diff options
79 files changed, 412 insertions, 112 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index a266b0c..696eb3e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling Version: 0.6.5 -Date: 2026-02-13 +Date: 2026-06-22 Authors@R: c( person("Johannes Ranke", email = "johannes.ranke@agroscope.admin.ch", role = c("aut", "cre"), @@ -1,5 +1,7 @@ ## version 0.6.5 +- R/PEC_sw_drift.R: Support specifying units for distances and widths using the units package. +- R/TOXSWA_cwa.R: Adapt to readr (>= 2.2.0) requiring to wrap literal input as used for reading .out files with I(). - R/PEC_sw_drainage_UK.R: Create a function `drainage_date_UK` that does not only respect the beginning of the drainage period on 1 October, but also the end of the drainage period on 30 April, and use it for determining the degradation time. Applications early in the year before 1 May will now correctly be calculated without degradation time. - R/PEC_sw_drift.R: Vectorise the function not only with respect to distances, rates and water depths, but also with respect to crop groups. Closes issue #2 reported by Julian Klein (@juklei). @@ -1,7 +1,7 @@ #' Groundwater ubiquity score based on Gustafson (1989) #' -#' The groundwater ubiquity score GUS is calculated according to -#' the following equation +#' The groundwater ubiquity score GUS is calculated according to the +#' equation #' \deqn{GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})}{GUS = log10 DT50soil * (4 - log10 Koc)} #' #' @references Gustafson, David I. (1989) Groundwater ubiquity score: a simple diff --git a/R/PEC_sw_drift.R b/R/PEC_sw_drift.R index 05f90dd..621a0b6 100644 --- a/R/PEC_sw_drift.R +++ b/R/PEC_sw_drift.R @@ -40,7 +40,7 @@ utils::globalVariables(c("A", "B", "C", "D", "H", "hinge", "z1", "z2", "distance #' @importFrom dplyr bind_rows #' @importFrom tidyr pivot_longer #' @return A numeric vector with the predicted concentration in surface water. -#' In some cases, the vector is named with distances or drift percentages, for +#' In some cases, the vector is named with distances or drift percentages, for #' backward compatibility with versions before the vectorisation of arguments #' other than 'distances' was introduced in v0.6.5. #' @export @@ -54,6 +54,10 @@ utils::globalVariables(c("A", "B", "C", "D", "H", "hinge", "z1", "z2", "distance #' # This makes it possible to also use different distances #' PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = "RF") #' +#' # We can also specify distance units explicitly +#' library(units) +#' PEC_sw_drift(100, distances = set_units(c(1, 3, 5, 6, 10, 20, 50, 100), "m"), drift_data = "RF") +#' #' # or consider aerial application #' PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = "RF", #' crop_group_RF = "aerial") @@ -115,6 +119,7 @@ PEC_sw_drift <- function(rate, rate_units <- match.arg(rate_units) PEC_units <- match.arg(PEC_units) if (!inherits(rate, "units")) rate <- set_units(rate, rate_units, mode = "symbolic") + if (!inherits(distances, "units")) distances <- set_units(distances, "m") if (!inherits(water_width, "units")) water_width <- set_units(water_width, "cm") if (!inherits(water_depth, "units")) water_depth <- set_units(water_depth, "cm") drift_data <- match.arg(drift_data) @@ -143,17 +148,17 @@ PEC_sw_drift <- function(rate, else water_width - (water_depth / tanpi(side_angle/180)) if (as.numeric(mean_water_width) < 0) stop("Undefined geometry") relative_mean_water_width <- mean_water_width / water_width # Always <= 1 - + # Check lengths of arguments advertised as vectorised for compatibility arg_lengths <- sapply( - list(rate = rate, applications = applications, distances = distances, - water_depth = water_depth, crop_group_JKI = crop_group_JKI, + list(rate = rate, applications = applications, distances = distances, + water_depth = water_depth, crop_group_JKI = crop_group_JKI, crop_group_RF = crop_group_RF), length) - + arg_lengths_not_one <- arg_lengths[arg_lengths != 1] if (length(unique(arg_lengths_not_one)) > 1) { - stop("The following argument lengths do not match:\n", + stop("The following argument lengths do not match:\n", capture_output(print(arg_lengths_not_one))) } @@ -173,13 +178,13 @@ PEC_sw_drift <- function(rate, ) |> left_join(drift_data_JKI_long, by = c("applications", "distance", "crop_group_JKI")) |> pull(pctg) - names(drift_percentages) <- paste(distances, "m") + names(drift_percentages) <- paste(as.character(distances), "m") } if (drift_data == "RF") { drift_percentages <- drift_percentages_rautmann(distances, applications, formula = formula, crop_group_RF, widths = as.numeric(set_units(water_width, "m"))) - names(drift_percentages) <- paste(distances, "m") + names(drift_percentages) <- paste(as.character(distances), "m") } } else { names(drift_percentages) <- paste(drift_percentages, "%") @@ -250,9 +255,13 @@ drift_percentages_rautmann <- function(distances, applications = 1, ) { unmatched_crop_groups <- setdiff(crop_group_RF, unique(pfm::drift_parameters_focus$crop_group)) + if (!inherits(distances, "units")) distances <- set_units(distances, "m") + if (!inherits(widths, "units")) widths <- set_units(widths, "m") if (length(unmatched_crop_groups) > 0) stop("Crop group(s) ", unmatched_crop_groups, " not supported") if (!all(applications %in% 1:8)) stop("Only 1 to 8 applications are supported") formula <- match.arg(formula) + distances <- drop_units(distances) + widths <- drop_units(widths) # To avoid recycling of components with length != 1 but smaller than the longest argument, # which would likely be unintended, we use tibble here diff --git a/_pkgdown.yml b/_pkgdown.yml index 9b0c204..6c45ae8 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -5,6 +5,7 @@ title: pfm template: bootstrap: 5 bootswatch: spacelab + math-rendering: mathjax news: cran_dates: false diff --git a/docs/404.html b/docs/404.html index 712b3c2..9303a96 100644 --- a/docs/404.html +++ b/docs/404.html @@ -6,7 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <title>Page not found (404) • pfm</title> -<script src="https://pkgdown.jrwb.de/pfm/deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> +<!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script src="https://pkgdown.jrwb.de/pfm/NA"> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="https://pkgdown.jrwb.de/pfm/deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <link href="https://pkgdown.jrwb.de/pfm/deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"> <script src="https://pkgdown.jrwb.de/pfm/deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="https://pkgdown.jrwb.de/pfm/deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"> <link href="https://pkgdown.jrwb.de/pfm/deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"> diff --git a/docs/authors.html b/docs/authors.html index 6c14ec6..1794acc 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Authors and Citation • pfm</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script 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src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> diff --git a/docs/index.html b/docs/index.html index 160afaa..fa302bb 100644 --- a/docs/index.html +++ b/docs/index.html @@ -6,7 +6,13 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <title>Utilities for Pesticide Fate Modelling • pfm</title> -<script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> +<!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"> <script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"> <link href="deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"> diff --git a/docs/index.md b/docs/index.md index 62199a9..859dcdf 100644 --- a/docs/index.md +++ b/docs/index.md @@ -49,7 +49,6 @@ The easiest way to install the package is probably to use the [r-universe repo](https://jranke.r-universe.dev/pfm): ``` r - install.packages("pfm", repos = c("https://jranke.r-universe.dev", "https://cran.r-project.org")) ``` @@ -59,7 +58,6 @@ Alternatively, you can install the package directly from github, e.g. by using [`pak`](https://pak.r-lib.org). ``` r - # install.packages("pak") pak::pak("jranke/pfm") ``` @@ -81,8 +79,8 @@ overlays of mkinfit predictions as shown Calculations of predicted environmental concentrations using this package have been used in some publications by Agroscope. -| | -|----| -| Korkaric M, Lehto M, Poiger T, de Baan L, Mathis M, Ammann L, Hanke I, Balmer M, Blom JF (2023) Risikoindikatoren für Pflanzenschutzmittel: weiterführende Analysen zur Berechnung. Agroscope Science, 154, 1-48, [doi:10.34776/as154g](https://doi.org/10.34776/as154g) | -| Korkaric M, Ammann L, Hanke I, Schneuwly J, Lehto M, Poiger T, de Baan L, Daniel O, Blom JF (2022) Neue Pflanzenschutzmittel-Risikoindikatoren für die Schweiz. Agrarforschung Schweiz 13, 1-10, [doi:10.34776/afs13-1](https://doi.org/10.34776/afs13-1) | +| | +|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| Korkaric M, Lehto M, Poiger T, de Baan L, Mathis M, Ammann L, Hanke I, Balmer M, Blom JF (2023) Risikoindikatoren für Pflanzenschutzmittel: weiterführende Analysen zur Berechnung. Agroscope Science, 154, 1-48, [doi:10.34776/as154g](https://doi.org/10.34776/as154g) | +| Korkaric M, Ammann L, Hanke I, Schneuwly J, Lehto M, Poiger T, de Baan L, Daniel O, Blom JF (2022) Neue Pflanzenschutzmittel-Risikoindikatoren für die Schweiz. Agrarforschung Schweiz 13, 1-10, [doi:10.34776/afs13-1](https://doi.org/10.34776/afs13-1) | | Korkaric M, Hanke I, Grossar D, Neuweiler R, Christ B, Wirth J, Hochstrasser M, Dubuis PH, Kuster T, Breitenmoser S, Egger B, Perren S, Schürch S, Aldrich A, Jeker L, Poiger T, Daniel O (2020) Datengrundlage und Kriterien für eine Einschränkung der PSM-Auswahl im ÖLN: Schutz der Oberflächengewässer, der Bienen und des Grundwassers (Metaboliten), sowie agronomische Folgen der Einschränkungen. Agroscope Science, 106, 2020, 1-31. [doi:10.34776/as106g](https://doi.org/10.34776/as106g) | diff --git a/docs/llms.txt b/docs/llms.txt index fed8f27..412fd7e 100644 --- a/docs/llms.txt +++ b/docs/llms.txt @@ -49,7 +49,6 @@ The easiest way to install the package is probably to use the [r-universe repo](https://jranke.r-universe.dev/pfm): ``` r - install.packages("pfm", repos = c("https://jranke.r-universe.dev", "https://cran.r-project.org")) ``` @@ -59,7 +58,6 @@ Alternatively, you can install the package directly from github, e.g. by using [`pak`](https://pak.r-lib.org). ``` r - # install.packages("pak") pak::pak("jranke/pfm") ``` @@ -81,10 +79,10 @@ overlays of mkinfit predictions as shown Calculations of predicted environmental concentrations using this package have been used in some publications by Agroscope. -| | -|----| -| Korkaric M, Lehto M, Poiger T, de Baan L, Mathis M, Ammann L, Hanke I, Balmer M, Blom JF (2023) Risikoindikatoren für Pflanzenschutzmittel: weiterführende Analysen zur Berechnung. Agroscope Science, 154, 1-48, [doi:10.34776/as154g](https://doi.org/10.34776/as154g) | -| Korkaric M, Ammann L, Hanke I, Schneuwly J, Lehto M, Poiger T, de Baan L, Daniel O, Blom JF (2022) Neue Pflanzenschutzmittel-Risikoindikatoren für die Schweiz. Agrarforschung Schweiz 13, 1-10, [doi:10.34776/afs13-1](https://doi.org/10.34776/afs13-1) | +| | +|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| Korkaric M, Lehto M, Poiger T, de Baan L, Mathis M, Ammann L, Hanke I, Balmer M, Blom JF (2023) Risikoindikatoren für Pflanzenschutzmittel: weiterführende Analysen zur Berechnung. Agroscope Science, 154, 1-48, [doi:10.34776/as154g](https://doi.org/10.34776/as154g) | +| Korkaric M, Ammann L, Hanke I, Schneuwly J, Lehto M, Poiger T, de Baan L, Daniel O, Blom JF (2022) Neue Pflanzenschutzmittel-Risikoindikatoren für die Schweiz. Agrarforschung Schweiz 13, 1-10, [doi:10.34776/afs13-1](https://doi.org/10.34776/afs13-1) | | Korkaric M, Hanke I, Grossar D, Neuweiler R, Christ B, Wirth J, Hochstrasser M, Dubuis PH, Kuster T, Breitenmoser S, Egger B, Perren S, Schürch S, Aldrich A, Jeker L, Poiger T, Daniel O (2020) Datengrundlage und Kriterien für eine Einschränkung der PSM-Auswahl im ÖLN: Schutz der Oberflächengewässer, der Bienen und des Grundwassers (Metaboliten), sowie agronomische Folgen der Einschränkungen. Agroscope Science, 106, 2020, 1-31. [doi:10.34776/as106g](https://doi.org/10.34776/as106g) | # Package index diff --git a/docs/news/index.html b/docs/news/index.html index 6b1dec0..4a1fb22 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Changelog • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Changelog"></head><body> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Changelog • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Changelog"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -34,7 +40,9 @@ <div class="section level2"> <h2 class="pkg-version" data-toc-text="0.6.5" id="version-065">version 0.6.5<a class="anchor" aria-label="anchor" href="#version-065"></a></h2> -<ul><li><p>R/PEC_sw_drainage_UK.R: Create a function <code>drainage_date_UK</code> that does not only respect the beginning of the drainage period on 1 October, but also the end of the drainage period on 30 April, and use it for determining the degradation time. Applications early in the year before 1 May will now correctly be calculated without degradation time.</p></li> +<ul><li><p>R/PEC_sw_drift.R: Support specifying units for distances and widths using the units package.</p></li> +<li><p>R/TOXSWA_cwa.R: Adapt to readr (>= 2.2.0) requiring to wrap literal input as used for reading .out files with I().</p></li> +<li><p>R/PEC_sw_drainage_UK.R: Create a function <code>drainage_date_UK</code> that does not only respect the beginning of the drainage period on 1 October, but also the end of the drainage period on 30 April, and use it for determining the degradation time. Applications early in the year before 1 May will now correctly be calculated without degradation time.</p></li> <li><p>R/PEC_sw_drift.R: Vectorise the function not only with respect to distances, rates and water depths, but also with respect to crop groups. Closes issue <a href="https://github.com/jranke/pfm/issues/2" class="external-link">#2</a> reported by Julian Klein (<a href="https://github.com/juklei" class="external-link">@juklei</a>).</p></li> </ul></div> <div class="section level2"> diff --git a/docs/news/index.md b/docs/news/index.md index 1b86e03..3077509 100644 --- a/docs/news/index.md +++ b/docs/news/index.md @@ -2,6 +2,12 @@ ## version 0.6.5 +- R/PEC_sw_drift.R: Support specifying units for distances and widths + using the units package. + +- R/TOXSWA_cwa.R: Adapt to readr (\>= 2.2.0) requiring to wrap literal + input as used for reading .out files with I(). + - R/PEC_sw_drainage_UK.R: Create a function `drainage_date_UK` that does not only respect the beginning of the drainage period on 1 October, but also the end of the drainage period on 30 April, and use it for diff --git a/docs/reference/EFSA_GW_interception_2014.html b/docs/reference/EFSA_GW_interception_2014.html index 411533f..4c20985 100644 --- a/docs/reference/EFSA_GW_interception_2014.html +++ b/docs/reference/EFSA_GW_interception_2014.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; 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charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Subset of EFSA crop washoff default values — EFSA_washoff_2017 • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Subset of EFSA crop washoff default values — EFSA_washoff_2017"><meta name="description" content="Subset of EFSA crop washoff default values"><meta property="og:description" content="Subset of EFSA crop washoff default values"></head><body> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Subset of EFSA crop washoff default values — EFSA_washoff_2017 • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Subset of EFSA crop washoff default values — EFSA_washoff_2017"><meta name="description" content="Subset of EFSA crop washoff default values"><meta property="og:description" content="Subset of EFSA crop washoff default values"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html index 86bbc9b..d21d340 100644 --- a/docs/reference/FOCUS_GW_scenarios_2012.html +++ b/docs/reference/FOCUS_GW_scenarios_2012.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012 • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012"><meta name="description" content="Currently, only scenario names with acronyms and a small subset of the soil definitions are provided. The +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012 • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012"><meta name="description" content="Currently, only scenario names with acronyms and a small subset of the soil definitions are provided. The soil definitions are from page 46ff. from FOCUS (2012)."><meta property="og:description" content="Currently, only scenario names with acronyms and a small subset of the soil definitions are provided. The soil definitions are from page 46ff. from FOCUS (2012)."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html index 1da0901..41d4547 100644 --- a/docs/reference/FOCUS_Step_12_scenarios.html +++ b/docs/reference/FOCUS_Step_12_scenarios.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios"><meta name="description" content="The data were extracted from the scenario.txt file using the R code shown below. +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios"><meta name="description" content="The data were extracted from the scenario.txt file using the R code shown below. The text file is not included in the package as its licence is not clear."><meta property="og:description" content="The data were extracted from the scenario.txt file using the R code shown below. The text file is not included in the package as its licence is not clear."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> diff --git a/docs/reference/FOCUS_Step_12_scenarios.md b/docs/reference/FOCUS_Step_12_scenarios.md index 3bf1ae2..63d1959 100644 --- a/docs/reference/FOCUS_Step_12_scenarios.md +++ b/docs/reference/FOCUS_Step_12_scenarios.md @@ -14,7 +14,6 @@ percentages for Step 2 calculations in a matrix called 'rd'. ## Examples ``` r - # \dontrun{ # This is the code that was used to extract the data scenario_path <- "inst/extdata/FOCUS_Step_12_scenarios.txt" diff --git a/docs/reference/FOMC_actual_twa.html b/docs/reference/FOMC_actual_twa.html index 98eac90..2a772a1 100644 --- a/docs/reference/FOMC_actual_twa.html +++ b/docs/reference/FOMC_actual_twa.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa"><meta name="description" content="Actual and maximum moving window time average concentrations for FOMC kinetics"><meta property="og:description" content="Actual and maximum moving window time average concentrations for FOMC kinetics"></head><body> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa"><meta name="description" content="Actual and maximum moving window time average concentrations for FOMC kinetics"><meta property="og:description" content="Actual and maximum moving window time average concentrations for FOMC kinetics"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html index b5a65e9..0e86666 100644 --- a/docs/reference/GUS.html +++ b/docs/reference/GUS.html @@ -1,8 +1,14 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Groundwater ubiquity score based on Gustafson (1989) — GUS • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Groundwater ubiquity score based on Gustafson (1989) — GUS"><meta name="description" content="The groundwater ubiquity score GUS is calculated according to -the following equation -$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$"><meta property="og:description" content="The groundwater ubiquity score GUS is calculated according to -the following equation +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Groundwater ubiquity score based on Gustafson (1989) — GUS • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Groundwater ubiquity score based on Gustafson (1989) — GUS"><meta name="description" content="The groundwater ubiquity score GUS is calculated according to the +equation +$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$"><meta property="og:description" content="The groundwater ubiquity score GUS is calculated according to the +equation $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -38,8 +44,8 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$"></head><body> </div> <div class="ref-description section level2"> - <p>The groundwater ubiquity score GUS is calculated according to -the following equation + <p>The groundwater ubiquity score GUS is calculated according to the +equation $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$</p> </div> diff --git a/docs/reference/GUS.md b/docs/reference/GUS.md index b81f464..8bc2a62 100644 --- a/docs/reference/GUS.md +++ b/docs/reference/GUS.md @@ -1,8 +1,7 @@ # Groundwater ubiquity score based on Gustafson (1989) The groundwater ubiquity score GUS is calculated according to the -following equation \$\$GUS = \log\_{10} DT50\_{soil} (4 - \log\_{10} -K\_{oc})\$\$ +equation \$\$GUS = \log\_{10} DT50\_{soil} (4 - \log\_{10} K\_{oc})\$\$ ## Usage diff --git a/docs/reference/PEC_FOMC_accu_rel.html b/docs/reference/PEC_FOMC_accu_rel.html index c9c7b6a..6139c28 100644 --- a/docs/reference/PEC_FOMC_accu_rel.html +++ b/docs/reference/PEC_FOMC_accu_rel.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel"><meta name="description" content="Get the relative accumulation of an FOMC model over multiples of an interval"><meta property="og:description" content="Get the relative accumulation of an FOMC model over multiples of an interval"></head><body> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel"><meta name="description" content="Get the relative accumulation of an FOMC model over multiples of an interval"><meta property="og:description" content="Get the relative accumulation of an FOMC model over multiples of an interval"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index b148280..7ef86fd 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate predicted environmental concentrations in soil — PEC_soil • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate predicted environmental concentrations in soil — PEC_soil"><meta name="description" content="This is a basic calculation of a contaminant concentration in bulk soil +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate predicted environmental concentrations in soil — PEC_soil • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate predicted environmental concentrations in soil — PEC_soil"><meta name="description" content="This is a basic calculation of a contaminant concentration in bulk soil based on complete, instantaneous mixing. If an interval is given, an attempt is made at calculating a long term maximum concentration using the concepts layed out in the PPR panel opinion (EFSA PPR panel 2012 diff --git a/docs/reference/PEC_soil_mets.html b/docs/reference/PEC_soil_mets.html index d615c46..950d17a 100644 --- a/docs/reference/PEC_soil_mets.html +++ b/docs/reference/PEC_soil_mets.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets"><meta name="description" content="Calculate initial and accumulation PEC soil for a set of metabolites"><meta property="og:description" content="Calculate initial and accumulation PEC soil for a set of metabolites"></head><body> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets"><meta name="description" content="Calculate initial and accumulation PEC soil for a set of metabolites"><meta property="og:description" content="Calculate initial and accumulation PEC soil for a set of metabolites"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html index 8dbfc78..30a146e 100644 --- a/docs/reference/PEC_sw_drainage_UK.html +++ b/docs/reference/PEC_sw_drainage_UK.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK"><meta name="description" content="This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK"><meta name="description" content="This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRC website. Degradation between the end (30 April) and the start (1 October) of the drainage period is taken into account if latest_application is specified and the degradation parameters are given either as a soil_DT50 or a model."><meta property="og:description" content="This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html index ee2f973..04fb9b0 100644 --- a/docs/reference/PEC_sw_drift.html +++ b/docs/reference/PEC_sw_drift.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift"><meta name="description" content="This is a basic, vectorised form of a simple calculation of a contaminant +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift"><meta name="description" content="This is a basic, vectorised form of a simple calculation of a contaminant concentration in surface water based on complete, instantaneous mixing with input via spray drift."><meta property="og:description" content="This is a basic, vectorised form of a simple calculation of a contaminant concentration in surface water based on complete, instantaneous mixing @@ -178,6 +184,16 @@ applications, water depth, crop groups and distances</p> <span class="r-out co"><span class="r-pr">#></span> 100 m </span> <span class="r-out co"><span class="r-pr">#></span> 0.01018774 </span> <span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># We can also specify distance units explicitly</span></span></span> +<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://r-quantities.github.io/units/" class="external-link">units</a></span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> udunits database from /usr/share/xml/udunits/udunits2.xml</span> +<span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, distances <span class="op">=</span> <span class="fu"><a href="https://r-quantities.github.io/units/reference/units.html" class="external-link">set_units</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">5</span>, <span class="fl">6</span>, <span class="fl">10</span>, <span class="fl">20</span>, <span class="fl">50</span>, <span class="fl">100</span><span class="op">)</span>, <span class="st">"m"</span><span class="op">)</span>, drift_data <span class="op">=</span> <span class="st">"RF"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Units: [µg/L]</span> +<span class="r-out co"><span class="r-pr">#></span> 1 m 3 m 5 m 6 m 10 m 20 m 50 m </span> +<span class="r-out co"><span class="r-pr">#></span> 0.91976667 0.31415827 0.19064473 0.15951494 0.09680051 0.04915079 0.02006434 </span> +<span class="r-out co"><span class="r-pr">#></span> 100 m </span> +<span class="r-out co"><span class="r-pr">#></span> 0.01018774 </span> +<span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># or consider aerial application</span></span></span> <span class="r-in"><span><span class="fu">PEC_sw_drift</span><span class="op">(</span><span class="fl">100</span>, distances <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">5</span>, <span class="fl">6</span>, <span class="fl">10</span>, <span class="fl">20</span>, <span class="fl">50</span>, <span class="fl">100</span><span class="op">)</span>, drift_data <span class="op">=</span> <span class="st">"RF"</span>,</span></span> <span class="r-in"><span> crop_group_RF <span class="op">=</span> <span class="st">"aerial"</span><span class="op">)</span></span></span> diff --git a/docs/reference/PEC_sw_drift.md b/docs/reference/PEC_sw_drift.md index c16a02a..375427e 100644 --- a/docs/reference/PEC_sw_drift.md +++ b/docs/reference/PEC_sw_drift.md @@ -148,6 +148,16 @@ PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = "RF") #> 100 m #> 0.01018774 +# We can also specify distance units explicitly +library(units) +#> udunits database from /usr/share/xml/udunits/udunits2.xml +PEC_sw_drift(100, distances = set_units(c(1, 3, 5, 6, 10, 20, 50, 100), "m"), drift_data = "RF") +#> Units: [µg/L] +#> 1 m 3 m 5 m 6 m 10 m 20 m 50 m +#> 0.91976667 0.31415827 0.19064473 0.15951494 0.09680051 0.04915079 0.02006434 +#> 100 m +#> 0.01018774 + # or consider aerial application PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = "RF", crop_group_RF = "aerial") diff --git a/docs/reference/PEC_sw_exposit_drainage.html b/docs/reference/PEC_sw_exposit_drainage.html index 792e774..59e0ef5 100644 --- a/docs/reference/PEC_sw_exposit_drainage.html +++ b/docs/reference/PEC_sw_exposit_drainage.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage"><meta name="description" content='This is a reimplementation of the calculation described in the Exposit 3.02 spreadsheet file, +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage"><meta name="description" content='This is a reimplementation of the calculation described in the Exposit 3.02 spreadsheet file, in the worksheet "Konzept Drainage". Although there are four groups of compounds ("Gefährdungsgruppen"), only one distinction is made in the calculations, between compounds with low mobility (group 1) and compounds @@ -68,10 +74,10 @@ It is recommened to specify the arguments <code>rate</code>, <code>Koc</code>, < <span> interception <span class="op">=</span> <span class="fl">0</span>,</span> <span> Koc <span class="op">=</span> <span class="cn">NA</span>,</span> <span> mobility <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="cn">NA</span>, <span class="st">"low"</span>, <span class="st">"high"</span><span class="op">)</span>,</span> -<span> DT50 <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="cn">Inf</span>, <span class="st">"d"</span><span class="op">)</span>,</span> -<span> t_drainage <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="fl">3</span>, <span class="st">"days"</span><span class="op">)</span>,</span> -<span> V_ditch <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="fl">30</span>, <span class="st">"m3"</span><span class="op">)</span>,</span> -<span> V_drainage <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>spring <span class="op">=</span> <span class="fl">10</span>, autumn <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="st">"m3"</span><span class="op">)</span>,</span> +<span> DT50 <span class="op">=</span> <span class="fu"><a href="https://r-quantities.github.io/units/reference/units.html" class="external-link">set_units</a></span><span class="op">(</span><span class="cn">Inf</span>, <span class="st">"d"</span><span class="op">)</span>,</span> +<span> t_drainage <span class="op">=</span> <span class="fu"><a href="https://r-quantities.github.io/units/reference/units.html" class="external-link">set_units</a></span><span class="op">(</span><span class="fl">3</span>, <span class="st">"days"</span><span class="op">)</span>,</span> +<span> V_ditch <span class="op">=</span> <span class="fu"><a href="https://r-quantities.github.io/units/reference/units.html" class="external-link">set_units</a></span><span class="op">(</span><span class="fl">30</span>, <span class="st">"m3"</span><span class="op">)</span>,</span> +<span> V_drainage <span class="op">=</span> <span class="fu"><a href="https://r-quantities.github.io/units/reference/units.html" class="external-link">set_units</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>spring <span class="op">=</span> <span class="fl">10</span>, autumn <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="st">"m3"</span><span class="op">)</span>,</span> <span> dilution <span class="op">=</span> <span class="fl">2</span></span> <span><span class="op">)</span></span></code></pre></div> </div> diff --git a/docs/reference/PEC_sw_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html index 8104913..b5f8f85 100644 --- a/docs/reference/PEC_sw_exposit_runoff.html +++ b/docs/reference/PEC_sw_exposit_runoff.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff"><meta name="description" content='This is a reimplementation of the calculation described in the Exposit 3.02 spreadsheet file, +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff"><meta name="description" content='This is a reimplementation of the calculation described in the Exposit 3.02 spreadsheet file, in the worksheet "Konzept Runoff".'><meta property="og:description" content='This is a reimplementation of the calculation described in the Exposit 3.02 spreadsheet file, in the worksheet "Konzept Runoff".'></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -46,11 +52,11 @@ in the worksheet "Konzept Runoff".</p> <span> <span class="va">rate</span>,</span> <span> interception <span class="op">=</span> <span class="fl">0</span>,</span> <span> <span class="va">Koc</span>,</span> -<span> DT50 <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="cn">Inf</span>, <span class="st">"d"</span><span class="op">)</span>,</span> -<span> t_runoff <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="fl">3</span>, <span class="st">"days"</span><span class="op">)</span>,</span> +<span> DT50 <span class="op">=</span> <span class="fu"><a href="https://r-quantities.github.io/units/reference/units.html" class="external-link">set_units</a></span><span class="op">(</span><span class="cn">Inf</span>, <span class="st">"d"</span><span class="op">)</span>,</span> +<span> t_runoff <span class="op">=</span> <span class="fu"><a href="https://r-quantities.github.io/units/reference/units.html" class="external-link">set_units</a></span><span class="op">(</span><span class="fl">3</span>, <span class="st">"days"</span><span class="op">)</span>,</span> <span> exposit_reduction_version <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"3.02"</span>, <span class="st">"3.01a"</span>, <span class="st">"3.01a2"</span>, <span class="st">"2.0"</span><span class="op">)</span>,</span> -<span> V_ditch <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="fl">30</span>, <span class="st">"m3"</span><span class="op">)</span>,</span> -<span> V_event <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="fl">100</span>, <span class="st">"m3"</span><span class="op">)</span>,</span> +<span> V_ditch <span class="op">=</span> <span class="fu"><a href="https://r-quantities.github.io/units/reference/units.html" class="external-link">set_units</a></span><span class="op">(</span><span class="fl">30</span>, <span class="st">"m3"</span><span class="op">)</span>,</span> +<span> V_event <span class="op">=</span> <span class="fu"><a href="https://r-quantities.github.io/units/reference/units.html" class="external-link">set_units</a></span><span class="op">(</span><span class="fl">100</span>, <span class="st">"m3"</span><span class="op">)</span>,</span> <span> dilution <span class="op">=</span> <span class="fl">2</span></span> <span><span class="op">)</span></span></code></pre></div> </div> diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html index a315bdc..61887c1 100644 --- a/docs/reference/PEC_sw_focus.html +++ b/docs/reference/PEC_sw_focus.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus"><meta name="description" content="This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2, +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus"><meta name="description" content="This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2, authored by Michael Klein, in R. Note that results for multiple applications should be compared to the corresponding results for a single application. At current, this is not done automatically in diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html index 8346564..45afb87 100644 --- a/docs/reference/PEC_sw_sed.html +++ b/docs/reference/PEC_sw_sed.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed"><meta name="description" content="The method 'percentage' is equivalent to what is used in the CRD spreadsheet +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed"><meta name="description" content="The method 'percentage' is equivalent to what is used in the CRD spreadsheet PEC calculator"><meta property="og:description" content="The method 'percentage' is equivalent to what is used in the CRD spreadsheet PEC calculator"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> @@ -46,9 +52,9 @@ PEC calculator</p> <span> <span class="va">PEC_sw</span>,</span> <span> percentage <span class="op">=</span> <span class="fl">100</span>,</span> <span> method <span class="op">=</span> <span class="st">"percentage"</span>,</span> -<span> sediment_depth <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="fl">5</span>, <span class="st">"cm"</span><span class="op">)</span>,</span> -<span> water_depth <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="fl">30</span>, <span class="st">"cm"</span><span class="op">)</span>,</span> -<span> sediment_density <span class="op">=</span> <span class="fu">set_units</span><span class="op">(</span><span class="fl">1.3</span>, <span class="st">"kg/L"</span><span class="op">)</span>,</span> +<span> sediment_depth <span class="op">=</span> <span class="fu"><a href="https://r-quantities.github.io/units/reference/units.html" class="external-link">set_units</a></span><span class="op">(</span><span class="fl">5</span>, <span class="st">"cm"</span><span class="op">)</span>,</span> +<span> water_depth <span class="op">=</span> <span class="fu"><a href="https://r-quantities.github.io/units/reference/units.html" class="external-link">set_units</a></span><span class="op">(</span><span class="fl">30</span>, <span class="st">"cm"</span><span class="op">)</span>,</span> +<span> sediment_density <span class="op">=</span> <span class="fu"><a href="https://r-quantities.github.io/units/reference/units.html" class="external-link">set_units</a></span><span class="op">(</span><span class="fl">1.3</span>, <span class="st">"kg/L"</span><span class="op">)</span>,</span> <span> PEC_sed_units <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"µg/kg"</span>, <span class="st">"mg/kg"</span><span class="op">)</span></span> <span><span class="op">)</span></span></code></pre></div> </div> @@ -100,7 +106,6 @@ g/cm3)</p></dd> <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/pfm">pfm</a></span><span class="op">)</span></span></span> <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://r-quantities.github.io/units/" class="external-link">units</a></span><span class="op">)</span></span></span> -<span class="r-msg co"><span class="r-pr">#></span> udunits database from /usr/share/xml/udunits/udunits2.xml</span> <span class="r-in"><span><span class="fu">PEC_sw_sed</span><span class="op">(</span><span class="fu"><a href="PEC_sw_drift.html">PEC_sw_drift</a></span><span class="op">(</span><span class="fl">100</span>, distances <span class="op">=</span> <span class="fl">1</span><span class="op">)</span>, percentage <span class="op">=</span> <span class="fl">50</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.130769 [µg/kg]</span> </code></pre></div> diff --git a/docs/reference/PEC_sw_sed.md b/docs/reference/PEC_sw_sed.md index 21d9748..6f03a84 100644 --- a/docs/reference/PEC_sw_sed.md +++ b/docs/reference/PEC_sw_sed.md @@ -61,7 +61,6 @@ Johannes Ranke ``` r library(pfm) library(units) -#> udunits database from /usr/share/xml/udunits/udunits2.xml PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50) #> 2.130769 [µg/kg] ``` diff --git a/docs/reference/SFO_actual_twa.html b/docs/reference/SFO_actual_twa.html index bcfeb05..842d288 100644 --- a/docs/reference/SFO_actual_twa.html +++ b/docs/reference/SFO_actual_twa.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" 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pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script 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content="Actual and maximum moving window time average concentrations for SFO kinetics"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> diff --git a/docs/reference/SSLRC_mobility_classification.html b/docs/reference/SSLRC_mobility_classification.html index 5dd600c..fbbbd0a 100644 --- a/docs/reference/SSLRC_mobility_classification.html +++ b/docs/reference/SSLRC_mobility_classification.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification"><meta name="description" content="This implements the method specified in the UK data requirements handbook and was +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification"><meta name="description" content="This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRD website"><meta property="og:description" content="This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRD website"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index 2087177..48e6b44 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script 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Usually, an instance of this class will be generated diff --git a/docs/reference/TSCF-1.png b/docs/reference/TSCF-1.png Binary files differindex 71b1825..8d7df74 100644 --- a/docs/reference/TSCF-1.png +++ b/docs/reference/TSCF-1.png diff --git a/docs/reference/TSCF.html b/docs/reference/TSCF.html index 4ad4475..90fcfbb 100644 --- a/docs/reference/TSCF.html +++ b/docs/reference/TSCF.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Estimation of the transpiration stream concentration factor — TSCF • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Estimation of the transpiration stream concentration factor — TSCF"><meta name="description" content="The FOCUS groundwater guidance (FOCUS 2014, p. 41) states that a reliable measured +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Estimation of the transpiration stream concentration factor — TSCF • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Estimation of the transpiration stream concentration factor — TSCF"><meta name="description" content="The FOCUS groundwater guidance (FOCUS 2014, p. 41) states that a reliable measured log Kow for neutral pH must be available in order to apply the Briggs equation. It is not clarified when it can be regarded reliable, but the equation is stated to be produced for non-ionic compounds, suggesting that diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html index 4fe4400..869b643 100644 --- a/docs/reference/chent_focus_sw.html +++ b/docs/reference/chent_focus_sw.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw"><meta name="description" content="Create a chemical compound object for FOCUS Step 1 calculations"><meta property="og:description" content="Create a chemical compound object for FOCUS Step 1 calculations"></head><body> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; 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charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI"><meta name="description" content="Deposition from spray drift expressed as percent of the applied dose as +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; 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charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Regression parameters for the Rautmann drift data — drift_parameters_focus • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Regression parameters for the Rautmann drift data — drift_parameters_focus"><meta name="description" content="The parameters were extracted from Appendix B to the FOCUS surface water guidance +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Regression parameters for the Rautmann drift data — drift_parameters_focus • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Regression parameters for the Rautmann drift data — drift_parameters_focus"><meta name="description" content="The parameters were extracted from Appendix B to the FOCUS surface water guidance using the R code given in the file data_generation/drift_parameters_focus.R installed with this package. The appendix itself is not included in the package, as its licence is not clear."><meta property="og:description" content="The parameters were extracted from Appendix B to the FOCUS surface water guidance diff --git a/docs/reference/drift_percentages_rautmann-1.png b/docs/reference/drift_percentages_rautmann-1.png Binary files differindex 8e40b84..f046ca0 100644 --- a/docs/reference/drift_percentages_rautmann-1.png +++ b/docs/reference/drift_percentages_rautmann-1.png diff --git a/docs/reference/drift_percentages_rautmann.html b/docs/reference/drift_percentages_rautmann.html index 96dfebf..9659752 100644 --- a/docs/reference/drift_percentages_rautmann.html +++ b/docs/reference/drift_percentages_rautmann.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate drift percentages based on Rautmann data — drift_percentages_rautmann • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate drift percentages based on Rautmann data — drift_percentages_rautmann"><meta name="description" content="Calculate drift percentages based on Rautmann data"><meta property="og:description" content="Calculate drift percentages based on Rautmann data"></head><body> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate drift percentages based on Rautmann data — drift_percentages_rautmann • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate drift percentages based on Rautmann data — drift_percentages_rautmann"><meta name="description" content="Calculate drift percentages based on Rautmann data"><meta property="og:description" content="Calculate drift percentages based on Rautmann data"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html index cbcb9f4..08c4bf9 100644 --- a/docs/reference/endpoint.html +++ b/docs/reference/endpoint.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Retrieve endpoint information from the chyaml field of a chent object — endpoint • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Retrieve endpoint information from the chyaml field of a chent object — endpoint"><meta name="description" content="R6 class objects of class chent represent chemical entities +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Retrieve endpoint information from the chyaml field of a chent object — endpoint • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Retrieve endpoint information from the chyaml field of a chent object — endpoint"><meta name="description" content="R6 class objects of class chent represent chemical entities and can hold a list of information loaded from a chemical yaml file in their chyaml field. Such information is extracted and optionally aggregated by this function."><meta property="og:description" content="R6 class objects of class chent represent chemical entities diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html index 76a309d..2a0bc3a 100644 --- a/docs/reference/geomean.html +++ b/docs/reference/geomean.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate the geometric mean — geomean • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate the geometric mean — geomean"><meta name="description" content="Based on some posts in a thread on Stackoverflow +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate the geometric mean — geomean • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate the geometric mean — geomean"><meta name="description" content="Based on some posts in a thread on Stackoverflow http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in This function returns NA if NA values are present and na.rm = FALSE (default). If negative values are present, it gives an error message. diff --git a/docs/reference/get_vertex.html b/docs/reference/get_vertex.html index d721667..fc35914 100644 --- a/docs/reference/get_vertex.html +++ b/docs/reference/get_vertex.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Fit a parabola through three points — get_vertex • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fit a parabola through three points — get_vertex"><meta name="description" content="This was inspired by an answer on stackoverflow +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Fit a parabola through three points — get_vertex • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Fit a parabola through three points — get_vertex"><meta name="description" content="This was inspired by an answer on stackoverflow https://stackoverflow.com/a/717791"><meta property="og:description" content="This was inspired by an answer on stackoverflow https://stackoverflow.com/a/717791"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> diff --git a/docs/reference/index.html b/docs/reference/index.html index 6d7b495..249a2f3 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; 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charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Package index • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Package index"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html index f1ebfeb..8ceca6c 100644 --- a/docs/reference/max_twa.html +++ b/docs/reference/max_twa.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>The maximum time weighted average concentration for a moving window — max_twa • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="The maximum time weighted average concentration for a moving window — max_twa"><meta name="description" content="If you generate your time series using sawtooth, +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>The maximum time weighted average concentration for a moving window — max_twa • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="The maximum time weighted average concentration for a moving window — max_twa"><meta name="description" content="If you generate your time series using sawtooth, you need to make sure that the length of the time series allows for finding the maximum. It is therefore recommended to check this using plot.one_box using the window size for the argument diff --git a/docs/reference/one_box-1.png b/docs/reference/one_box-1.png Binary files differindex 62ed361..1e4b517 100644 --- a/docs/reference/one_box-1.png +++ b/docs/reference/one_box-1.png diff --git a/docs/reference/one_box-2.png b/docs/reference/one_box-2.png Binary files differindex 9cf9480..6a4d0de 100644 --- a/docs/reference/one_box-2.png +++ b/docs/reference/one_box-2.png diff --git a/docs/reference/one_box-3.png b/docs/reference/one_box-3.png Binary files differindex 59943e5..d659e3a 100644 --- a/docs/reference/one_box-3.png +++ b/docs/reference/one_box-3.png diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html index 7b73a42..4987f15 100644 --- a/docs/reference/one_box.html +++ b/docs/reference/one_box.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Create a time series of decline data — one_box • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create a time series of decline data — one_box"><meta name="description" content="Create a time series of decline data"><meta property="og:description" content="Create a time series of decline data"></head><body> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Create a time series of decline data — one_box • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create a time series of decline data — one_box"><meta name="description" content="Create a time series of decline data"><meta property="og:description" content="Create a time series of decline data"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> diff --git a/docs/reference/perc_runoff_exposit.html b/docs/reference/perc_runoff_exposit.html index ee5dda0..0591ef1 100644 --- a/docs/reference/perc_runoff_exposit.html +++ b/docs/reference/perc_runoff_exposit.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; 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charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Read TOXSWA surface water concentrations — read.TOXSWA_cwa • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Read TOXSWA surface water concentrations — read.TOXSWA_cwa"><meta name="description" content="Read TOXSWA hourly concentrations of a chemical substance in a specific segment of a TOXSWA surface water body. Per default, the data for the last segment are imported. As TOXSWA 4 reports the values at the end of the hour (ConLiqWatLayCur) in its summary file, we use this value as well instead diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index bbd10af..02cba58 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Objects exported from other packages — reexports • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Objects exported from other packages — reexports"><meta name="description" content="These objects are imported from other packages. Follow the links +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Objects exported from other packages — reexports • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Objects exported from other packages — reexports"><meta name="description" content="These objects are imported from other packages. Follow the links below to see their documentation. mkin diff --git a/docs/reference/sawtooth-1.png b/docs/reference/sawtooth-1.png Binary files differindex b6fca96..b87b54a 100644 --- a/docs/reference/sawtooth-1.png +++ b/docs/reference/sawtooth-1.png diff --git a/docs/reference/sawtooth-2.png b/docs/reference/sawtooth-2.png Binary files differindex d4e93f7..64e3574 100644 --- a/docs/reference/sawtooth-2.png +++ b/docs/reference/sawtooth-2.png diff --git a/docs/reference/sawtooth-3.png b/docs/reference/sawtooth-3.png Binary files differindex 338feef..7537b54 100644 --- a/docs/reference/sawtooth-3.png +++ b/docs/reference/sawtooth-3.png diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html index 57467f0..6043eb8 100644 --- a/docs/reference/sawtooth.html +++ b/docs/reference/sawtooth.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Create decline time series for multiple applications — sawtooth • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create decline time series for multiple applications — sawtooth"><meta name="description" content="If the application pattern is specified in applications, +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Create decline time series for multiple applications — sawtooth • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create decline time series for multiple applications — sawtooth"><meta name="description" content="If the application pattern is specified in applications, n and i are disregarded."><meta property="og:description" content="If the application pattern is specified in applications, n and i are disregarded."></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html index f6900f3..d6a21e6 100644 --- a/docs/reference/soil_scenario_data_EFSA_2015.html +++ b/docs/reference/soil_scenario_data_EFSA_2015.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015 • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015"><meta name="description" content="Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015 • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015"><meta name="description" content="Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the scenario and model adjustment factors from p. 15 and p. 17 are included."><meta property="og:description" content="Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the diff --git a/docs/reference/soil_scenario_data_EFSA_2017.html b/docs/reference/soil_scenario_data_EFSA_2017.html index 60dfed5..0640d8f 100644 --- a/docs/reference/soil_scenario_data_EFSA_2017.html +++ b/docs/reference/soil_scenario_data_EFSA_2017.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017 • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017"><meta name="description" content="Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017 • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017"><meta name="description" content="Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the concentration in soil as given in the EFSA guidance (2017, p. 14/15). Also, the scenario and model adjustment factors from p. 16 and p. 18 are included."><meta property="og:description" content="Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the concentration in soil as given in the EFSA guidance (2017, p. 14/15). Also, the diff --git a/docs/reference/twa.html b/docs/reference/twa.html index ca6d605..74bad9c 100644 --- a/docs/reference/twa.html +++ b/docs/reference/twa.html @@ -1,5 +1,11 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate a time weighted average concentration — twa • pfm</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate a time weighted average concentration — twa"><meta name="description" content="The moving average is built only using the values in the past, so +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Calculate a time weighted average concentration — twa • pfm</title><!-- mathjax math --><script src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-mml-chtml.js" integrity="sha256-MASABpB4tYktI2Oitl4t+78w/lyA+D7b/s9GEP0JOGI=" crossorigin="anonymous"></script><script> + window.MathJax = { + chtml: { + fontURL: "https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/output/chtml/fonts/woff-v2" + } + }; +</script><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate a time weighted average concentration — twa"><meta name="description" content="The moving average is built only using the values in the past, so the earliest possible time for the maximum in the time series returned is after one window has passed."><meta property="og:description" content="The moving average is built only using the values in the past, so the earliest possible time for the maximum in the time series returned diff --git a/docs/search.json b/docs/search.json index 097f74a..e470deb 100644 --- a/docs/search.json +++ b/docs/search.json @@ -1 +1 @@ -[{"path":"https://pkgdown.jrwb.de/pfm/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Johannes Ranke. Author, maintainer. Elisabeth Lutz. Contributor.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Johannes Ranke (2026). pfm: Utilities Pesticide Fate Modelling. R package version 0.6.5, https://pkgdown.jrwb.de/pfm.","code":"@Manual{, title = {pfm: Utilities for Pesticide Fate Modelling}, author = {{Johannes Ranke}}, year = {2026}, note = {R package version 0.6.5}, url = {https://pkgdown.jrwb.de/pfm}, }"},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"pfm","dir":"","previous_headings":"","what":"Utilities for Pesticide Fate Modelling","title":"Utilities for Pesticide Fate Modelling","text":"R package pfm provides utilities fate modelling, including simple routines calculating predicted environmental concentrations (PEC) routines dealing FOCUS pesticide fate modelling tools made available GNU public license. specifically, pfm includes facilities simple one-box modelling saw-tooth-like curves resulting multiple repeated applications, calculation PEC soil based 1997 SANCO guidance first tiers EFSA PEC soil guidance 2012 2015, well functions calculating PEC surface water. PEC drift calculations can based Rautmann drift percentiles published JKI, exponential formulas published Rautmann inter- extrapolate arbitrary distances, integrated Rautmann formulas (integrated width surface water body) used FOCUS drift calculations. PEC drainage calculations, methods used UK tier 1 Germany implemented. runoff, German method used tier 1 available. output FOCUS TOXSWA calculations can read , plotted, evaluated using TOXSWA cwa class giving maximum time weighted average concentrations peak statistics way available using EPAT tool.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Utilities for Pesticide Fate Modelling","text":"easiest way install package probably use r-universe repo: packages R-universe provided slight delay. Alternatively, can install package directly github, e.g. using pak.","code":"install.packages(\"pfm\", repos = c(\"https://jranke.r-universe.dev\", \"https://cran.r-project.org\")) # install.packages(\"pak\") pak::pak(\"jranke/pfm\")"},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"use","dir":"","previous_headings":"","what":"Use","title":"Utilities for Pesticide Fate Modelling","text":"Please refer reference.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Utilities for Pesticide Fate Modelling","text":"One nice example usage package visualisation time weighted average sawtooth curve obtained several overlays mkinfit predictions shown .","code":""},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"applications","dir":"","previous_headings":"","what":"Applications","title":"Utilities for Pesticide Fate Modelling","text":"Calculations predicted environmental concentrations using package used publications Agroscope.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"Subset EFSA crop interception default values groundwater modelling","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"","code":"EFSA_GW_interception_2014"},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"matrix containing interception values, currently selected crops","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"European Food Safety Authority (2014) EFSA Guidance Document evaluating laboratory field dissipation studies obtain DegT50 values active substances plant protection products transformation products active substances soil. EFSA Journal 12(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"","code":"EFSA_GW_interception_2014 #> BBCH #> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x #> Beans (field + vegetable) 0 0.25 0.40 0.40 0.70 0.70 0.70 0.70 0.70 0.80 #> Peas 0 0.35 0.55 0.55 0.85 0.85 0.85 0.85 0.85 0.85 #> Summer oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90 #> Winter oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90 #> Tomatoes 0 0.50 0.70 0.70 0.80 0.80 0.80 0.80 0.80 0.50 #> Spring cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80 #> Winter cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80"},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"Subset EFSA crop washoff default values","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"","code":"EFSA_washoff_2017"},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"matrix containing wash-factors, currently selected crops","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"European Food Safety Authority (2017) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 15(10) 4982 doi:10.2903/j.efsa.2017.4982","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"","code":"EFSA_washoff_2017 #> BBCH #> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x #> Beans (field + vegetable) NA 0.60 0.75 0.75 0.80 0.80 0.80 0.80 0.80 0.35 #> Peas NA 0.40 0.60 0.60 0.65 0.65 0.65 0.65 0.65 0.35 #> Summer oilseed rape NA 0.40 0.50 0.50 0.60 0.60 0.60 0.60 0.60 0.50 #> Winter oilseed rape NA 0.10 0.40 0.40 0.55 0.55 0.55 0.55 0.55 0.30 #> Tomatoes NA 0.55 0.75 0.75 0.70 0.70 0.70 0.70 0.70 0.35 #> Spring cereals NA 0.40 0.50 0.50 0.65 0.65 0.65 0.65 0.65 0.55 #> Winter cereals NA 0.10 0.40 0.60 0.55 0.55 0.55 0.60 0.60 0.40"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html","id":null,"dir":"Reference","previous_headings":"","what":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"Currently, scenario names acronyms small subset soil definitions provided. soil definitions page 46ff. FOCUS (2012).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"","code":"FOCUS_GW_scenarios_2012"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"FOCUS (2012) Generic guidance Tier 1 FOCUS ground water assessments. Version 2.1. FOrum Co-ordination pesticde fate models USe. http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"","code":"FOCUS_GW_scenarios_2012 #> $names #> Cha Ham Jok Kre Oke #> \"Châteadun\" \"Hamburg\" \"Jokioinen\" \"Kremsmünster\" \"Okehampton\" #> Pia Por Sev Thi #> \"Piacenza\" \"Porto\" \"Sevilla\" \"Thiva\" #> #> $soils #> location horizon number pH_H2O perc_clay perc_oc rel_deg #> 1 Cha Ap 1 8.0 30.0 1.39 1.0 #> 2 Cha B1 2 8.1 31.0 0.93 0.5 #> 3 Cha B2 3 8.2 25.0 0.70 0.5 #> 4 Cha II C1 4 8.5 26.0 0.30 0.3 #> 5 Cha II C1 5 8.5 26.0 0.30 0.0 #> 6 Cha II C2 6 8.5 24.0 0.27 0.0 #> 7 Cha M 7 8.3 31.0 0.21 0.0 #> 8 Ham Ap 1 6.4 7.2 1.50 1.0 #> 9 Ham BvI 2 5.6 6.7 1.00 0.5 #> 10 Ham BvII 3 5.6 0.9 0.20 0.3 #> 11 Ham Bv/Cv 4 5.7 0.0 0.00 0.3 #> 12 Ham Cv 5 5.5 0.0 0.00 0.3 #> 13 Ham Cv 6 5.5 0.0 0.00 0.0 #> 14 Jok Ap 1 6.2 3.6 4.06 1.0 #> 15 Jok Bs 2 5.6 1.8 0.84 0.5 #> 16 Jok BC1 3 5.4 1.2 0.36 0.3 #> 17 Jok BC2 4 5.4 1.7 0.29 0.3 #> 18 Jok BC2 5 5.4 1.7 0.29 0.0 #> 19 Jok Cg 6 5.3 1.9 0.21 0.0 #> 20 Kre <NA> 1 7.7 14.0 3.60 1.0 #> 21 Kre <NA> 2 7.0 25.0 1.00 0.5 #> 22 Kre <NA> 3 7.1 27.0 0.50 0.5 #> 23 Kre <NA> 4 7.1 27.0 0.50 0.3 #> 24 Kre <NA> 5 7.1 27.0 0.50 0.0 #> 25 Oke A 1 5.8 18.0 2.20 1.0 #> 26 Oke Bw1 2 6.3 17.0 0.70 0.5 #> 27 Oke BC 3 6.5 14.0 0.40 0.3 #> 28 Oke C 4 6.6 9.0 0.10 0.3 #> 29 Oke C 5 6.6 9.0 0.10 0.0 #> 30 Pia Ap 1 7.0 15.0 1.26 1.0 #> 31 Pia Ap 2 7.0 15.0 1.26 0.5 #> 32 Pia Bw 3 6.3 7.0 0.47 0.5 #> 33 Pia Bw 4 6.3 7.0 0.47 0.3 #> 34 Pia 2C 5 6.4 0.0 0.00 0.3 #> 35 Pia 2C 6 6.4 0.0 0.00 0.0 #> 36 Por <NA> 1 4.9 10.0 1.42 1.0 #> 37 Por <NA> 2 4.8 8.0 0.78 0.5 #> 38 Por <NA> 3 4.8 8.0 0.78 0.3 #> 39 Por <NA> 4 4.8 8.0 0.78 0.0 #> 40 Sev <NA> 1 7.3 14.0 0.93 1.0 #> 41 Sev <NA> 2 7.3 13.0 0.93 1.0 #> 42 Sev <NA> 3 7.8 15.0 0.70 0.5 #> 43 Sev <NA> 4 8.1 16.0 0.58 0.3 #> 44 Sev <NA> 5 8.1 16.0 0.58 0.0 #> 45 Sev <NA> 6 8.2 22.0 0.49 0.0 #> 46 Thi Ap1 1 7.7 25.3 0.74 1.0 #> 47 Thi Ap2 2 7.7 25.3 0.74 0.5 #> 48 Thi Bw 3 7.8 29.6 0.57 0.5 #> 49 Thi Bw 4 7.8 31.9 0.31 0.3 #> 50 Thi Ck1 5 7.8 32.9 0.18 0.3 #> 51 Thi Ck1 6 7.8 32.9 0.18 0.0 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.html","id":null,"dir":"Reference","previous_headings":"","what":"Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios","title":"Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios","text":"data extracted scenario.txt file using R code shown . text file included package licence clear.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios","text":"list containing scenario names character vector called 'names', drift percentiles matrix called 'drift', interception percentages matrix called 'interception' runoff/drainage percentages Step 2 calculations matrix called 'rd'.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios","text":"","code":"# \\dontrun{ # This is the code that was used to extract the data scenario_path <- \"inst/extdata/FOCUS_Step_12_scenarios.txt\" scenarios <- readLines(scenario_path)[9:38] #> Warning: cannot open file 'inst/extdata/FOCUS_Step_12_scenarios.txt': No such file or directory #> Error in file(con, \"r\"): cannot open the connection FOCUS_Step_12_scenarios <- list() sce <- read.table(text = scenarios, sep = \"\\t\", header = TRUE, check.names = FALSE, stringsAsFactors = FALSE) #> Error: object 'scenarios' not found FOCUS_Step_12_scenarios$names = sce$Crop #> Error: object 'sce' not found rownames(sce) <- sce$Crop #> Error: object 'sce' not found FOCUS_Step_12_scenarios$drift = sce[, 3:11] #> Error: object 'sce' not found FOCUS_Step_12_scenarios$interception = sce[, 12:15] #> Error: object 'sce' not found sce_2 <- readLines(scenario_path)[41:46] #> Warning: cannot open file 'inst/extdata/FOCUS_Step_12_scenarios.txt': No such file or directory #> Error in file(con, \"r\"): cannot open the connection rd <- read.table(text = sce_2, sep = \"\\t\")[1:2] #> Error: object 'sce_2' not found rd_mat <- matrix(rd$V2, nrow = 3, byrow = FALSE) #> Error: object 'rd' not found dimnames(rd_mat) = list(Time = c(\"Oct-Feb\", \"Mar-May\", \"Jun-Sep\"), Region = c(\"North\", \"South\")) #> Error: object 'rd_mat' not found FOCUS_Step_12_scenarios$rd = rd_mat #> Error: object 'rd_mat' not found save(FOCUS_Step_12_scenarios, file = \"data/FOCUS_Step_12_scenarios.RData\") #> Warning: cannot open compressed file 'data/FOCUS_Step_12_scenarios.RData', probable reason 'No such file or directory' #> Error in gzfile(file, \"wb\"): cannot open the connection # } # And this is the resulting data FOCUS_Step_12_scenarios #> list()"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":null,"dir":"Reference","previous_headings":"","what":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"Actual maximum moving window time average concentrations FOMC kinetics","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"","code":"FOMC_actual_twa( alpha = 1.0001, beta = 10, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100) )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"FOCUS (2014) Generic Guidance Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration, Version 1.1, 18 December 2014, p. 251","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"alpha Parameter FOMC model beta Parameter FOMC model times output times, window sizes time weighted average concentrations","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"","code":"FOMC_actual_twa(alpha = 1.0001, beta = 10) #> actual twa #> 0 1.00000000 NaN #> 1 0.90908224 0.9530973 #> 2 0.83331814 0.9115995 #> 4 0.71426168 0.8411664 #> 7 0.58820408 0.7580202 #> 14 0.41663019 0.6253074 #> 21 0.32254415 0.5387324 #> 28 0.26312277 0.4767543 #> 42 0.19227599 0.3925054 #> 50 0.16663681 0.3583198 #> 100 0.09088729 0.2397608"},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":null,"dir":"Reference","previous_headings":"","what":"Groundwater ubiquity score based on Gustafson (1989) — GUS","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"groundwater ubiquity score GUS calculated according following equation $$GUS = \\log_{10} DT50_{soil} (4 - \\log_{10} K_{oc})$$","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"","code":"GUS(...) # S3 method for class 'numeric' GUS(DT50, Koc, ...) # S3 method for class 'chent' GUS( chent, degradation_value = \"DT50ref\", lab_field = \"laboratory\", redox = \"aerobic\", sorption_value = \"Kfoc\", degradation_aggregator = geomean, sorption_aggregator = geomean, ... ) # S3 method for class 'GUS_result' print(x, ..., digits = 1)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"... Included generic allow arguments later. Therefore also added specific methods. DT50 Half-life chemical soil. field half-life according Gustafson (1989). However, leaching sub-soil can completely excluded field dissipation experiments Gustafson refer normalisation procedure, says field study conducted use conditions. Koc sorption constant normalised organic carbon. Gustafson mention nonlinearity sorption constant commonly found usually described Freundlich sorption, therefore unclear reference concentration Koc observed (reference concentration soil porewater). chent chent given appropriate information present chyaml field, information used, defaults specified . degradation_value available degradation values used? lab_field laboratory field half-lives used? defaults lab implementation, order avoid double-accounting mobility. comparability original GUS values given Gustafson (1989) desired, non-normalised first-order field half-lives obtained actual use conditions used. redox Aerobic anaerobic degradation data sorption_value available sorption values used? Defaults Kfoc generally available European pesticide peer review process. values generally use reference concentration 1 mg/L porewater, means expected Koc values concentration 1 mg/L water phase. degradation_aggregator Function aggregating half-lives sorption_aggregator Function aggregation Koc values x object class GUS_result printed digits number digits used print method","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"list DT50 Koc used well resulting score class GUS_result","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"Gustafson, David . (1989) Groundwater ubiquity score: simple method assessing pesticide leachability. Environmental toxicology chemistry 8(4) 339–57.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","title":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","text":"Get relative accumulation FOMC model multiples interval","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","text":"","code":"PEC_FOMC_accu_rel(n, interval, FOMC)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","text":"n number applications interval Time applications FOMC Named numeric vector containing FOMC parameters alpha beta","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","text":"numeric vector containing n accumulation factors n applications","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate predicted environmental concentrations in soil — PEC_soil","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"basic calculation contaminant concentration bulk soil based complete, instantaneous mixing. interval given, attempt made calculating long term maximum concentration using concepts layed PPR panel opinion (EFSA PPR panel 2012 EFSA guidance PEC soil calculations (EFSA, 2015, 2017).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"","code":"PEC_soil( rate, rate_units = \"g/ha\", interception = 0, mixing_depth = 5, PEC_units = \"mg/kg\", PEC_pw_units = \"mg/L\", interval = NA, n_periods = Inf, tillage_depth = 20, leaching_depth = tillage_depth, crop = \"annual\", cultivation = FALSE, chent = NA, DT50 = NA, FOMC = NA, Koc = NA, Kom = Koc/1.724, t_avg = 0, t_act = NULL, scenarios = c(\"default\", \"EFSA_2017\", \"EFSA_2015\"), leaching = scenarios == \"EFSA_2017\", porewater = FALSE )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"rate Application rate units specified rate_units Defaults g/ha interception fraction application rate reach soil mixing_depth Mixing depth cm PEC_units Requested units calculated PEC. mg/kg currently supported PEC_pw_units mg/L currently supported interval Period deeper mixing. default NA, .e. deeper mixing. annual deeper mixing, set 365 degradation units days n_periods Number periods considered long term PEC calculations tillage_depth Periodic (see interval) deeper mixing cm leaching_depth EFSA (2017) uses mixing depth (ecotoxicological evaluation depth) calculate leaching annual crops tillage takes place. default, losses layer tillage depth taken account implementation. crop Ignored scenarios EFSA_2017. annual crops supported scenarios used. crops single cropping cycle per year currently supported. cultivation mechanical cultivation sense EFSA (2017) take place, .e. twice year depth 5 cm? Ignored scenarios EFSA_2017 chent optional chent object holding substance specific information. Can also name substance character string DT50 specified, overrides soil DT50 endpoints chent object DT50 specified available chent object, zero degradation assumed FOMC specified, named numeric vector containing FOMC parameters alpha beta. overrides degradation endpoints, degradation interval maximum PEC calculated using parameters without temperature correction Koc specified, overrides Koc endpoints chent object Kom Calculated Koc default, can explicitly specified Kom t_avg Averaging times time weighted average concentrations t_act Time series actual concentrations scenarios 'default', soil bulk density 1.5 kg/L used. DT50 used without correction soil properties specified REACH guidance (R.16, Table R.16-9) used porewater PEC calculations. \"EFSA_2015\", DT50 taken modelling half-life 20°C pF2 ('chent' specified, DegT50 destination 'PECgw' used), corrected using Arrhenius activation energy 65.4 kJ/mol. Also model scenario adjustment factors EFSA guidance used. leaching leaching taken account? default FALSE, except EFSA_2017 scenarios used. porewater equilibrium porewater concentrations estimated based Kom organic carbon fraction soil instead total soil concentrations? Based equation (7) given PPR panel opinion (EFSA 2012, p. 24) scenarios specified EFSA guidance (2015, p. 13).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"predicted concentration soil","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"assumes complete load soil time specified 'interval' (typically 365 days) dosed . PPR panel opinion cited (EFSA PPR panel 2012), temperature correction using Arrhenius equation performed. Total soil porewater PEC values scenarios defined EFSA guidance (2017, p. 14/15) can easily calculated.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"time weighted average (TWA) concentrations given examples EFSA guidance 2015 (p. 80) can reproduced, true TWA concentrations given example EFSA guidance 2017 (p. 92). According EFSA guidance (EFSA, 2017, p. 43), leaching taken account EFSA 2017 scenarios, using evaluation depth (mixing depth) depth layer leaching takes place. However, amount leaching evaluation depth (often 5 cm) partly mixed back tillage, default function use tillage depth calculation leaching rate. temperature information available selected scenarios, e.g. EFSA scenarios, DT50 groundwater modelling (destination 'PECgw') taken chent object, otherwise DT50 destination 'PECsoil'.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"EFSA Panel Plant Protection Products Residues (2012) Scientific Opinion science behind guidance scenario selection scenario parameterisation predicting environmental concentrations plant protection products soil. EFSA Journal 10(2) 2562, doi:10.2903/j.efsa.2012.2562 EFSA (European Food Safety Authority) 2017) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 15(10) 4982 doi:10.2903/j.efsa.2017.4982 EFSA (European Food Safety Authority) (2015) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 13(4) 4093 doi:10.2903/j.efsa.2015.4093","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"","code":"PEC_soil(100, interception = 0.25) #> scenario #> t_avg default #> 0 0.1 # This is example 1 starting at p. 92 of the EFSA guidance (2017) # Note that TWA concentrations differ from the ones given in the guidance # for an unknown reason (the values from EFSA (2015) can be reproduced). PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), Kom = 1000, scenarios = \"EFSA_2017\") #> scenario #> t_avg CTN CTC CTS #> 0 19.76834 13.8619 10.53795 #> 21 19.59345 13.7169 10.39882 PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), Kom = 1000, scenarios = \"EFSA_2017\", porewater = TRUE) #> scenario #> t_avg CLN CLC CLS #> 0 0.5541984 0.6779249 0.9816693 #> 21 0.5484576 0.6693125 0.9609119 # This is example 1 starting at p. 79 of the EFSA guidance (2015) PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), scenarios = \"EFSA_2015\") #> scenario #> t_avg CTN CTC CTS #> 0 21.96827 11.53750 9.145259 #> 21 21.78517 11.40701 9.017370 PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), Kom = 1000, scenarios = \"EFSA_2015\", porewater = TRUE) #> scenario #> t_avg CLN CLC CLS #> 0 0.7589401 0.6674322 0.9147861 #> 21 0.7506036 0.6590345 0.8987279 # The following is from example 4 starting at p. 85 of the EFSA guidance (2015) # Metabolite M2 # Calculate total and porewater soil concentrations for tier 1 scenarios # Relative molar mass is 100/300, formation fraction is 0.7 * 1 results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), scenarios = \"EFSA_2015\") results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), Kom = 100, scenarios = \"EFSA_2015\", porewater = TRUE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil_mets.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets","title":"Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets","text":"Calculate initial accumulation PEC soil set metabolites","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil_mets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets","text":"","code":"PEC_soil_mets(rate, mw_parent, mets, interval = 365, ...)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil_mets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets","text":"rate Application rate units specified mw_parent molecular weight parent compound mets dataframe metabolite identifiers rownames columns \"mw\", \"occ\" \"DT50\" holding molecular weight, maximum occurrence soil soil DT50 interval interval accumulation calculations ... arguments passed PEC_soil","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"implements method specified UK data requirements handbook checked spreadsheet published CRC website. Degradation end (30 April) start (1 October) drainage period taken account latest_application specified degradation parameters given either soil_DT50 model.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"","code":"PEC_sw_drainage_UK( rate, interception = 0, Koc, latest_application = NULL, soil_DT50 = NULL, model = NULL, model_parms = NULL ) drainage_date_UK(application_date)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"rate Application rate g/ha compatible unit specified units package interception fraction application rate reach soil Koc sorption coefficient normalised organic carbon L/kg unit specified units package latest_application Latest application date, formatted e.g. \"01 July\" soil_DT50 Soil degradation half-life, SFO kinetics used, days time unit specified units package model soil degradation model used. Either one \"FOMC\", \"DFOP\", \"HS\", \"IORE\", mkinmod object model_parms named numeric vector containing model parameters application_date Application date","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"predicted concentration surface water µg/L","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"HSE's Chemicals Regulation Division (CRD) Active substance PECsw calculations (UK specific authorisation requests) https://www.hse.gov.uk/pesticides/data-requirements-handbook/fate/pecsw-sed-via-drainflow.htm accessed 2026-02-13 PECsw/sed spray drift tier 1 drainflow calculator Version 2.1.1 (2025) Spreadsheet published https://www.hse.gov.uk/pesticides/assets/docs/PEC%20sw-sed%20(spraydrift).xlsx) accessed 2026-02-13","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"","code":"PEC_sw_drainage_UK(150, Koc = 100) #> 8.076923 [µg/L] PEC_sw_drainage_UK(60, interception = 0.5, Koc = 550, latest_application = \"01 July\", soil_DT50 = 200) #> 0.8388303 [µg/L] drainage_date_UK(\"2023-07-10\") #> [1] \"2023-10-01\" drainage_date_UK(\"2020-12-01\") #> [1] \"2020-12-01\" drainage_date_UK(as.Date(\"2022-01-15\")) #> [1] \"2022-01-15\""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"basic, vectorised form simple calculation contaminant concentration surface water based complete, instantaneous mixing input via spray drift.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"","code":"PEC_sw_drift( rate, applications = 1, water_depth = as_units(\"30 cm\"), drift_percentages = NULL, drift_data = c(\"JKI\", \"RF\"), crop_group_JKI = \"Ackerbau\", crop_group_RF = \"arable\", distances = c(1, 5, 10, 20), formula = c(\"Rautmann\", \"FOCUS\"), water_width = as_units(\"100 cm\"), side_angle = 90, rate_units = \"g/ha\", PEC_units = \"µg/L\" )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"rate Application rate units specified , units defined via units package. applications Number applications selection drift percentile water_depth Depth water body cm drift_percentages Percentage drift values calculate PECsw. Overrides 'drift_data', 'distances', 'applications', crop group formula arguments NULL. drift_data Source drift percentage data. 'JKI', drift_data_JKI included package used. 'RF', Rautmann drift data calculated either original form integrated width water body, depending 'formula' argument. crop_group_JKI using 'JKI' drift data, one German names used drift_data_JKI. used drift_data 'JKI'. Available crop groups \"Ackerbau\", \"Obstbau frueh\", \"Obstbau spaet\", \"Weinbau frueh\", \"Weinbau spaet\", \"Hopfenbau\", \"Flaechenkulturen > 900 l/ha\" \"Gleisanlagen\". crop_group_RF Crop group(s) used drift_parameters_focus, .e. \"arable\", \"hops\", \"vines, late\", \"vines, early\", \"fruit, late\", \"fruit, early\" \"aerial\". distances distances m get PEC values formula default, original Rautmann formula used. specify \"FOCUS\", mean drift input width water body calculated described Chapter 5.4.5 FOCUS surface water guidance water_width Width water body cm side_angle angle side water relative bottom assumed horizontal, degrees. SYNOPS model assumes 45 degrees . rate_units Defaults g/ha. backwards compatibility, used specified rate units::units]. PEC_units Requested units calculated PEC. µg/L currently supported","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"numeric vector predicted concentration surface water. cases, vector named distances drift percentages, backward compatibility versions vectorisation arguments 'distances' introduced v0.6.5.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"recommened specify arguments rate, water_depth water_width using units::units units package. Since pfm version 0.6.5, function vectorised respect rates, applications, water depth, crop groups distances","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"","code":"PEC_sw_drift(100) #> Units: [µg/L] #> 1 m 5 m 10 m 20 m #> 0.92333333 0.19000000 0.09666667 0.05000000 # Alternatively, we can use the formula for a single application to # \"Ackerbau\" from the paper PEC_sw_drift(100, drift_data = \"RF\") #> Units: [µg/L] #> 1 m 5 m 10 m 20 m #> 0.91976667 0.19064473 0.09680051 0.04915079 # This makes it possible to also use different distances PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = \"RF\") #> Units: [µg/L] #> 1 m 3 m 5 m 6 m 10 m 20 m 50 m #> 0.91976667 0.31415827 0.19064473 0.15951494 0.09680051 0.04915079 0.02006434 #> 100 m #> 0.01018774 # or consider aerial application PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = \"RF\", crop_group_RF = \"aerial\") #> Units: [µg/L] #> 1 m 3 m 5 m 6 m 10 m 20 m 50 m #> 16.8233333 11.0585820 9.0986174 8.4866460 6.9825178 4.7004640 1.8820816 #> 100 m #> 0.9417586 # Using custom drift percentages is also supported PEC_sw_drift(100, drift_percentages = c(2.77, 0.95, 0.57, 0.48, 0.29, 0.15, 0.06, 0.03)) #> Units: [µg/L] #> 2.77 % 0.95 % 0.57 % 0.48 % 0.29 % 0.15 % 0.06 % #> 0.92333333 0.31666667 0.19000000 0.16000000 0.09666667 0.05000000 0.02000000 #> 0.03 % #> 0.01000000 # The influence of assuming a 45° angle of the sides of the waterbody and the width of the # waterbody can be illustrated PEC_sw_drift(100) #> Units: [µg/L] #> 1 m 5 m 10 m 20 m #> 0.92333333 0.19000000 0.09666667 0.05000000 PEC_sw_drift(100, drift_data = \"RF\") #> Units: [µg/L] #> 1 m 5 m 10 m 20 m #> 0.91976667 0.19064473 0.09680051 0.04915079 PEC_sw_drift(100, drift_data = \"RF\", formula = \"FOCUS\") #> Units: [µg/L] #> 1 m 5 m 10 m 20 m #> 0.64246407 0.17414541 0.09235842 0.04798749 PEC_sw_drift(100, drift_data = \"RF\", formula = \"FOCUS\", side_angle = 45) #> Units: [µg/L] #> 1 m 5 m 10 m 20 m #> 0.91780582 0.24877916 0.13194060 0.06855356 PEC_sw_drift(100, drift_data = \"RF\", formula = \"FOCUS\", side_angle = 45, water_width = 200) #> Units: [µg/L] #> 1 m 5 m 10 m 20 m #> 0.60169999 0.18937304 0.10402698 0.05517095 # The function is vectorised with respect to rates, applications, water depth, # crop groups and distances PEC_sw_drift( rate = rep(100, 6), applications = c(1, 2, rep(1, 4)), water_depth = c(30, 30, 30, 60, 30, 30), crop_group_JKI = c(rep(\"Ackerbau\", 4), rep(\"Obstbau frueh\", 2)), distances = c(rep(5, 4), 10, 5)) #> Units: [µg/L] #> 5 m 5 m 5 m 5 m 10 m 5 m #> 0.1900000 0.1566667 0.1900000 0.0950000 3.9366667 6.6300000 # Try the same with the Rautmann formula PEC_sw_drift( rate = rep(100, 6), applications = c(1, 2, rep(1, 4)), water_depth = c(30, 30, 30, 60, 30, 30), drift_data = \"RF\", crop_group_RF = c(rep(\"arable\", 4), rep(\"fruit, early\", 2)), distances = c(rep(5, 4), 10, 5)) #> Units: [µg/L] #> 5 m 5 m 5 m 5 m 10 m 5 m #> 0.19064473 0.15991216 0.19064473 0.09532236 3.93566026 6.62814740 # And with the FOCUS variant PEC_sw_drift( rate = rep(100, 6), applications = c(1, 2, rep(1, 4)), water_depth = c(30, 30, 30, 60, 30, 30), drift_data = \"RF\", formula = \"FOCUS\", crop_group_RF = c(rep(\"arable\", 4), rep(\"fruit, early\", 2)), distances = c(rep(5, 4), 10, 5)) #> Units: [µg/L] #> 5 m 5 m 5 m 5 m 10 m 5 m #> 0.1741454 0.1456444 0.1741454 0.0870727 3.7957683 6.1809560"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"reimplementation calculation described Exposit 3.02 spreadsheet file, worksheet \"Konzept Drainage\". Although four groups compounds (\"Gefährdungsgruppen\"), one distinction made calculations, compounds low mobility (group 1) compounds modest high mobility (groups 2, 3 4). implementation, group derived Koc, given explicitly. details, see discussion function arguments . recommened specify arguments rate, Koc, DT50, t_drainage, V_ditch V_drainage using units::units units package.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"","code":"PEC_sw_exposit_drainage( rate, interception = 0, Koc = NA, mobility = c(NA, \"low\", \"high\"), DT50 = set_units(Inf, \"d\"), t_drainage = set_units(3, \"days\"), V_ditch = set_units(30, \"m3\"), V_drainage = set_units(c(spring = 10, autumn = 100), \"m3\"), dilution = 2 )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"Excel 3.02 spreadsheet available https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"rate application rate g/ha interception fraction intercepted crop Koc sorption coefficient soil organic carbon used determine mobility. trigger value 550 L/kg used order decide Koc >> 500. mobility Overrides determined Koc. DT50 soil half-life days t_drainage time application drainage event, degradation occurs, days V_ditch volume ditch assumed 1 m * 100 m * 30 cm = 30 m3 V_drainage drainage volume, equivalent 1 mm precipitation 1 ha spring/summer 10 mm autumn/winter/early spring. dilution dilution factor","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"list containing following components perc_drainage_total Gesamtaustrag (total fraction residue drained) perc_peak Stoßbelastung (fraction drained event) PEC_sw_drainage matrix containing PEC values spring autumn scenarios. rate given g/ha, PECsw microg/L.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"","code":"PEC_sw_exposit_drainage(500, Koc = 150) #> $perc_drainage_total #> spring autumn #> 0.2 1.0 #> #> $perc_peak #> spring autumn #> 12.5 25.0 #> #> $PEC_sw_drainage #> Units: [µg/L] #> spring autumn #> 1.562500 4.807692 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"reimplementation calculation described Exposit 3.02 spreadsheet file, worksheet \"Konzept Runoff\".","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"","code":"PEC_sw_exposit_runoff( rate, interception = 0, Koc, DT50 = set_units(Inf, \"d\"), t_runoff = set_units(3, \"days\"), exposit_reduction_version = c(\"3.02\", \"3.01a\", \"3.01a2\", \"2.0\"), V_ditch = set_units(30, \"m3\"), V_event = set_units(100, \"m3\"), dilution = 2 )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"Excel 3.02 spreadsheet available https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"rate Application rate g/ha compatible unit specified units package interception fraction intercepted crop Koc sorption coefficient soil organic carbon DT50 soil half-life days t_runoff time application runoff event, degradation occurs, days exposit_reduction_version version reduction factors used. \"3.02\" current version used Germany, \"3.01a\" version additional percentages 3 m 6 m buffer zones used Switzerland. \"3.01a2\" version introduced consistency previous calculations performed 3 m buffer zone Switzerland, reduction applied dissolved bound fraction. V_ditch volume ditch assumed 1 m * 100 m * 30 cm = 30 m3 V_event unreduced runoff volume, equivalent 10 mm precipitation 1 ha dilution dilution factor","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"list containing following components perc_runoff runoff percentages dissolved bound substance runoff matrix containing dissolved bound input different distances PEC_sw_runoff dataframe containing PEC values dissolved bound substance different distances. rate given g/ha, PECsw microg/L.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"recommened specify arguments rate, Koc, DT50, t_runoff, V_ditch V_event using units::units units package.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"","code":"PEC_sw_exposit_runoff(500, Koc = 150) #> $perc_runoff #> dissolved bound #> 0.248 0.001 #> #> $runoff #> dissolved bound total #> No buffer 1.240 [g] 0.00500 [g] 1.24500 [g] #> 5 m 0.744 [g] 0.00300 [g] 0.74700 [g] #> 10 m 0.496 [g] 0.00075 [g] 0.49675 [g] #> 20 m 0.248 [g] 0.00025 [g] 0.24825 [g] #> #> $PEC_sw_runoff #> dissolved bound total #> No buffer 4.769231 [µg/L] 0.019230769 [µg/L] 4.788462 [µg/L] #> 5 m 4.133333 [µg/L] 0.016666667 [µg/L] 4.150000 [µg/L] #> 10 m 3.542857 [µg/L] 0.005357143 [µg/L] 3.548214 [µg/L] #> 20 m 2.480000 [µg/L] 0.002500000 [µg/L] 2.482500 [µg/L] #> PEC_sw_exposit_runoff(600, Koc = 10000, DT50 = 195, exposit = \"3.01a\") #> $perc_runoff #> dissolved bound #> 0.037 0.159 #> #> $runoff #> dissolved bound total #> No buffer 0.21964521 [g] 0.94388078 [g] 1.16352600 [g] #> 3 m 0.16473391 [g] 0.66071655 [g] 0.82545046 [g] #> 5 m 0.13178713 [g] 0.56632847 [g] 0.69811560 [g] #> 6 m 0.12080487 [g] 0.42474635 [g] 0.54555122 [g] #> 10 m 0.08785809 [g] 0.14158212 [g] 0.22944020 [g] #> 20 m 0.04392904 [g] 0.04719404 [g] 0.09112308 [g] #> #> $PEC_sw_runoff #> dissolved bound total #> No buffer 0.8447893 [µg/L] 3.6303107 [µg/L] 4.4751000 [µg/L] #> 3 m 0.7844472 [µg/L] 3.1462693 [µg/L] 3.9307165 [µg/L] #> 5 m 0.7321507 [µg/L] 3.1462693 [µg/L] 3.8784200 [µg/L] #> 6 m 0.7106169 [µg/L] 2.4985080 [µg/L] 3.2091248 [µg/L] #> 10 m 0.6275578 [µg/L] 1.0113008 [µg/L] 1.6388586 [µg/L] #> 20 m 0.4392904 [µg/L] 0.4719404 [µg/L] 0.9112308 [µg/L] #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"reimplementation FOCUS Step 1 2 calculator version 3.2, authored Michael Klein, R. Note results multiple applications compared corresponding results single application. current, done automatically implementation. Step 1 PECs calculated. However, input files can generated suitable input FOCUS calculator.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"","code":"PEC_sw_focus( parent, rate, n = 1, i = NA, comment = \"\", met = NULL, f_drift = NA, f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names, region = c(\"n\", \"s\"), season = c(NA, \"of\", \"mm\", \"js\"), interception = c(\"no interception\", \"minimal crop cover\", \"average crop cover\", \"full canopy\"), met_form_water = TRUE, txt_file = \"pesticide.txt\", overwrite = FALSE, append = FALSE )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"parent list containing substance specific parameters, e.g. conveniently generated chent_focus_sw. rate application rate g/ha. Overriden applications given explicitly n number applications application interval comment comment input file met list containing metabolite specific parameters. e.g. conveniently generated chent_focus_sw. NULL, PEC calculated compound, parent. f_drift fraction application rate reaching waterbody via drift. NA, derived scenario name number applications via drift data defined FOCUS_Step_12_scenarios f_rd fraction amount applied reaching waterbody via runoff/drainage. Step 1, assumed 10%, parent metabolite scenario name scenario. Must one scenario names given FOCUS_Step_12_scenarios region 'n' Northern Europe 's' Southern Europe. NA, Step 1 PECsw calculated season '' October February, 'mm' March May, 'js' June September. NA, step 1 PECsw calculated interception One 'interception' (default), 'minimal crop cover', 'average crop cover' 'full canopy' met_form_water metabolite formation water taken account? can switched check influence compare previous versions Steps 12 calculator txt_file name, potentially full path Steps.12 input text file specification run(s) written overwrite existing file location specified txt_file overwritten? takes effect append FALSE. append input text file appended, exists?","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"formulas input waterbody via runoff/drainage parent subsequent formation metabolite water documented model description coming calculator. one expect, appears (get results) calculated multiplying application rate molar weight correction formation fraction water/sediment systems. Step 2 implemented.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"FOCUS (2014) Generic guidance Surface Water Scenarios (version 1.4). FOrum Co-ordination pesticde fate models USe. http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf Website Steps 1 2 calculator Joint Research Center European Union: http://esdac.jrc.ec.europa.eu/projects/stepsonetwo","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"","code":"# Parent only dummy_1 <- chent_focus_sw(\"Dummy 1\", cwsat = 6000, DT50_ws = 6, Koc = 344.8) PEC_sw_focus(dummy_1, 3000, f_drift = 0) #> $f_drift #> [1] 0 #> #> $eq_rate_drift_s #> [1] 3000 #> #> $eq_rate_rd_s #> [1] 3000 #> #> $eq_rate_rd_parent_s #> [1] NA #> #> $input_drift_s #> [1] 0 #> #> $input_rd_s #> [1] 300 #> #> $f_rd_sw #> [1] 0.6850566 #> #> $f_rd_sed #> [1] 0.3149434 #> #> $PEC #> type #> Time PECsw TWAECsw PECsed TWAECsed #> 0 6.850566e+02 NA 2.362075e+03 NA #> 1 6.103161e+02 647.68635 2.104370e+03 2233.2225 #> 2 5.437298e+02 612.03420 1.874780e+03 2110.2939 #> 4 4.315586e+02 548.76030 1.488014e+03 1892.1255 #> 7 3.051580e+02 469.88375 1.052185e+03 1620.1592 #> 14 1.359325e+02 339.57370 4.686951e+02 1170.8501 #> 21 6.055102e+01 257.45458 2.087799e+02 887.7034 #> 28 2.697241e+01 203.47173 9.300089e+01 701.5705 #> 42 5.352005e+00 140.10377 1.845371e+01 483.0778 #> 50 2.123945e+00 118.24602 7.323361e+00 407.7123 #> 100 6.585062e-03 59.30629 2.270529e-02 204.4881 #> #> $PEC_sw_max #> [1] 685.0566 #> #> $PEC_sed_max #> [1] 2362.075 #> # Metabolite new_dummy <- chent_focus_sw(\"New Dummy\", mw = 250, Koc = 100) M1 <- chent_focus_sw(\"M1\", mw = 100, cwsat = 100, DT50_ws = 100, Koc = 50, max_ws = 0, max_soil = 0.5) PEC_sw_focus(new_dummy, 1000, scenario = \"cereals, winter\", met = M1) #> $f_drift #> [1] 0.02759 #> #> $eq_rate_drift_s #> [1] 0 #> #> $eq_rate_rd_s #> [1] 200 #> #> $eq_rate_rd_parent_s #> [1] 0 #> #> $input_drift_s #> [1] 0 #> #> $input_rd_s #> [1] 20 #> #> $f_rd_sw #> [1] 0.9375 #> #> $f_rd_sed #> [1] 0.0625 #> #> $PEC #> type #> Time PECsw TWAECsw PECsed TWAECsed #> 0 62.50000 NA 31.25000 NA #> 1 62.06828 62.28414 31.03414 31.14207 #> 2 61.63954 62.06890 30.81977 31.03445 #> 4 60.79093 61.64158 30.39547 30.82079 #> 7 59.53987 61.00800 29.76994 30.50400 #> 14 56.71995 59.56326 28.35997 29.78163 #> 21 54.03358 58.16414 27.01679 29.08207 #> 28 51.47444 56.80902 25.73722 28.40451 #> 42 46.71404 54.22460 23.35702 27.11230 #> 50 44.19417 52.81945 22.09709 26.40973 #> 100 31.25000 45.08422 15.62500 22.54211 #> #> $PEC_sw_max #> [1] 62.5 #> #> $PEC_sed_max #> [1] 31.25 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","title":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","text":"method 'percentage' equivalent used CRD spreadsheet PEC calculator","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","text":"","code":"PEC_sw_sed( PEC_sw, percentage = 100, method = \"percentage\", sediment_depth = set_units(5, \"cm\"), water_depth = set_units(30, \"cm\"), sediment_density = set_units(1.3, \"kg/L\"), PEC_sed_units = c(\"µg/kg\", \"mg/kg\") )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","text":"PEC_sw Numeric vector matrix surface water concentrations µg/L corresponding sediment concentration estimated percentage percentage sediment, used percentage method method method used calculation sediment_depth Depth sediment layer water_depth Depth water body cm sediment_density density sediment kg/L (equivalent g/cm3) PEC_sed_units units estimated sediment PEC value","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","text":"predicted concentration sediment","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","text":"","code":"library(pfm) library(units) #> udunits database from /usr/share/xml/udunits/udunits2.xml PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50) #> 2.130769 [µg/kg]"},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":null,"dir":"Reference","previous_headings":"","what":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"Actual maximum moving window time average concentrations SFO kinetics","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"","code":"SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100))"},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"FOCUS (2014) Generic Guidance Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration, Version 1.1, 18 December 2014, p. 251","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"DT50 half-life. times output times, window sizes time weighted average concentrations","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"","code":"SFO_actual_twa(10) #> actual twa #> 0 1.0000000000 NaN #> 1 0.9330329915 0.9661297 #> 2 0.8705505633 0.9337803 #> 4 0.7578582833 0.8733416 #> 7 0.6155722067 0.7923030 #> 14 0.3789291416 0.6400113 #> 21 0.2332582479 0.5267498 #> 28 0.1435872944 0.4412651 #> 42 0.0544094102 0.3248093 #> 50 0.0312500000 0.2795222 #> 100 0.0009765625 0.1441286"},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"implements method specified UK data requirements handbook checked spreadsheet published CRD website","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"","code":"SSLRC_mobility_classification(Koc)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"Koc sorption coefficient normalised organic carbon L/kg","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"list containing classification percentage compound transported per 10 mm drain water","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"HSE's Chemicals Regulation Division (CRD) Active substance PECsw calculations (UK specific authorisation requests) https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm accessed 2019-09-27 Drainage PECs Version 1.0 (2015) Spreadsheet published https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx accessed 2019-09-27","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"","code":"SSLRC_mobility_classification(100) #> $`Mobility classification` #> [1] \"Moderately mobile\" #> #> $`Percentage drained per mm of drain water` #> [1] 0.7 #> SSLRC_mobility_classification(10000) #> $`Mobility classification` #> [1] \"Non mobile\" #> #> $`Percentage drained per mm of drain water` #> [1] 0.008 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"R6 class holding TOXSWA water concentration (cwa) data associated statistics. like maximum moving window average concentrations, dataframes holding events exceeding specified thresholds. Usually, instance class generated read.TOXSWA_cwa.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"R6::R6Class generator object.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"filename Length one character vector holding filename. basedir Length one character vector holding directory file came . zipfile null, giving path zip file file read. segment Length one integer, specifying segment cwa data read. substance TOXSWA name substance. cwas Dataframe holding concentrations. events List dataframes holding event statistics threshold. windows Matrix maximum time weighted average concentrations (TWAC_max) areas curve µg/day * h (AUC_max_h) µg/day * d (AUC_max_d) requested moving window sizes days.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"TOXSWA_cwa$new() TOXSWA_cwa$moving_windows() TOXSWA_cwa$get_events() TOXSWA_cwa$print() TOXSWA_cwa$clone()","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"toxswa-cwa-new-","dir":"Reference","previous_headings":"","what":"TOXSWA_cwa$new()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"Create TOXSWA_cwa object file","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$new( filename, basedir, zipfile = NULL, segment = \"last\", substance = \"parent\", total = FALSE )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"filename filename basedir directory look zipfile Optional path zipfile holding file segment Either \"last\" number segment read data substance TOXSWA substance name (TOXSWA 4 higher) total total concentrations read ? FALSE, free concentrations read","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"toxswa-cwa-moving-windows-","dir":"Reference","previous_headings":"","what":"TOXSWA_cwa$moving_windows()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"Add windows field described .","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$moving_windows(windows, total = FALSE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"windows Window sizes days total TRUE, total concentration including amount adsorbed suspended matter used.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"toxswa-cwa-get-events-","dir":"Reference","previous_headings":"","what":"TOXSWA_cwa$get_events()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"Populate datataframe event information specified threshold value. resulting dataframe stored events field object.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$get_events(thresholds, total = FALSE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"thresholds Threshold values µg/L. total TRUE, total concentration including amount adsorbed suspended matter used.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"toxswa-cwa-print-","dir":"Reference","previous_headings":"","what":"TOXSWA_cwa$print()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"Print TOXSWA_cwa object","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$print()"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"toxswa-cwa-clone-","dir":"Reference","previous_headings":"","what":"TOXSWA_cwa$clone()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"H_sw_R1_stream <- read.TOXSWA_cwa(\"00003s_pa.cwa\", basedir = \"SwashProjects/project_H_sw/TOXSWA\", zipfile = system.file(\"testdata/SwashProjects.zip\", package = \"pfm\")) H_sw_R1_stream$get_events(c(2, 10)) H_sw_R1_stream$moving_windows(c(7, 21)) print(H_sw_R1_stream) #> <TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 #> datetime t t_firstjan t_rel_to_max cwa_mug_per_L #> 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0 #> 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0 #> 60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0 #> 80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0 #> 100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0 #> 120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0 #> cwa_tot_mug_per_L #> 20 0 #> 40 0 #> 60 0 #> 80 0 #> 100 0 #> 120 0 #> Moving window analysis #> window max_TWAC max_AUC_h max_AUC_d #> 1 7 days 2.3926551 401.9660 16.74859 #> 2 21 days 0.8369248 421.8101 17.57542 #> Event statistics for threshold 2 #> t_start cwa_max duration pre_interval AUC_h AUC_d #> 1 44.375 4.167238 0.208 44.375 17.77202 0.740501 #> 2 55.042 40.584010 0.583 10.459 398.21189 16.592162 #> Event statistics for threshold 10 #> t_start cwa_max duration pre_interval AUC_h AUC_d #> 1 55.083 40.58401 0.459 55.083 379.433 15.80971"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":null,"dir":"Reference","previous_headings":"","what":"Estimation of the transpiration stream concentration factor — TSCF","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"FOCUS groundwater guidance (FOCUS 2014, p. 41) states reliable measured log Kow neutral pH must available order apply Briggs equation. clarified can regarded reliable, equation stated produced non-ionic compounds, suggesting compound ionogenic (weak acid/base) ionic.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"","code":"TSCF(log_Kow, method = c(\"briggs82\", \"dettenmaier09\"))"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"log_Kow decadic logarithm octanol-water partition constant method Short name estimation method.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"Dettenmaier equation given show views subject exist.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"FOCUS (2014) Generic Guidance Tier 1 FOCUS Ground Water Assessments. Version 2.2, May 2014 Dettenmaier EM, Doucette WJ Bugbee B (2009) Chemical hydrophobicity uptake plant roots. Environ. Sci. Technol 43, 324 - 329","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"","code":"plot(TSCF, -1, 5, xlab = \"log Kow\", ylab = \"TSCF\", ylim = c(0, 1.1)) TSCF_2 <- function(x) TSCF(x, method = \"dettenmaier09\") curve(TSCF_2, -1, 5, add = TRUE, lty = 2) legend(\"topright\", lty = 1:2, bty = \"n\", legend = c(\"Briggs et al. (1982)\", \"Dettenmaier et al. (2009)\"))"},{"path":"https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","title":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","text":"Create chemical compound object FOCUS Step 1 calculations","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","text":"","code":"chent_focus_sw( name, Koc, DT50_ws = NA, DT50_soil = NA, DT50_water = NA, DT50_sediment = NA, cwsat = 1000, mw = NA, max_soil = 1, max_ws = 1 )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","text":"name Length one character vector containing name Koc Partition coefficient organic carbon water L/kg. DT50_ws Half-life water/sediment systems days DT50_soil Half-life soil days DT50_water Half-life water days (Step 2) DT50_sediment Half-life sediment days (Step 2) cwsat Water solubility mg/L mw Molar weight g/mol. max_soil Maximum observed fraction (dimensionless) soil max_ws Maximum observed fraction (dimensionless) water/sediment systems","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","text":"list substance specific properties","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":null,"dir":"Reference","previous_headings":"","what":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","title":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","text":"Deposition spray drift expressed percent applied dose published German Julius-Kühn Institute (JKI).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","text":"","code":"drift_data_JKI"},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","text":"list currently containing matrices spray drift percentage data field crops (Ackerbau), Pome/stone fruit, early late (Obstbau frueh, spaet).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","text":"JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html 2015-06-11, present 2024-01-31 Rautmann, D., Streloke, M Winkler, R (2001) New basic drift values authorization procedure plant protection products Mitt. Biol. Bundesanst. Land- Forstwirtsch. 383, 133-141","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","text":"data extracted spreadsheet cited using R code given file data_generation/drift_data_JKI.R installed package. file included package, licence clear. Additional spray drift values taken publication Rautmann et al. (2001). Specifically, values early vines, values 3 m buffer incomplete spreadsheet. Note vegetables, ornamentals small fruit, values field crops used crops < 50 cm, vales late vines used crops > 50 cm. JKI spreadsheet, indicated values used spray applications handheld/knapsack equipment (tragbare Spritz- und Sprühgerate). Values non-professional use listed JKI spreadsheet included.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","text":"","code":"drift_data_JKI #> [[1]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 2.77 NA NA NA NA #> 3 0.95 29.20 15.73 2.70 8.02 #> 5 0.57 19.89 8.41 1.18 3.62 #> 10 0.29 11.81 3.60 0.39 1.23 #> 15 0.20 5.55 1.81 0.20 0.65 #> 20 0.15 2.77 1.09 0.13 0.42 #> 30 0.10 1.04 0.54 0.07 0.22 #> 40 0.07 0.52 0.32 0.04 0.14 #> 50 0.06 0.30 0.22 0.03 0.10 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 4.440 NA #> 3 19.33 NA 0.018721696 #> 5 11.57 0.180 0.014363896 #> 10 5.77 0.050 0.010026007 #> 15 3.84 0.020 0.008124366 #> 20 1.79 0.012 0.006998158 #> 30 0.56 0.005 0.005670811 #> 40 0.25 0.003 NA #> 50 0.13 0.002 0.004350831 #> #> [[2]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 2.38 NA NA NA NA #> 3 0.79 25.53 12.13 2.53 7.23 #> 5 0.47 16.87 6.81 1.09 3.22 #> 10 0.24 9.61 3.11 0.35 1.07 #> 15 0.16 5.61 1.58 0.18 0.56 #> 20 0.12 2.59 0.90 0.11 0.36 #> 30 0.08 0.87 0.40 0.06 0.19 #> 40 0.06 0.40 0.23 0.03 0.12 #> 50 0.05 0.22 0.15 0.02 0.08 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 3.780 NA #> 3 17.73 NA NA #> 5 9.60 0.160 NA #> 10 4.18 0.040 NA #> 15 2.57 0.020 NA #> 20 1.21 0.011 NA #> 30 0.38 0.005 NA #> 40 0.17 0.003 NA #> 50 0.09 0.002 NA #> #> [[3]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 2.01 NA NA NA NA #> 3 0.68 23.96 11.01 2.49 6.90 #> 5 0.41 15.79 6.04 1.04 3.07 #> 10 0.20 8.96 2.67 0.32 1.02 #> 15 0.14 4.24 1.39 0.16 0.54 #> 20 0.10 2.01 0.80 0.10 0.34 #> 30 0.07 0.70 0.36 0.05 0.18 #> 40 0.05 0.33 0.21 0.03 0.11 #> 50 0.04 0.19 0.13 0.02 0.08 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 3.420 NA #> 3 15.93 NA NA #> 5 8.57 0.150 NA #> 10 3.70 0.040 NA #> 15 2.26 0.020 NA #> 20 1.05 0.010 NA #> 30 0.34 0.004 NA #> 40 0.15 0.003 NA #> 50 0.08 0.002 NA #> #> [[4]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.85 NA NA NA NA #> 3 0.62 23.61 10.12 2.44 6.71 #> 5 0.38 15.42 5.60 1.02 2.99 #> 10 0.19 8.66 2.50 0.31 0.99 #> 15 0.13 4.01 1.28 0.16 0.52 #> 20 0.10 1.89 0.75 0.10 0.33 #> 30 0.06 0.66 0.35 0.05 0.17 #> 40 0.05 0.31 0.20 0.03 0.11 #> 50 0.04 0.17 0.13 0.02 0.08 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 2.290 NA #> 3 15.38 NA NA #> 5 8.26 0.120 NA #> 10 3.55 0.030 NA #> 15 2.17 0.020 NA #> 20 0.93 0.009 NA #> 30 0.31 0.004 NA #> 40 0.14 0.002 NA #> 50 0.08 0.002 NA #> #> [[5]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.75 NA NA NA NA #> 3 0.59 23.12 9.74 2.37 6.59 #> 5 0.36 15.06 5.41 1.00 2.93 #> 10 0.18 8.42 2.43 0.31 0.98 #> 15 0.12 3.83 1.24 0.15 0.51 #> 20 0.09 1.81 0.72 0.09 0.33 #> 30 0.06 0.63 0.34 0.05 0.17 #> 40 0.05 0.30 0.20 0.03 0.11 #> 50 0.04 0.17 0.13 0.02 0.08 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 2.120 NA #> 3 15.12 NA NA #> 5 7.99 0.110 NA #> 10 3.36 0.030 NA #> 15 2.03 0.010 NA #> 20 0.88 0.008 NA #> 30 0.29 0.004 NA #> 40 0.14 0.002 NA #> 50 0.07 0.002 NA #> #> [[6]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.64 NA NA NA NA #> 3 0.56 22.76 9.21 2.29 6.41 #> 5 0.34 14.64 5.18 0.97 2.85 #> 10 0.17 8.04 2.38 0.30 0.95 #> 15 0.11 3.71 1.20 0.15 0.50 #> 20 0.09 1.75 0.68 0.09 0.32 #> 30 0.06 0.61 0.31 0.05 0.17 #> 40 0.04 0.29 0.17 0.03 0.11 #> 50 0.03 0.16 0.11 0.02 0.07 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 1.980 NA #> 3 14.90 NA NA #> 5 7.79 0.100 NA #> 10 3.23 0.030 NA #> 15 1.93 0.010 NA #> 20 0.83 0.008 NA #> 30 0.28 0.004 NA #> 40 0.13 0.002 NA #> 50 0.07 0.001 NA #> #> [[7]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.61 NA NA NA NA #> 3 0.55 22.69 9.10 2.24 6.33 #> 5 0.33 14.45 5.11 0.94 2.81 #> 10 0.17 7.83 2.33 0.29 0.94 #> 15 0.11 3.62 1.20 0.15 0.49 #> 20 0.08 1.71 0.67 0.09 0.31 #> 30 0.06 0.60 0.30 0.05 0.16 #> 40 0.04 0.28 0.17 0.03 0.10 #> 50 0.03 0.16 0.11 0.02 0.07 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 1.930 NA #> 3 14.63 NA NA #> 5 7.60 0.100 NA #> 10 3.13 0.030 NA #> 15 1.86 0.010 NA #> 20 0.81 0.008 NA #> 30 0.26 0.004 NA #> 40 0.12 0.002 NA #> 50 0.06 0.001 NA #> #> [[8]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.52 NA NA NA NA #> 3 0.52 22.24 8.66 2.16 6.26 #> 5 0.31 14.09 4.92 0.91 2.78 #> 10 0.16 7.58 2.29 0.28 0.93 #> 15 0.11 3.48 1.14 0.14 0.49 #> 20 0.08 1.65 0.65 0.09 0.31 #> 30 0.05 0.57 0.29 0.04 0.16 #> 40 0.04 0.27 0.16 0.03 0.10 #> 50 0.03 0.15 0.11 0.02 0.07 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 1.640 NA #> 3 13.53 NA NA #> 5 7.15 0.090 NA #> 10 3.01 0.020 NA #> 15 1.82 0.010 NA #> 20 0.78 0.007 NA #> 30 0.25 0.003 NA #> 40 0.12 0.002 NA #> 50 0.06 0.001 NA #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":null,"dir":"Reference","previous_headings":"","what":"Regression parameters for the Rautmann drift data — drift_parameters_focus","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"parameters extracted Appendix B FOCUS surface water guidance using R code given file data_generation/drift_parameters_focus.R installed package. appendix included package, licence clear.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"","code":"drift_parameters_focus"},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"tibble::tibble.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"hinge distance, Inf substituted cases hinge distance given data, way parameters C D never used distance B used case distance smaller hinge distance.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"FOCUS (2014) Generic guidance Surface Water Scenarios (version 1.4). FOrum Co-ordination pesticde fate models USe. http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf FOCUS (2001) FOCUS Surface Water Scenarios EU Evaluation Process 91/414/EEC. Report FOCUS Working Group Surface Water Scenarios, EC Document Reference SANCO/4802/2001-rev.2. 245, Appendix B. https://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/FOCUS_SWS_APPENDIX_B.doc Rautmann, D., Streloke, M Winkler, R (2001) New basic drift values authorization procedure plant protection products Mitt. Biol. Bundesanst. Land- Forstwirtsch. 383, 133-141","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"","code":"drift_parameters_focus #> # A tibble: 49 × 8 #> crop_group n_apps percentile A B C D hinge #> <chr> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 arable 1 90 2.76 -0.978 NA NA Inf #> 2 arable 2 82 2.44 -1.01 NA NA Inf #> 3 arable 3 77 2.02 -0.996 NA NA Inf #> 4 arable 4 74 1.86 -0.986 NA NA Inf #> 5 arable 5 72 1.79 -0.994 NA NA Inf #> 6 arable 6 70 1.63 -0.986 NA NA Inf #> 7 arable 7 69 1.58 -0.981 NA NA Inf #> 8 arable 8 67 1.51 -0.983 NA NA Inf #> 9 hops 1 90 58.2 -1.00 8655. -2.84 15.3 #> 10 hops 2 82 66.2 -1.20 5555. -2.82 15.3 #> # ℹ 39 more rows unique(drift_parameters_focus$crop_group) #> [1] \"arable\" \"hops\" \"vines, late\" \"vines, early\" \"fruit, late\" #> [6] \"fruit, early\" \"aerial\""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"Calculate drift percentages based Rautmann data","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"","code":"drift_percentages_rautmann( distances, applications = 1, crop_group_RF = \"arable\", formula = c(\"Rautmann\", \"FOCUS\"), widths = 1 )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"distances distances m get PEC values applications Number applications selection drift percentile crop_group_RF Crop group(s) used drift_parameters_focus, .e. \"arable\", \"hops\", \"vines, late\", \"vines, early\", \"fruit, late\", \"fruit, early\" \"aerial\". formula default, original Rautmann formula used. specify \"FOCUS\", mean drift input width water body calculated described Chapter 5.4.5 FOCUS surface water guidance widths widths water bodies (used FOCUS formula)","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"FOCUS (2014) Generic guidance Surface Water Scenarios (version 1.4). FOrum Co-ordination pesticde fate models USe. http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"","code":"# Compare JKI data with Rautmann and FOCUS formulas for arable crops (default) # One application on field crops, for 1 m, 3 m and 5 m distance drift_data_JKI[[1]][as.character(c(1, 3, 5)), \"Ackerbau\"] #> 1 3 5 #> 2.77 0.95 0.57 drift_percentages_rautmann(c(1, 3, 5)) #> [1] 2.7593000 0.9424748 0.5719342 drift_percentages_rautmann(c(1, 3, 5), formula = \"FOCUS\") #> [1] 1.9273922 0.8160023 0.5224362 # Since pfm 0.6.5, the function can also take a vector of crop groups drift_percentages_rautmann( distances = c(1, 5, 5), crop_group_RF = c(\"fruit, early\", \"fruit, early\", \"fruit, late\")) #> [1] 66.702000 19.884442 8.410849 # Two applications, all else equal drift_data_JKI[[2]][as.character(c(1, 3, 5)), \"Ackerbau\"] #> 1 3 5 #> 2.38 0.79 0.47 drift_percentages_rautmann(c(1, 3, 5), applications = 2) #> [1] 2.4376000 0.8036556 0.4797365 drift_percentages_rautmann(c(1, 3, 5), formula = \"FOCUS\", app = 2) #> [1] 1.6837733 0.6925952 0.4369331 # One application to early or late fruit crops drift_data_JKI[[1]][as.character(c(3, 5, 20, 50)), \"Obstbau frueh\"] #> 3 5 20 50 #> 29.20 19.89 2.77 0.30 drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = \"fruit, early\") #> [1] 29.1973659 19.8844422 2.7618138 0.3012008 drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = \"fruit, early\", formula = \"FOCUS\") #> [1] 26.1193421 18.5428680 2.6038558 0.2940792 drift_data_JKI[[1]][as.character(c(3, 5, 20, 50)), \"Obstbau spaet\"] #> 3 5 20 50 #> 15.73 8.41 1.09 0.22 drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = \"fruit, late\") #> [1] 15.7246994 8.4108487 1.0813887 0.2155992 drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = \"fruit, late\", formula = \"FOCUS\") #> [1] 13.1414350 7.5123244 1.0359007 0.2118734 # We get a continuum if the waterbody covers the hinge distance # (11.4 m for 1 early app to fruit) x <- seq(3, 30, by = 0.1) d <- drift_percentages_rautmann(x, crop_group_RF = \"fruit, early\", formula = \"FOCUS\") plot(x, d, type = \"l\", xlab = \"Distance of near edge [m]\", ylab = \"Mean drift percentage over waterbody width\", main = \"One application to fruit, early\") abline(v = 11.4, lty = 2)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"R6 class objects class chent represent chemical entities can hold list information loaded chemical yaml file chyaml field. information extracted optionally aggregated function.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"","code":"endpoint( chent, medium = \"soil\", type = c(\"degradation\", \"sorption\"), lab_field = c(NA, \"laboratory\", \"field\"), redox = c(NA, \"aerobic\", \"anaerobic\"), value = c(\"DT50ref\", \"Kfoc\", \"N\"), aggregator = geomean, raw = FALSE, signif = 3 ) soil_DT50( chent, aggregator = geomean, signif = 3, lab_field = \"laboratory\", value = \"DT50ref\", redox = \"aerobic\", raw = FALSE ) soil_Kfoc(chent, aggregator = geomean, signif = 3, value = \"Kfoc\", raw = FALSE) soil_N(chent, aggregator = mean, signif = 3, raw = FALSE) soil_sorption( chent, values = c(\"Kfoc\", \"N\"), aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3), raw = FALSE )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"chent chent object get information medium medium information sought type information type lab_field NA, want laboratory field endpoints redox NA, looking aerobic anaerobic data value name value want. list given usage section exclusive aggregator aggregator function. Can mean, geomean, identity, example. raw number(s) returned stored chent object (character value) retain original information precision? signif many significant digits want values values returned aggregators named vector aggregator functions used","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"result applying aggregator function values converted numeric vector, rounded given number significant digits, , raw = TRUE, values character value, retaining implicit information precision may present.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"functions soil_* functions extract soil specific endpoints. Freundlich exponent, capital letter N used order facilitate dealing data R. pesticide fate modelling, exponent often called 1/n.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the geometric mean — geomean","title":"Calculate the geometric mean — geomean","text":"Based posts thread Stackoverflow http://stackoverflow.com/questions/2602583/geometric-mean----built-function returns NA NA values present na.rm = FALSE (default). negative values present, gives error message. least one element vector 0, returns 0.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the geometric mean — geomean","text":"","code":"geomean(x, na.rm = FALSE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the geometric mean — geomean","text":"x Vector numbers na.rm NA values omitted?","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate the geometric mean — geomean","text":"geometric mean","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate the geometric mean — geomean","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the geometric mean — geomean","text":"","code":"geomean(c(1, 3, 9)) #> [1] 3 geomean(c(1, 3, NA, 9)) #> [1] NA geomean(c(1, -3, 9)) # returns an error #> Error in geomean(c(1, -3, 9)): Only defined for positive numbers"},{"path":"https://pkgdown.jrwb.de/pfm/reference/get_vertex.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a parabola through three points — get_vertex","title":"Fit a parabola through three points — get_vertex","text":"inspired answer stackoverflow https://stackoverflow.com//717791","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/get_vertex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a parabola through three points — get_vertex","text":"","code":"get_vertex(x, y)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/get_vertex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a parabola through three points — get_vertex","text":"x Three x coordinates y Three y coordinates","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":null,"dir":"Reference","previous_headings":"","what":"The maximum time weighted average concentration for a moving window — max_twa","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"generate time series using sawtooth, need make sure length time series allows finding maximum. therefore recommended check using plot.one_box using window size argument max_twa.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"","code":"max_twa(x, window = 21)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"x object type one_box window size moving window","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"method working directly fitted mkinfit objects uses equations given PEC soil section FOCUS guidance restricted SFO, FOMC DFOP models parent compound","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"","code":"pred <- sawtooth(one_box(10), applications = data.frame(time = c(0, 7), amount = c(1, 1))) max_twa(pred) #> $max #> parent #> 0.9537545 #> #> $window_start #> parent #> 0 #> #> $window_end #> parent #> 21 #> pred_FOMC <- mkinfit(\"FOMC\", FOCUS_2006_C, quiet = TRUE) max_twa(pred_FOMC) #> 21 #> 18.22124"},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a time series of decline data — one_box","title":"Create a time series of decline data — one_box","text":"Create time series decline data","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a time series of decline data — one_box","text":"","code":"one_box(x, ini, ..., t_end = 100, res = 0.01) # S3 method for class 'numeric' one_box(x, ini = 1, ..., t_end = 100, res = 0.01) # S3 method for class 'character' one_box(x, ini = 1, parms, ..., t_end = 100, res = 0.01) # S3 method for class 'mkinfit' one_box(x, ini = \"model\", ..., t_end = 100, res = 0.01)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a time series of decline data — one_box","text":"x numeric, half-life used exponential decline. character string specifying parent decline model given e.g. FOMC, parms must contain corresponding parameters. x mkinfit object, decline calculated object. ini initial amount. x mkinfit object, ini 'model', fitted initial concentrations used. Otherwise, ini must numeric. length one, used parent initial values metabolites zero, otherwise, must give values observed variables. ... arguments passed methods t_end End time series res Resolution time series parms named numeric vector containing model parameters","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a time series of decline data — one_box","text":"object class one_box, inheriting ts.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a time series of decline data — one_box","text":"","code":"# Only use a half-life pred_0 <- one_box(10) plot(pred_0) # Use a fitted mkinfit model require(mkin) fit <- mkinfit(\"FOMC\", FOCUS_2006_C, quiet = TRUE) pred_1 <- one_box(fit) plot(pred_1) # Use a model with more than one observed variable m_2 <- mkinmod(parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data pred_2 <- one_box(fit_2, ini = \"model\") plot(pred_2)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":null,"dir":"Reference","previous_headings":"","what":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"table loss percentages used Exposit 3 twelve different Koc classes","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"","code":"perc_runoff_exposit"},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"data frame percentage values dissolved fraction fraction bound eroding particles, Koc classes used row names Koc_lower_bound lower bound Koc class dissolved percentage applied substance transferred adjacent water body dissolved phase bound percentage applied substance transferred adjacent water body bound eroding particles","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"Excel 3.02 spreadsheet available https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"","code":"print(perc_runoff_exposit) #> Koc_lower_bound dissolved bound #> 0-20 0 [L/kg] 0.110 0.000 #> >20-50 20 [L/kg] 0.151 0.000 #> >50-100 50 [L/kg] 0.197 0.000 #> >100-200 100 [L/kg] 0.248 0.001 #> >200-500 200 [L/kg] 0.224 0.004 #> >500-1000 500 [L/kg] 0.184 0.020 #> >1000-2000 1000 [L/kg] 0.133 0.042 #> >2000-5000 2000 [L/kg] 0.084 0.091 #> >5000-10000 5000 [L/kg] 0.037 0.159 #> >10000-20000 10000 [L/kg] 0.031 0.192 #> >20000-50000 20000 [L/kg] 0.014 0.291 #> >50000 50000 [L/kg] 0.001 0.451"},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":null,"dir":"Reference","previous_headings":"","what":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"table runoff reduction percentages used Exposit 3 different vegetated buffer widths","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"","code":"perc_runoff_reduction_exposit"},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"named list data frames reduction percentage values dissolved fraction fraction bound eroding particles, vegetated buffer widths row names. names list items Exposit versions values taken. dissolved reduction percentage dissolved phase bound reduction percentage particulate phase","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"Excel 3.02 spreadsheet available https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html Agroscope version 3.01a additional runoff factors 3 m 6 m buffer zones received Muris Korkaric (published). variant 3.01a2 introduced consistency previous calculations performed Agroscope 3 m buffer zone.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"","code":"print(perc_runoff_reduction_exposit) #> $`3.02` #> dissolved bound #> No buffer 0 0 #> 5 m 40 40 #> 10 m 60 85 #> 20 m 80 95 #> #> $`3.01a` #> dissolved bound #> No buffer 0 0 #> 3 m 25 30 #> 5 m 40 40 #> 6 m 45 55 #> 10 m 60 85 #> 20 m 80 95 #> #> $`3.01a2` #> dissolved bound #> No buffer 0 0 #> 3 m 25 25 #> #> $`2.0` #> dissolved bound #> No buffer 0.0 0.0 #> 20 m 97.5 97.5 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"Calculate time course relative concentrations based mkinmod model","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"","code":"pfm_degradation( model = \"SFO\", DT50 = 1000, parms = c(k_parent = log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, by = step_days) )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"model degradation model used. Either parent model like 'SFO' 'FOMC', mkinmod object DT50 half-life. used simple exponential decline calculated (SFO model). parms parameters used degradation model years many years degradation predicted? step_days step size days output ? times output times","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"","code":"head(pfm_degradation(\"SFO\", DT50 = 10)) #> time parent #> 0 0 1.0000000 #> 1 1 0.9330330 #> 2 2 0.8705506 #> 3 3 0.8122524 #> 4 4 0.7578583 #> 5 5 0.7071068"},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"Plot TOXSWA hourly concentrations chemical substance specific segment TOXSWA surface water body.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"","code":"# S3 method for class 'TOXSWA_cwa' plot( x, time_column = c(\"datetime\", \"t\", \"t_firstjan\", \"t_rel_to_max\"), xlab = \"default\", ylab = \"default\", add = FALSE, threshold_factor = 1000, thin_low = 1, total = FALSE, LC_TIME = \"C\", ... )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"x TOXSWA_cwa object plotted. time_column used time axis. \"t_firstjan\" chosen, time given days relative first January first year. xlab, ylab Labels x y axis. add add existing plot? threshold_factor factor data lower maximum order get thinned plotting (see next argument). thin_low integer greater 1, data close zero (smaller 1/threshold_factor maximum) series thinned factor order decrease amount data included plots total total concentration water plotted, including substance sorbed suspended matter? LC_TIME Specification locale used format dates ... arguments passed plot adding existing plot","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"","code":"H_sw_D4_pond <- read.TOXSWA_cwa(\"00001p_pa.cwa\", basedir = \"SwashProjects/project_H_sw/TOXSWA\", zipfile = system.file(\"testdata/SwashProjects.zip\", package = \"pfm\")) plot(H_sw_D4_pond) plot(H_sw_D4_pond, time_column = \"t\") plot(H_sw_D4_pond, time_column = \"t_firstjan\") plot(H_sw_D4_pond, time_column = \"t_rel_to_max\") H_sw_R1_stream <- read.TOXSWA_cwa(\"00003s_pa.cwa\", basedir = \"SwashProjects/project_H_sw/TOXSWA\", zipfile = system.file(\"testdata/SwashProjects.zip\", package = \"pfm\")) plot(H_sw_R1_stream, time_column = \"t_rel_to_max\")"},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.one_box.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot time series of decline data — plot.one_box","title":"Plot time series of decline data — plot.one_box","text":"Plot time series decline data","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.one_box.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot time series of decline data — plot.one_box","text":"","code":"# S3 method for class 'one_box' plot( x, xlim = range(time(x)), ylim = c(0, max(x)), xlab = \"Time\", ylab = \"Residue\", max_twa = NULL, max_twa_var = dimnames(x)[[2]][1], ... )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.one_box.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot time series of decline data — plot.one_box","text":"x object type one_box plotted xlim Limits x axis ylim Limits y axis xlab Label x axis ylab Label y axis max_twa numeric value given, maximum time weighted average concentration(s) /shown graph. max_twa_var Variable maximum time weighted average shown max_twa NULL. ... arguments passed methods","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.one_box.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot time series of decline data — plot.one_box","text":"","code":"dfop_pred <- one_box(\"DFOP\", parms = c(k1 = 0.2, k2 = 0.02, g = 0.7)) plot(dfop_pred) plot(sawtooth(dfop_pred, 3, 7), max_twa = 21) # Use a fitted mkinfit model m_2 <- mkinmod(parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data pred_2 <- one_box(fit_2, ini = 1) pred_2_saw <- sawtooth(pred_2, 2, 7) plot(pred_2_saw) plot(pred_2_saw, max_twa = 21, max_twa_var = \"m1\")"},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":null,"dir":"Reference","previous_headings":"","what":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"Read TOXSWA hourly concentrations chemical substance specific segment TOXSWA surface water body. Per default, data last segment imported. TOXSWA 4 reports values end hour (ConLiqWatLayCur) summary file, use value well instead hourly averages (ConLiqWatLay). TOXSWA 5.5.3 variable renamed ConLiqWatLay file.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"","code":"read.TOXSWA_cwa( filename, basedir = \".\", zipfile = NULL, segment = \"last\", substance = \"parent\", total = FALSE, windows = NULL, thresholds = NULL )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"filename filename cwa file (TOXSWA 2.x.y similar) file using FOCUS TOXSWA 4 (.e. TOXSWA 4.4.2) higher. basedir path directory cwa file resides. zipfile Optional path zip file containing cwa file. segment segment data read. Either \"last\", segment number. substance .files, default value \"parent\" leads reading concentrations parent compound. Alternatively, substance interested can selected code name. total Set TRUE order read total concentrations well. necessary .files generated TOXSWA 4.4.2 similar, .cwa files. .cwa files, total concentration always read well. windows Numeric vector width moving windows days, calculating maximum time weighted average concentrations areas curve. thresholds Numeric vector threshold concentrations µg/L generating event statistics.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"instance R6 object class TOXSWA_cwa.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"","code":"H_sw_D4_pond <- read.TOXSWA_cwa(\"00001p_pa.cwa\", basedir = \"SwashProjects/project_H_sw/TOXSWA\", zipfile = system.file(\"testdata/SwashProjects.zip\", package = \"pfm\"))"},{"path":"https://pkgdown.jrwb.de/pfm/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. mkin set_nd_nq(), set_nd_nq_focus()","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/sawtooth.html","id":null,"dir":"Reference","previous_headings":"","what":"Create decline time series for multiple applications — sawtooth","title":"Create decline time series for multiple applications — sawtooth","text":"application pattern specified applications, n disregarded.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/sawtooth.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create decline time series for multiple applications — sawtooth","text":"","code":"sawtooth( x, n = 1, i = 365, applications = data.frame(time = seq(0, (n - 1) * i, length.out = n), amount = 1) )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/sawtooth.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create decline time series for multiple applications — sawtooth","text":"x one_box object n number applications. applications specified, n ignored interval applications. applications specified, ignored applications data frame holding application times first column corresponding amounts applied second column.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/sawtooth.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create decline time series for multiple applications — sawtooth","text":"","code":"applications = data.frame(time = seq(0, 14, by = 7), amount = c(1, 2, 3)) pred <- one_box(10) plot(sawtooth(pred, applications = applications)) m_2 <- mkinmod(parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data pred_2 <- one_box(fit_2, ini = 1) pred_2_saw <- sawtooth(pred_2, 2, 7) plot(pred_2_saw, max_twa = 21, max_twa_var = \"m1\") max_twa(pred_2_saw) #> $max #> parent m1 #> 0.7834481 0.8617049 #> #> $window_start #> parent m1 #> 0.00 26.85 #> #> $window_end #> parent m1 #> 21.00 47.85 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":null,"dir":"Reference","previous_headings":"","what":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"Properties predefined scenarios used Tier 1, Tier 2A Tier 3A concentration soil given EFSA guidance (2015, p. 13/14). Also, scenario model adjustment factors p. 15 p. 17 included.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"","code":"soil_scenario_data_EFSA_2015"},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"data frame one row scenario. Row names scenario codes, e.g. CTN Northern scenario total concentration soil. Columns mostly self-explanatory. rho dry bulk density top soil.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"EFSA (European Food Safety Authority) (2015) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 13(4) 4093 doi:10.2903/j.efsa.2015.4093","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"","code":"soil_scenario_data_EFSA_2015 #> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce #> CTN North Estonia 4.7 7.0 Coarse 0.118 0.244 0.95 3.0 #> CTC Central Germany 8.0 10.1 Coarse 0.086 0.244 1.05 2.0 #> CTS South France 11.0 12.3 Medium fine 0.048 0.385 1.22 2.0 #> CLN North Denmark 8.2 9.8 Medium 0.023 0.347 1.39 2.0 #> CLC Central Czech Republik 9.1 11.2 Medium 0.018 0.347 1.43 1.5 #> CLS South Spain 12.8 14.7 Medium 0.011 0.347 1.51 1.5 #> f_mod #> CTN 2 #> CTC 2 #> CTS 2 #> CLN 4 #> CLC 4 #> CLS 4"},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":null,"dir":"Reference","previous_headings":"","what":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"Properties predefined scenarios used Tier 1, Tier 2A Tier 3A concentration soil given EFSA guidance (2017, p. 14/15). Also, scenario model adjustment factors p. 16 p. 18 included.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"","code":"soil_scenario_data_EFSA_2017"},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"data frame one row scenario. Row names scenario codes, e.g. CTN Northern scenario total concentration soil. Columns mostly self-explanatory. rho dry bulk density top soil.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"EFSA (European Food Safety Authority) (2017) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 15(10) 4982 doi:10.2903/j.efsa.2017.4982","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"","code":"soil_scenario_data_EFSA_2017 #> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce f_mod #> CTN North Estonia 5.7 7.6 Coarse 0.220 0.244 0.707 1.4 3 #> CTC Central Poland 7.4 9.3 Coarse 0.122 0.244 0.934 1.4 3 #> CTS South France 10.2 11.7 Medium 0.070 0.349 1.117 1.4 3 #> CLN North Denmark 8.0 9.2 Medium 0.025 0.349 1.371 1.6 4 #> CLC Central Austria 9.3 11.3 Medium 0.018 0.349 1.432 1.6 4 #> CLS South Spain 15.4 16.7 Medium 0.010 0.349 1.521 1.6 4 #> FOCUS_zone prec #> CTN Hamburg 639 #> CTC Hamburg 617 #> CTS Hamburg 667 #> CLN Hamburg 602 #> CLC Châteaudun 589 #> CLS Sevilla 526 waldo::compare(soil_scenario_data_EFSA_2017, soil_scenario_data_EFSA_2015) #> `old` is length 12 #> `new` is length 10 #> #> `names(old)[8:12]`: \"rho\" \"f_sce\" \"f_mod\" \"FOCUS_zone\" \"prec\" #> `names(new)[8:10]`: \"rho\" \"f_sce\" \"f_mod\" #> #> `old$Country`: \"Estonia\" \"Poland\" \"France\" \"Denmark\" \"Austria\" \"Spain\" #> `new$Country`: \"Estonia\" \"Germany\" \"France\" \"Denmark\" \"Czech Republik\" \"Spain\" #> #> `old$T_arit`: 5.70 7.40 10.20 8.00 9.30 15.40 #> `new$T_arit`: 4.70 8.00 11.00 8.20 9.10 12.80 #> #> `old$T_arr`: 7.60 9.30 11.70 9.20 11.30 16.70 #> `new$T_arr`: 7.00 10.10 12.30 9.80 11.20 14.70 #> #> `old$Texture`: \"Coarse\" \"Coarse\" \"Medium\" \"Medium\" \"Medium\" \"Medium\" #> `new$Texture`: \"Coarse\" \"Coarse\" \"Medium fine\" \"Medium\" \"Medium\" \"Medium\" #> #> `old$f_om`: 0.2200 0.1220 0.0700 0.0250 0.0180 0.0100 #> `new$f_om`: 0.1180 0.0860 0.0480 0.0230 0.0180 0.0110 #> #> `old$theta_fc`: 0.2440 0.2440 0.3490 0.3490 0.3490 0.3490 #> `new$theta_fc`: 0.2440 0.2440 0.3850 0.3470 0.3470 0.3470 #> #> `old$rho`: 0.7070 0.9340 1.1170 1.3710 1.4320 1.5210 #> `new$rho`: 0.9500 1.0500 1.2200 1.3900 1.4300 1.5100 #> #> `old$f_sce`: 1.40 1.40 1.40 1.60 1.60 1.60 #> `new$f_sce`: 3.00 2.00 2.00 2.00 1.50 1.50 #> #> And 3 more differences ..."},{"path":"https://pkgdown.jrwb.de/pfm/reference/twa.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate a time weighted average concentration — twa","title":"Calculate a time weighted average concentration — twa","text":"moving average built using values past, earliest possible time maximum time series returned one window passed.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/twa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate a time weighted average concentration — twa","text":"","code":"twa(x, window = 21) # S3 method for class 'one_box' twa(x, window = 21)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/twa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate a time weighted average concentration — twa","text":"x object type one_box window size moving window","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/twa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate a time weighted average concentration — twa","text":"","code":"pred <- sawtooth(one_box(10), applications = data.frame(time = c(0, 7), amount = c(1, 1))) max_twa(pred) #> $max #> parent #> 0.9537545 #> #> $window_start #> parent #> 0 #> #> $window_end #> parent #> 21 #>"},{"path":"https://pkgdown.jrwb.de/pfm/news/index.html","id":"version-065","dir":"Changelog","previous_headings":"","what":"version 0.6.5","title":"version 0.6.5","text":"R/PEC_sw_drainage_UK.R: Create function drainage_date_UK respect beginning drainage period 1 October, also end drainage period 30 April, use determining degradation time. Applications early year 1 May now correctly calculated without degradation time. R/PEC_sw_drift.R: Vectorise function respect distances, rates water depths, also respect crop groups. Closes issue #2 reported Julian Klein (@juklei).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/news/index.html","id":"version-064","dir":"Changelog","previous_headings":"","what":"version 0.6.4","title":"version 0.6.4","text":"R/PEC_sw_drainage_uk.R: Fix bug preventing function work latest_application set 29 February. Also, make function correctly deal units. R/twa.R: Fix bug plotting one-box models class one_box affected plots displayed time weighted average. R/PEC_sw_drainage_uk.R: Fix bug leading increased PEC values case application date beginning drainage period soil_DT50 specified.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/news/index.html","id":"version-063","dir":"Changelog","previous_headings":"","what":"version 0.6.3","title":"version 0.6.3","text":"R/{PEC_sw_drift,PEC_sw_exposit_runoff,PEC_sw_sed}.R: Make use units package. R/PEC_sw_drift.R: Change argument name ‘crop_group_focus’ ‘crop_group_RF’, order make easier understand relation ‘drift_data’ argument.","code":""}] +[{"path":"https://pkgdown.jrwb.de/pfm/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Johannes Ranke. Author, maintainer. Elisabeth Lutz. Contributor.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Johannes Ranke (2026). pfm: Utilities Pesticide Fate Modelling. R package version 0.6.5, https://pkgdown.jrwb.de/pfm.","code":"@Manual{, title = {pfm: Utilities for Pesticide Fate Modelling}, author = {{Johannes Ranke}}, year = {2026}, note = {R package version 0.6.5}, url = {https://pkgdown.jrwb.de/pfm}, }"},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"pfm","dir":"","previous_headings":"","what":"Utilities for Pesticide Fate Modelling","title":"Utilities for Pesticide Fate Modelling","text":"R package pfm provides utilities fate modelling, including simple routines calculating predicted environmental concentrations (PEC) routines dealing FOCUS pesticide fate modelling tools made available GNU public license. specifically, pfm includes facilities simple one-box modelling saw-tooth-like curves resulting multiple repeated applications, calculation PEC soil based 1997 SANCO guidance first tiers EFSA PEC soil guidance 2012 2015, well functions calculating PEC surface water. PEC drift calculations can based Rautmann drift percentiles published JKI, exponential formulas published Rautmann inter- extrapolate arbitrary distances, integrated Rautmann formulas (integrated width surface water body) used FOCUS drift calculations. PEC drainage calculations, methods used UK tier 1 Germany implemented. runoff, German method used tier 1 available. output FOCUS TOXSWA calculations can read , plotted, evaluated using TOXSWA cwa class giving maximum time weighted average concentrations peak statistics way available using EPAT tool.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Utilities for Pesticide Fate Modelling","text":"easiest way install package probably use r-universe repo: packages R-universe provided slight delay. Alternatively, can install package directly github, e.g. using pak.","code":"install.packages(\"pfm\", repos = c(\"https://jranke.r-universe.dev\", \"https://cran.r-project.org\")) # install.packages(\"pak\") pak::pak(\"jranke/pfm\")"},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"use","dir":"","previous_headings":"","what":"Use","title":"Utilities for Pesticide Fate Modelling","text":"Please refer reference.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Utilities for Pesticide Fate Modelling","text":"One nice example usage package visualisation time weighted average sawtooth curve obtained several overlays mkinfit predictions shown .","code":""},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"applications","dir":"","previous_headings":"","what":"Applications","title":"Utilities for Pesticide Fate Modelling","text":"Calculations predicted environmental concentrations using package used publications Agroscope.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"Subset EFSA crop interception default values groundwater modelling","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"","code":"EFSA_GW_interception_2014"},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"matrix containing interception values, currently selected crops","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"European Food Safety Authority (2014) EFSA Guidance Document evaluating laboratory field dissipation studies obtain DegT50 values active substances plant protection products transformation products active substances soil. EFSA Journal 12(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"","code":"EFSA_GW_interception_2014 #> BBCH #> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x #> Beans (field + vegetable) 0 0.25 0.40 0.40 0.70 0.70 0.70 0.70 0.70 0.80 #> Peas 0 0.35 0.55 0.55 0.85 0.85 0.85 0.85 0.85 0.85 #> Summer oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90 #> Winter oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90 #> Tomatoes 0 0.50 0.70 0.70 0.80 0.80 0.80 0.80 0.80 0.50 #> Spring cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80 #> Winter cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80"},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"Subset EFSA crop washoff default values","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"","code":"EFSA_washoff_2017"},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"matrix containing wash-factors, currently selected crops","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"European Food Safety Authority (2017) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 15(10) 4982 doi:10.2903/j.efsa.2017.4982","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"","code":"EFSA_washoff_2017 #> BBCH #> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x #> Beans (field + vegetable) NA 0.60 0.75 0.75 0.80 0.80 0.80 0.80 0.80 0.35 #> Peas NA 0.40 0.60 0.60 0.65 0.65 0.65 0.65 0.65 0.35 #> Summer oilseed rape NA 0.40 0.50 0.50 0.60 0.60 0.60 0.60 0.60 0.50 #> Winter oilseed rape NA 0.10 0.40 0.40 0.55 0.55 0.55 0.55 0.55 0.30 #> Tomatoes NA 0.55 0.75 0.75 0.70 0.70 0.70 0.70 0.70 0.35 #> Spring cereals NA 0.40 0.50 0.50 0.65 0.65 0.65 0.65 0.65 0.55 #> Winter cereals NA 0.10 0.40 0.60 0.55 0.55 0.55 0.60 0.60 0.40"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html","id":null,"dir":"Reference","previous_headings":"","what":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"Currently, scenario names acronyms small subset soil definitions provided. soil definitions page 46ff. FOCUS (2012).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"","code":"FOCUS_GW_scenarios_2012"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"FOCUS (2012) Generic guidance Tier 1 FOCUS ground water assessments. Version 2.1. FOrum Co-ordination pesticde fate models USe. http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"","code":"FOCUS_GW_scenarios_2012 #> $names #> Cha Ham Jok Kre Oke #> \"Châteadun\" \"Hamburg\" \"Jokioinen\" \"Kremsmünster\" \"Okehampton\" #> Pia Por Sev Thi #> \"Piacenza\" \"Porto\" \"Sevilla\" \"Thiva\" #> #> $soils #> location horizon number pH_H2O perc_clay perc_oc rel_deg #> 1 Cha Ap 1 8.0 30.0 1.39 1.0 #> 2 Cha B1 2 8.1 31.0 0.93 0.5 #> 3 Cha B2 3 8.2 25.0 0.70 0.5 #> 4 Cha II C1 4 8.5 26.0 0.30 0.3 #> 5 Cha II C1 5 8.5 26.0 0.30 0.0 #> 6 Cha II C2 6 8.5 24.0 0.27 0.0 #> 7 Cha M 7 8.3 31.0 0.21 0.0 #> 8 Ham Ap 1 6.4 7.2 1.50 1.0 #> 9 Ham BvI 2 5.6 6.7 1.00 0.5 #> 10 Ham BvII 3 5.6 0.9 0.20 0.3 #> 11 Ham Bv/Cv 4 5.7 0.0 0.00 0.3 #> 12 Ham Cv 5 5.5 0.0 0.00 0.3 #> 13 Ham Cv 6 5.5 0.0 0.00 0.0 #> 14 Jok Ap 1 6.2 3.6 4.06 1.0 #> 15 Jok Bs 2 5.6 1.8 0.84 0.5 #> 16 Jok BC1 3 5.4 1.2 0.36 0.3 #> 17 Jok BC2 4 5.4 1.7 0.29 0.3 #> 18 Jok BC2 5 5.4 1.7 0.29 0.0 #> 19 Jok Cg 6 5.3 1.9 0.21 0.0 #> 20 Kre <NA> 1 7.7 14.0 3.60 1.0 #> 21 Kre <NA> 2 7.0 25.0 1.00 0.5 #> 22 Kre <NA> 3 7.1 27.0 0.50 0.5 #> 23 Kre <NA> 4 7.1 27.0 0.50 0.3 #> 24 Kre <NA> 5 7.1 27.0 0.50 0.0 #> 25 Oke A 1 5.8 18.0 2.20 1.0 #> 26 Oke Bw1 2 6.3 17.0 0.70 0.5 #> 27 Oke BC 3 6.5 14.0 0.40 0.3 #> 28 Oke C 4 6.6 9.0 0.10 0.3 #> 29 Oke C 5 6.6 9.0 0.10 0.0 #> 30 Pia Ap 1 7.0 15.0 1.26 1.0 #> 31 Pia Ap 2 7.0 15.0 1.26 0.5 #> 32 Pia Bw 3 6.3 7.0 0.47 0.5 #> 33 Pia Bw 4 6.3 7.0 0.47 0.3 #> 34 Pia 2C 5 6.4 0.0 0.00 0.3 #> 35 Pia 2C 6 6.4 0.0 0.00 0.0 #> 36 Por <NA> 1 4.9 10.0 1.42 1.0 #> 37 Por <NA> 2 4.8 8.0 0.78 0.5 #> 38 Por <NA> 3 4.8 8.0 0.78 0.3 #> 39 Por <NA> 4 4.8 8.0 0.78 0.0 #> 40 Sev <NA> 1 7.3 14.0 0.93 1.0 #> 41 Sev <NA> 2 7.3 13.0 0.93 1.0 #> 42 Sev <NA> 3 7.8 15.0 0.70 0.5 #> 43 Sev <NA> 4 8.1 16.0 0.58 0.3 #> 44 Sev <NA> 5 8.1 16.0 0.58 0.0 #> 45 Sev <NA> 6 8.2 22.0 0.49 0.0 #> 46 Thi Ap1 1 7.7 25.3 0.74 1.0 #> 47 Thi Ap2 2 7.7 25.3 0.74 0.5 #> 48 Thi Bw 3 7.8 29.6 0.57 0.5 #> 49 Thi Bw 4 7.8 31.9 0.31 0.3 #> 50 Thi Ck1 5 7.8 32.9 0.18 0.3 #> 51 Thi Ck1 6 7.8 32.9 0.18 0.0 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.html","id":null,"dir":"Reference","previous_headings":"","what":"Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios","title":"Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios","text":"data extracted scenario.txt file using R code shown . text file included package licence clear.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios","text":"list containing scenario names character vector called 'names', drift percentiles matrix called 'drift', interception percentages matrix called 'interception' runoff/drainage percentages Step 2 calculations matrix called 'rd'.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios","text":"","code":"# \\dontrun{ # This is the code that was used to extract the data scenario_path <- \"inst/extdata/FOCUS_Step_12_scenarios.txt\" scenarios <- readLines(scenario_path)[9:38] #> Warning: cannot open file 'inst/extdata/FOCUS_Step_12_scenarios.txt': No such file or directory #> Error in file(con, \"r\"): cannot open the connection FOCUS_Step_12_scenarios <- list() sce <- read.table(text = scenarios, sep = \"\\t\", header = TRUE, check.names = FALSE, stringsAsFactors = FALSE) #> Error: object 'scenarios' not found FOCUS_Step_12_scenarios$names = sce$Crop #> Error: object 'sce' not found rownames(sce) <- sce$Crop #> Error: object 'sce' not found FOCUS_Step_12_scenarios$drift = sce[, 3:11] #> Error: object 'sce' not found FOCUS_Step_12_scenarios$interception = sce[, 12:15] #> Error: object 'sce' not found sce_2 <- readLines(scenario_path)[41:46] #> Warning: cannot open file 'inst/extdata/FOCUS_Step_12_scenarios.txt': No such file or directory #> Error in file(con, \"r\"): cannot open the connection rd <- read.table(text = sce_2, sep = \"\\t\")[1:2] #> Error: object 'sce_2' not found rd_mat <- matrix(rd$V2, nrow = 3, byrow = FALSE) #> Error: object 'rd' not found dimnames(rd_mat) = list(Time = c(\"Oct-Feb\", \"Mar-May\", \"Jun-Sep\"), Region = c(\"North\", \"South\")) #> Error: object 'rd_mat' not found FOCUS_Step_12_scenarios$rd = rd_mat #> Error: object 'rd_mat' not found save(FOCUS_Step_12_scenarios, file = \"data/FOCUS_Step_12_scenarios.RData\") #> Warning: cannot open compressed file 'data/FOCUS_Step_12_scenarios.RData', probable reason 'No such file or directory' #> Error in gzfile(file, \"wb\"): cannot open the connection # } # And this is the resulting data FOCUS_Step_12_scenarios #> list()"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":null,"dir":"Reference","previous_headings":"","what":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"Actual maximum moving window time average concentrations FOMC kinetics","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"","code":"FOMC_actual_twa( alpha = 1.0001, beta = 10, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100) )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"FOCUS (2014) Generic Guidance Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration, Version 1.1, 18 December 2014, p. 251","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"alpha Parameter FOMC model beta Parameter FOMC model times output times, window sizes time weighted average concentrations","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"","code":"FOMC_actual_twa(alpha = 1.0001, beta = 10) #> actual twa #> 0 1.00000000 NaN #> 1 0.90908224 0.9530973 #> 2 0.83331814 0.9115995 #> 4 0.71426168 0.8411664 #> 7 0.58820408 0.7580202 #> 14 0.41663019 0.6253074 #> 21 0.32254415 0.5387324 #> 28 0.26312277 0.4767543 #> 42 0.19227599 0.3925054 #> 50 0.16663681 0.3583198 #> 100 0.09088729 0.2397608"},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":null,"dir":"Reference","previous_headings":"","what":"Groundwater ubiquity score based on Gustafson (1989) — GUS","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"groundwater ubiquity score GUS calculated according equation $$GUS = \\log_{10} DT50_{soil} (4 - \\log_{10} K_{oc})$$","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"","code":"GUS(...) # S3 method for class 'numeric' GUS(DT50, Koc, ...) # S3 method for class 'chent' GUS( chent, degradation_value = \"DT50ref\", lab_field = \"laboratory\", redox = \"aerobic\", sorption_value = \"Kfoc\", degradation_aggregator = geomean, sorption_aggregator = geomean, ... ) # S3 method for class 'GUS_result' print(x, ..., digits = 1)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"... Included generic allow arguments later. Therefore also added specific methods. DT50 Half-life chemical soil. field half-life according Gustafson (1989). However, leaching sub-soil can completely excluded field dissipation experiments Gustafson refer normalisation procedure, says field study conducted use conditions. Koc sorption constant normalised organic carbon. Gustafson mention nonlinearity sorption constant commonly found usually described Freundlich sorption, therefore unclear reference concentration Koc observed (reference concentration soil porewater). chent chent given appropriate information present chyaml field, information used, defaults specified . degradation_value available degradation values used? lab_field laboratory field half-lives used? defaults lab implementation, order avoid double-accounting mobility. comparability original GUS values given Gustafson (1989) desired, non-normalised first-order field half-lives obtained actual use conditions used. redox Aerobic anaerobic degradation data sorption_value available sorption values used? Defaults Kfoc generally available European pesticide peer review process. values generally use reference concentration 1 mg/L porewater, means expected Koc values concentration 1 mg/L water phase. degradation_aggregator Function aggregating half-lives sorption_aggregator Function aggregation Koc values x object class GUS_result printed digits number digits used print method","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"list DT50 Koc used well resulting score class GUS_result","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"Gustafson, David . (1989) Groundwater ubiquity score: simple method assessing pesticide leachability. Environmental toxicology chemistry 8(4) 339–57.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","title":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","text":"Get relative accumulation FOMC model multiples interval","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","text":"","code":"PEC_FOMC_accu_rel(n, interval, FOMC)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","text":"n number applications interval Time applications FOMC Named numeric vector containing FOMC parameters alpha beta","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","text":"numeric vector containing n accumulation factors n applications","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate predicted environmental concentrations in soil — PEC_soil","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"basic calculation contaminant concentration bulk soil based complete, instantaneous mixing. interval given, attempt made calculating long term maximum concentration using concepts layed PPR panel opinion (EFSA PPR panel 2012 EFSA guidance PEC soil calculations (EFSA, 2015, 2017).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"","code":"PEC_soil( rate, rate_units = \"g/ha\", interception = 0, mixing_depth = 5, PEC_units = \"mg/kg\", PEC_pw_units = \"mg/L\", interval = NA, n_periods = Inf, tillage_depth = 20, leaching_depth = tillage_depth, crop = \"annual\", cultivation = FALSE, chent = NA, DT50 = NA, FOMC = NA, Koc = NA, Kom = Koc/1.724, t_avg = 0, t_act = NULL, scenarios = c(\"default\", \"EFSA_2017\", \"EFSA_2015\"), leaching = scenarios == \"EFSA_2017\", porewater = FALSE )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"rate Application rate units specified rate_units Defaults g/ha interception fraction application rate reach soil mixing_depth Mixing depth cm PEC_units Requested units calculated PEC. mg/kg currently supported PEC_pw_units mg/L currently supported interval Period deeper mixing. default NA, .e. deeper mixing. annual deeper mixing, set 365 degradation units days n_periods Number periods considered long term PEC calculations tillage_depth Periodic (see interval) deeper mixing cm leaching_depth EFSA (2017) uses mixing depth (ecotoxicological evaluation depth) calculate leaching annual crops tillage takes place. default, losses layer tillage depth taken account implementation. crop Ignored scenarios EFSA_2017. annual crops supported scenarios used. crops single cropping cycle per year currently supported. cultivation mechanical cultivation sense EFSA (2017) take place, .e. twice year depth 5 cm? Ignored scenarios EFSA_2017 chent optional chent object holding substance specific information. Can also name substance character string DT50 specified, overrides soil DT50 endpoints chent object DT50 specified available chent object, zero degradation assumed FOMC specified, named numeric vector containing FOMC parameters alpha beta. overrides degradation endpoints, degradation interval maximum PEC calculated using parameters without temperature correction Koc specified, overrides Koc endpoints chent object Kom Calculated Koc default, can explicitly specified Kom t_avg Averaging times time weighted average concentrations t_act Time series actual concentrations scenarios 'default', soil bulk density 1.5 kg/L used. DT50 used without correction soil properties specified REACH guidance (R.16, Table R.16-9) used porewater PEC calculations. \"EFSA_2015\", DT50 taken modelling half-life 20°C pF2 ('chent' specified, DegT50 destination 'PECgw' used), corrected using Arrhenius activation energy 65.4 kJ/mol. Also model scenario adjustment factors EFSA guidance used. leaching leaching taken account? default FALSE, except EFSA_2017 scenarios used. porewater equilibrium porewater concentrations estimated based Kom organic carbon fraction soil instead total soil concentrations? Based equation (7) given PPR panel opinion (EFSA 2012, p. 24) scenarios specified EFSA guidance (2015, p. 13).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"predicted concentration soil","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"assumes complete load soil time specified 'interval' (typically 365 days) dosed . PPR panel opinion cited (EFSA PPR panel 2012), temperature correction using Arrhenius equation performed. Total soil porewater PEC values scenarios defined EFSA guidance (2017, p. 14/15) can easily calculated.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"time weighted average (TWA) concentrations given examples EFSA guidance 2015 (p. 80) can reproduced, true TWA concentrations given example EFSA guidance 2017 (p. 92). According EFSA guidance (EFSA, 2017, p. 43), leaching taken account EFSA 2017 scenarios, using evaluation depth (mixing depth) depth layer leaching takes place. However, amount leaching evaluation depth (often 5 cm) partly mixed back tillage, default function use tillage depth calculation leaching rate. temperature information available selected scenarios, e.g. EFSA scenarios, DT50 groundwater modelling (destination 'PECgw') taken chent object, otherwise DT50 destination 'PECsoil'.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"EFSA Panel Plant Protection Products Residues (2012) Scientific Opinion science behind guidance scenario selection scenario parameterisation predicting environmental concentrations plant protection products soil. EFSA Journal 10(2) 2562, doi:10.2903/j.efsa.2012.2562 EFSA (European Food Safety Authority) 2017) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 15(10) 4982 doi:10.2903/j.efsa.2017.4982 EFSA (European Food Safety Authority) (2015) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 13(4) 4093 doi:10.2903/j.efsa.2015.4093","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"","code":"PEC_soil(100, interception = 0.25) #> scenario #> t_avg default #> 0 0.1 # This is example 1 starting at p. 92 of the EFSA guidance (2017) # Note that TWA concentrations differ from the ones given in the guidance # for an unknown reason (the values from EFSA (2015) can be reproduced). PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), Kom = 1000, scenarios = \"EFSA_2017\") #> scenario #> t_avg CTN CTC CTS #> 0 19.76834 13.8619 10.53795 #> 21 19.59345 13.7169 10.39882 PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), Kom = 1000, scenarios = \"EFSA_2017\", porewater = TRUE) #> scenario #> t_avg CLN CLC CLS #> 0 0.5541984 0.6779249 0.9816693 #> 21 0.5484576 0.6693125 0.9609119 # This is example 1 starting at p. 79 of the EFSA guidance (2015) PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), scenarios = \"EFSA_2015\") #> scenario #> t_avg CTN CTC CTS #> 0 21.96827 11.53750 9.145259 #> 21 21.78517 11.40701 9.017370 PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), Kom = 1000, scenarios = \"EFSA_2015\", porewater = TRUE) #> scenario #> t_avg CLN CLC CLS #> 0 0.7589401 0.6674322 0.9147861 #> 21 0.7506036 0.6590345 0.8987279 # The following is from example 4 starting at p. 85 of the EFSA guidance (2015) # Metabolite M2 # Calculate total and porewater soil concentrations for tier 1 scenarios # Relative molar mass is 100/300, formation fraction is 0.7 * 1 results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), scenarios = \"EFSA_2015\") results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), Kom = 100, scenarios = \"EFSA_2015\", porewater = TRUE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil_mets.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets","title":"Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets","text":"Calculate initial accumulation PEC soil set metabolites","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil_mets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets","text":"","code":"PEC_soil_mets(rate, mw_parent, mets, interval = 365, ...)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil_mets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets","text":"rate Application rate units specified mw_parent molecular weight parent compound mets dataframe metabolite identifiers rownames columns \"mw\", \"occ\" \"DT50\" holding molecular weight, maximum occurrence soil soil DT50 interval interval accumulation calculations ... arguments passed PEC_soil","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"implements method specified UK data requirements handbook checked spreadsheet published CRC website. Degradation end (30 April) start (1 October) drainage period taken account latest_application specified degradation parameters given either soil_DT50 model.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"","code":"PEC_sw_drainage_UK( rate, interception = 0, Koc, latest_application = NULL, soil_DT50 = NULL, model = NULL, model_parms = NULL ) drainage_date_UK(application_date)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"rate Application rate g/ha compatible unit specified units package interception fraction application rate reach soil Koc sorption coefficient normalised organic carbon L/kg unit specified units package latest_application Latest application date, formatted e.g. \"01 July\" soil_DT50 Soil degradation half-life, SFO kinetics used, days time unit specified units package model soil degradation model used. Either one \"FOMC\", \"DFOP\", \"HS\", \"IORE\", mkinmod object model_parms named numeric vector containing model parameters application_date Application date","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"predicted concentration surface water µg/L","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"HSE's Chemicals Regulation Division (CRD) Active substance PECsw calculations (UK specific authorisation requests) https://www.hse.gov.uk/pesticides/data-requirements-handbook/fate/pecsw-sed-via-drainflow.htm accessed 2026-02-13 PECsw/sed spray drift tier 1 drainflow calculator Version 2.1.1 (2025) Spreadsheet published https://www.hse.gov.uk/pesticides/assets/docs/PEC%20sw-sed%20(spraydrift).xlsx) accessed 2026-02-13","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"","code":"PEC_sw_drainage_UK(150, Koc = 100) #> 8.076923 [µg/L] PEC_sw_drainage_UK(60, interception = 0.5, Koc = 550, latest_application = \"01 July\", soil_DT50 = 200) #> 0.8388303 [µg/L] drainage_date_UK(\"2023-07-10\") #> [1] \"2023-10-01\" drainage_date_UK(\"2020-12-01\") #> [1] \"2020-12-01\" drainage_date_UK(as.Date(\"2022-01-15\")) #> [1] \"2022-01-15\""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"basic, vectorised form simple calculation contaminant concentration surface water based complete, instantaneous mixing input via spray drift.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"","code":"PEC_sw_drift( rate, applications = 1, water_depth = as_units(\"30 cm\"), drift_percentages = NULL, drift_data = c(\"JKI\", \"RF\"), crop_group_JKI = \"Ackerbau\", crop_group_RF = \"arable\", distances = c(1, 5, 10, 20), formula = c(\"Rautmann\", \"FOCUS\"), water_width = as_units(\"100 cm\"), side_angle = 90, rate_units = \"g/ha\", PEC_units = \"µg/L\" )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"rate Application rate units specified , units defined via units package. applications Number applications selection drift percentile water_depth Depth water body cm drift_percentages Percentage drift values calculate PECsw. Overrides 'drift_data', 'distances', 'applications', crop group formula arguments NULL. drift_data Source drift percentage data. 'JKI', drift_data_JKI included package used. 'RF', Rautmann drift data calculated either original form integrated width water body, depending 'formula' argument. crop_group_JKI using 'JKI' drift data, one German names used drift_data_JKI. used drift_data 'JKI'. Available crop groups \"Ackerbau\", \"Obstbau frueh\", \"Obstbau spaet\", \"Weinbau frueh\", \"Weinbau spaet\", \"Hopfenbau\", \"Flaechenkulturen > 900 l/ha\" \"Gleisanlagen\". crop_group_RF Crop group(s) used drift_parameters_focus, .e. \"arable\", \"hops\", \"vines, late\", \"vines, early\", \"fruit, late\", \"fruit, early\" \"aerial\". distances distances m get PEC values formula default, original Rautmann formula used. specify \"FOCUS\", mean drift input width water body calculated described Chapter 5.4.5 FOCUS surface water guidance water_width Width water body cm side_angle angle side water relative bottom assumed horizontal, degrees. SYNOPS model assumes 45 degrees . rate_units Defaults g/ha. backwards compatibility, used specified rate units::units]. PEC_units Requested units calculated PEC. µg/L currently supported","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"numeric vector predicted concentration surface water. cases, vector named distances drift percentages, backward compatibility versions vectorisation arguments 'distances' introduced v0.6.5.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"recommened specify arguments rate, water_depth water_width using units::units units package. Since pfm version 0.6.5, function vectorised respect rates, applications, water depth, crop groups distances","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"","code":"PEC_sw_drift(100) #> Units: [µg/L] #> 1 m 5 m 10 m 20 m #> 0.92333333 0.19000000 0.09666667 0.05000000 # Alternatively, we can use the formula for a single application to # \"Ackerbau\" from the paper PEC_sw_drift(100, drift_data = \"RF\") #> Units: [µg/L] #> 1 m 5 m 10 m 20 m #> 0.91976667 0.19064473 0.09680051 0.04915079 # This makes it possible to also use different distances PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = \"RF\") #> Units: [µg/L] #> 1 m 3 m 5 m 6 m 10 m 20 m 50 m #> 0.91976667 0.31415827 0.19064473 0.15951494 0.09680051 0.04915079 0.02006434 #> 100 m #> 0.01018774 # We can also specify distance units explicitly library(units) #> udunits database from /usr/share/xml/udunits/udunits2.xml PEC_sw_drift(100, distances = set_units(c(1, 3, 5, 6, 10, 20, 50, 100), \"m\"), drift_data = \"RF\") #> Units: [µg/L] #> 1 m 3 m 5 m 6 m 10 m 20 m 50 m #> 0.91976667 0.31415827 0.19064473 0.15951494 0.09680051 0.04915079 0.02006434 #> 100 m #> 0.01018774 # or consider aerial application PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = \"RF\", crop_group_RF = \"aerial\") #> Units: [µg/L] #> 1 m 3 m 5 m 6 m 10 m 20 m 50 m #> 16.8233333 11.0585820 9.0986174 8.4866460 6.9825178 4.7004640 1.8820816 #> 100 m #> 0.9417586 # Using custom drift percentages is also supported PEC_sw_drift(100, drift_percentages = c(2.77, 0.95, 0.57, 0.48, 0.29, 0.15, 0.06, 0.03)) #> Units: [µg/L] #> 2.77 % 0.95 % 0.57 % 0.48 % 0.29 % 0.15 % 0.06 % #> 0.92333333 0.31666667 0.19000000 0.16000000 0.09666667 0.05000000 0.02000000 #> 0.03 % #> 0.01000000 # The influence of assuming a 45° angle of the sides of the waterbody and the width of the # waterbody can be illustrated PEC_sw_drift(100) #> Units: [µg/L] #> 1 m 5 m 10 m 20 m #> 0.92333333 0.19000000 0.09666667 0.05000000 PEC_sw_drift(100, drift_data = \"RF\") #> Units: [µg/L] #> 1 m 5 m 10 m 20 m #> 0.91976667 0.19064473 0.09680051 0.04915079 PEC_sw_drift(100, drift_data = \"RF\", formula = \"FOCUS\") #> Units: [µg/L] #> 1 m 5 m 10 m 20 m #> 0.64246407 0.17414541 0.09235842 0.04798749 PEC_sw_drift(100, drift_data = \"RF\", formula = \"FOCUS\", side_angle = 45) #> Units: [µg/L] #> 1 m 5 m 10 m 20 m #> 0.91780582 0.24877916 0.13194060 0.06855356 PEC_sw_drift(100, drift_data = \"RF\", formula = \"FOCUS\", side_angle = 45, water_width = 200) #> Units: [µg/L] #> 1 m 5 m 10 m 20 m #> 0.60169999 0.18937304 0.10402698 0.05517095 # The function is vectorised with respect to rates, applications, water depth, # crop groups and distances PEC_sw_drift( rate = rep(100, 6), applications = c(1, 2, rep(1, 4)), water_depth = c(30, 30, 30, 60, 30, 30), crop_group_JKI = c(rep(\"Ackerbau\", 4), rep(\"Obstbau frueh\", 2)), distances = c(rep(5, 4), 10, 5)) #> Units: [µg/L] #> 5 m 5 m 5 m 5 m 10 m 5 m #> 0.1900000 0.1566667 0.1900000 0.0950000 3.9366667 6.6300000 # Try the same with the Rautmann formula PEC_sw_drift( rate = rep(100, 6), applications = c(1, 2, rep(1, 4)), water_depth = c(30, 30, 30, 60, 30, 30), drift_data = \"RF\", crop_group_RF = c(rep(\"arable\", 4), rep(\"fruit, early\", 2)), distances = c(rep(5, 4), 10, 5)) #> Units: [µg/L] #> 5 m 5 m 5 m 5 m 10 m 5 m #> 0.19064473 0.15991216 0.19064473 0.09532236 3.93566026 6.62814740 # And with the FOCUS variant PEC_sw_drift( rate = rep(100, 6), applications = c(1, 2, rep(1, 4)), water_depth = c(30, 30, 30, 60, 30, 30), drift_data = \"RF\", formula = \"FOCUS\", crop_group_RF = c(rep(\"arable\", 4), rep(\"fruit, early\", 2)), distances = c(rep(5, 4), 10, 5)) #> Units: [µg/L] #> 5 m 5 m 5 m 5 m 10 m 5 m #> 0.1741454 0.1456444 0.1741454 0.0870727 3.7957683 6.1809560"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"reimplementation calculation described Exposit 3.02 spreadsheet file, worksheet \"Konzept Drainage\". Although four groups compounds (\"Gefährdungsgruppen\"), one distinction made calculations, compounds low mobility (group 1) compounds modest high mobility (groups 2, 3 4). implementation, group derived Koc, given explicitly. details, see discussion function arguments . recommened specify arguments rate, Koc, DT50, t_drainage, V_ditch V_drainage using units::units units package.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"","code":"PEC_sw_exposit_drainage( rate, interception = 0, Koc = NA, mobility = c(NA, \"low\", \"high\"), DT50 = set_units(Inf, \"d\"), t_drainage = set_units(3, \"days\"), V_ditch = set_units(30, \"m3\"), V_drainage = set_units(c(spring = 10, autumn = 100), \"m3\"), dilution = 2 )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"Excel 3.02 spreadsheet available https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"rate application rate g/ha interception fraction intercepted crop Koc sorption coefficient soil organic carbon used determine mobility. trigger value 550 L/kg used order decide Koc >> 500. mobility Overrides determined Koc. DT50 soil half-life days t_drainage time application drainage event, degradation occurs, days V_ditch volume ditch assumed 1 m * 100 m * 30 cm = 30 m3 V_drainage drainage volume, equivalent 1 mm precipitation 1 ha spring/summer 10 mm autumn/winter/early spring. dilution dilution factor","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"list containing following components perc_drainage_total Gesamtaustrag (total fraction residue drained) perc_peak Stoßbelastung (fraction drained event) PEC_sw_drainage matrix containing PEC values spring autumn scenarios. rate given g/ha, PECsw microg/L.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"","code":"PEC_sw_exposit_drainage(500, Koc = 150) #> $perc_drainage_total #> spring autumn #> 0.2 1.0 #> #> $perc_peak #> spring autumn #> 12.5 25.0 #> #> $PEC_sw_drainage #> Units: [µg/L] #> spring autumn #> 1.562500 4.807692 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"reimplementation calculation described Exposit 3.02 spreadsheet file, worksheet \"Konzept Runoff\".","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"","code":"PEC_sw_exposit_runoff( rate, interception = 0, Koc, DT50 = set_units(Inf, \"d\"), t_runoff = set_units(3, \"days\"), exposit_reduction_version = c(\"3.02\", \"3.01a\", \"3.01a2\", \"2.0\"), V_ditch = set_units(30, \"m3\"), V_event = set_units(100, \"m3\"), dilution = 2 )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"Excel 3.02 spreadsheet available https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"rate Application rate g/ha compatible unit specified units package interception fraction intercepted crop Koc sorption coefficient soil organic carbon DT50 soil half-life days t_runoff time application runoff event, degradation occurs, days exposit_reduction_version version reduction factors used. \"3.02\" current version used Germany, \"3.01a\" version additional percentages 3 m 6 m buffer zones used Switzerland. \"3.01a2\" version introduced consistency previous calculations performed 3 m buffer zone Switzerland, reduction applied dissolved bound fraction. V_ditch volume ditch assumed 1 m * 100 m * 30 cm = 30 m3 V_event unreduced runoff volume, equivalent 10 mm precipitation 1 ha dilution dilution factor","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"list containing following components perc_runoff runoff percentages dissolved bound substance runoff matrix containing dissolved bound input different distances PEC_sw_runoff dataframe containing PEC values dissolved bound substance different distances. rate given g/ha, PECsw microg/L.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"recommened specify arguments rate, Koc, DT50, t_runoff, V_ditch V_event using units::units units package.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"","code":"PEC_sw_exposit_runoff(500, Koc = 150) #> $perc_runoff #> dissolved bound #> 0.248 0.001 #> #> $runoff #> dissolved bound total #> No buffer 1.240 [g] 0.00500 [g] 1.24500 [g] #> 5 m 0.744 [g] 0.00300 [g] 0.74700 [g] #> 10 m 0.496 [g] 0.00075 [g] 0.49675 [g] #> 20 m 0.248 [g] 0.00025 [g] 0.24825 [g] #> #> $PEC_sw_runoff #> dissolved bound total #> No buffer 4.769231 [µg/L] 0.019230769 [µg/L] 4.788462 [µg/L] #> 5 m 4.133333 [µg/L] 0.016666667 [µg/L] 4.150000 [µg/L] #> 10 m 3.542857 [µg/L] 0.005357143 [µg/L] 3.548214 [µg/L] #> 20 m 2.480000 [µg/L] 0.002500000 [µg/L] 2.482500 [µg/L] #> PEC_sw_exposit_runoff(600, Koc = 10000, DT50 = 195, exposit = \"3.01a\") #> $perc_runoff #> dissolved bound #> 0.037 0.159 #> #> $runoff #> dissolved bound total #> No buffer 0.21964521 [g] 0.94388078 [g] 1.16352600 [g] #> 3 m 0.16473391 [g] 0.66071655 [g] 0.82545046 [g] #> 5 m 0.13178713 [g] 0.56632847 [g] 0.69811560 [g] #> 6 m 0.12080487 [g] 0.42474635 [g] 0.54555122 [g] #> 10 m 0.08785809 [g] 0.14158212 [g] 0.22944020 [g] #> 20 m 0.04392904 [g] 0.04719404 [g] 0.09112308 [g] #> #> $PEC_sw_runoff #> dissolved bound total #> No buffer 0.8447893 [µg/L] 3.6303107 [µg/L] 4.4751000 [µg/L] #> 3 m 0.7844472 [µg/L] 3.1462693 [µg/L] 3.9307165 [µg/L] #> 5 m 0.7321507 [µg/L] 3.1462693 [µg/L] 3.8784200 [µg/L] #> 6 m 0.7106169 [µg/L] 2.4985080 [µg/L] 3.2091248 [µg/L] #> 10 m 0.6275578 [µg/L] 1.0113008 [µg/L] 1.6388586 [µg/L] #> 20 m 0.4392904 [µg/L] 0.4719404 [µg/L] 0.9112308 [µg/L] #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"reimplementation FOCUS Step 1 2 calculator version 3.2, authored Michael Klein, R. Note results multiple applications compared corresponding results single application. current, done automatically implementation. Step 1 PECs calculated. However, input files can generated suitable input FOCUS calculator.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"","code":"PEC_sw_focus( parent, rate, n = 1, i = NA, comment = \"\", met = NULL, f_drift = NA, f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names, region = c(\"n\", \"s\"), season = c(NA, \"of\", \"mm\", \"js\"), interception = c(\"no interception\", \"minimal crop cover\", \"average crop cover\", \"full canopy\"), met_form_water = TRUE, txt_file = \"pesticide.txt\", overwrite = FALSE, append = FALSE )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"parent list containing substance specific parameters, e.g. conveniently generated chent_focus_sw. rate application rate g/ha. Overriden applications given explicitly n number applications application interval comment comment input file met list containing metabolite specific parameters. e.g. conveniently generated chent_focus_sw. NULL, PEC calculated compound, parent. f_drift fraction application rate reaching waterbody via drift. NA, derived scenario name number applications via drift data defined FOCUS_Step_12_scenarios f_rd fraction amount applied reaching waterbody via runoff/drainage. Step 1, assumed 10%, parent metabolite scenario name scenario. Must one scenario names given FOCUS_Step_12_scenarios region 'n' Northern Europe 's' Southern Europe. NA, Step 1 PECsw calculated season '' October February, 'mm' March May, 'js' June September. NA, step 1 PECsw calculated interception One 'interception' (default), 'minimal crop cover', 'average crop cover' 'full canopy' met_form_water metabolite formation water taken account? can switched check influence compare previous versions Steps 12 calculator txt_file name, potentially full path Steps.12 input text file specification run(s) written overwrite existing file location specified txt_file overwritten? takes effect append FALSE. append input text file appended, exists?","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"formulas input waterbody via runoff/drainage parent subsequent formation metabolite water documented model description coming calculator. one expect, appears (get results) calculated multiplying application rate molar weight correction formation fraction water/sediment systems. Step 2 implemented.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"FOCUS (2014) Generic guidance Surface Water Scenarios (version 1.4). FOrum Co-ordination pesticde fate models USe. http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf Website Steps 1 2 calculator Joint Research Center European Union: http://esdac.jrc.ec.europa.eu/projects/stepsonetwo","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"","code":"# Parent only dummy_1 <- chent_focus_sw(\"Dummy 1\", cwsat = 6000, DT50_ws = 6, Koc = 344.8) PEC_sw_focus(dummy_1, 3000, f_drift = 0) #> $f_drift #> [1] 0 #> #> $eq_rate_drift_s #> [1] 3000 #> #> $eq_rate_rd_s #> [1] 3000 #> #> $eq_rate_rd_parent_s #> [1] NA #> #> $input_drift_s #> [1] 0 #> #> $input_rd_s #> [1] 300 #> #> $f_rd_sw #> [1] 0.6850566 #> #> $f_rd_sed #> [1] 0.3149434 #> #> $PEC #> type #> Time PECsw TWAECsw PECsed TWAECsed #> 0 6.850566e+02 NA 2.362075e+03 NA #> 1 6.103161e+02 647.68635 2.104370e+03 2233.2225 #> 2 5.437298e+02 612.03420 1.874780e+03 2110.2939 #> 4 4.315586e+02 548.76030 1.488014e+03 1892.1255 #> 7 3.051580e+02 469.88375 1.052185e+03 1620.1592 #> 14 1.359325e+02 339.57370 4.686951e+02 1170.8501 #> 21 6.055102e+01 257.45458 2.087799e+02 887.7034 #> 28 2.697241e+01 203.47173 9.300089e+01 701.5705 #> 42 5.352005e+00 140.10377 1.845371e+01 483.0778 #> 50 2.123945e+00 118.24602 7.323361e+00 407.7123 #> 100 6.585062e-03 59.30629 2.270529e-02 204.4881 #> #> $PEC_sw_max #> [1] 685.0566 #> #> $PEC_sed_max #> [1] 2362.075 #> # Metabolite new_dummy <- chent_focus_sw(\"New Dummy\", mw = 250, Koc = 100) M1 <- chent_focus_sw(\"M1\", mw = 100, cwsat = 100, DT50_ws = 100, Koc = 50, max_ws = 0, max_soil = 0.5) PEC_sw_focus(new_dummy, 1000, scenario = \"cereals, winter\", met = M1) #> $f_drift #> [1] 0.02759 #> #> $eq_rate_drift_s #> [1] 0 #> #> $eq_rate_rd_s #> [1] 200 #> #> $eq_rate_rd_parent_s #> [1] 0 #> #> $input_drift_s #> [1] 0 #> #> $input_rd_s #> [1] 20 #> #> $f_rd_sw #> [1] 0.9375 #> #> $f_rd_sed #> [1] 0.0625 #> #> $PEC #> type #> Time PECsw TWAECsw PECsed TWAECsed #> 0 62.50000 NA 31.25000 NA #> 1 62.06828 62.28414 31.03414 31.14207 #> 2 61.63954 62.06890 30.81977 31.03445 #> 4 60.79093 61.64158 30.39547 30.82079 #> 7 59.53987 61.00800 29.76994 30.50400 #> 14 56.71995 59.56326 28.35997 29.78163 #> 21 54.03358 58.16414 27.01679 29.08207 #> 28 51.47444 56.80902 25.73722 28.40451 #> 42 46.71404 54.22460 23.35702 27.11230 #> 50 44.19417 52.81945 22.09709 26.40973 #> 100 31.25000 45.08422 15.62500 22.54211 #> #> $PEC_sw_max #> [1] 62.5 #> #> $PEC_sed_max #> [1] 31.25 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","title":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","text":"method 'percentage' equivalent used CRD spreadsheet PEC calculator","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","text":"","code":"PEC_sw_sed( PEC_sw, percentage = 100, method = \"percentage\", sediment_depth = set_units(5, \"cm\"), water_depth = set_units(30, \"cm\"), sediment_density = set_units(1.3, \"kg/L\"), PEC_sed_units = c(\"µg/kg\", \"mg/kg\") )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","text":"PEC_sw Numeric vector matrix surface water concentrations µg/L corresponding sediment concentration estimated percentage percentage sediment, used percentage method method method used calculation sediment_depth Depth sediment layer water_depth Depth water body cm sediment_density density sediment kg/L (equivalent g/cm3) PEC_sed_units units estimated sediment PEC value","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","text":"predicted concentration sediment","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","text":"","code":"library(pfm) library(units) PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50) #> 2.130769 [µg/kg]"},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":null,"dir":"Reference","previous_headings":"","what":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"Actual maximum moving window time average concentrations SFO kinetics","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"","code":"SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100))"},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"FOCUS (2014) Generic Guidance Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration, Version 1.1, 18 December 2014, p. 251","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"DT50 half-life. times output times, window sizes time weighted average concentrations","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"","code":"SFO_actual_twa(10) #> actual twa #> 0 1.0000000000 NaN #> 1 0.9330329915 0.9661297 #> 2 0.8705505633 0.9337803 #> 4 0.7578582833 0.8733416 #> 7 0.6155722067 0.7923030 #> 14 0.3789291416 0.6400113 #> 21 0.2332582479 0.5267498 #> 28 0.1435872944 0.4412651 #> 42 0.0544094102 0.3248093 #> 50 0.0312500000 0.2795222 #> 100 0.0009765625 0.1441286"},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"implements method specified UK data requirements handbook checked spreadsheet published CRD website","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"","code":"SSLRC_mobility_classification(Koc)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"Koc sorption coefficient normalised organic carbon L/kg","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"list containing classification percentage compound transported per 10 mm drain water","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"HSE's Chemicals Regulation Division (CRD) Active substance PECsw calculations (UK specific authorisation requests) https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm accessed 2019-09-27 Drainage PECs Version 1.0 (2015) Spreadsheet published https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx accessed 2019-09-27","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"","code":"SSLRC_mobility_classification(100) #> $`Mobility classification` #> [1] \"Moderately mobile\" #> #> $`Percentage drained per mm of drain water` #> [1] 0.7 #> SSLRC_mobility_classification(10000) #> $`Mobility classification` #> [1] \"Non mobile\" #> #> $`Percentage drained per mm of drain water` #> [1] 0.008 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"R6 class holding TOXSWA water concentration (cwa) data associated statistics. like maximum moving window average concentrations, dataframes holding events exceeding specified thresholds. Usually, instance class generated read.TOXSWA_cwa.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"R6::R6Class generator object.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"filename Length one character vector holding filename. basedir Length one character vector holding directory file came . zipfile null, giving path zip file file read. segment Length one integer, specifying segment cwa data read. substance TOXSWA name substance. cwas Dataframe holding concentrations. events List dataframes holding event statistics threshold. windows Matrix maximum time weighted average concentrations (TWAC_max) areas curve µg/day * h (AUC_max_h) µg/day * d (AUC_max_d) requested moving window sizes days.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"TOXSWA_cwa$new() TOXSWA_cwa$moving_windows() TOXSWA_cwa$get_events() TOXSWA_cwa$print() TOXSWA_cwa$clone()","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"toxswa-cwa-new-","dir":"Reference","previous_headings":"","what":"TOXSWA_cwa$new()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"Create TOXSWA_cwa object file","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$new( filename, basedir, zipfile = NULL, segment = \"last\", substance = \"parent\", total = FALSE )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"filename filename basedir directory look zipfile Optional path zipfile holding file segment Either \"last\" number segment read data substance TOXSWA substance name (TOXSWA 4 higher) total total concentrations read ? FALSE, free concentrations read","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"toxswa-cwa-moving-windows-","dir":"Reference","previous_headings":"","what":"TOXSWA_cwa$moving_windows()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"Add windows field described .","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$moving_windows(windows, total = FALSE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"windows Window sizes days total TRUE, total concentration including amount adsorbed suspended matter used.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"toxswa-cwa-get-events-","dir":"Reference","previous_headings":"","what":"TOXSWA_cwa$get_events()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"Populate datataframe event information specified threshold value. resulting dataframe stored events field object.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$get_events(thresholds, total = FALSE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"thresholds Threshold values µg/L. total TRUE, total concentration including amount adsorbed suspended matter used.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"toxswa-cwa-print-","dir":"Reference","previous_headings":"","what":"TOXSWA_cwa$print()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"Print TOXSWA_cwa object","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$print()"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"toxswa-cwa-clone-","dir":"Reference","previous_headings":"","what":"TOXSWA_cwa$clone()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"H_sw_R1_stream <- read.TOXSWA_cwa(\"00003s_pa.cwa\", basedir = \"SwashProjects/project_H_sw/TOXSWA\", zipfile = system.file(\"testdata/SwashProjects.zip\", package = \"pfm\")) H_sw_R1_stream$get_events(c(2, 10)) H_sw_R1_stream$moving_windows(c(7, 21)) print(H_sw_R1_stream) #> <TOXSWA_cwa> data from file 00003s_pa.cwa segment 20 #> datetime t t_firstjan t_rel_to_max cwa_mug_per_L #> 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0 #> 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0 #> 60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0 #> 80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0 #> 100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0 #> 120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0 #> cwa_tot_mug_per_L #> 20 0 #> 40 0 #> 60 0 #> 80 0 #> 100 0 #> 120 0 #> Moving window analysis #> window max_TWAC max_AUC_h max_AUC_d #> 1 7 days 2.3926551 401.9660 16.74859 #> 2 21 days 0.8369248 421.8101 17.57542 #> Event statistics for threshold 2 #> t_start cwa_max duration pre_interval AUC_h AUC_d #> 1 44.375 4.167238 0.208 44.375 17.77202 0.740501 #> 2 55.042 40.584010 0.583 10.459 398.21189 16.592162 #> Event statistics for threshold 10 #> t_start cwa_max duration pre_interval AUC_h AUC_d #> 1 55.083 40.58401 0.459 55.083 379.433 15.80971"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":null,"dir":"Reference","previous_headings":"","what":"Estimation of the transpiration stream concentration factor — TSCF","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"FOCUS groundwater guidance (FOCUS 2014, p. 41) states reliable measured log Kow neutral pH must available order apply Briggs equation. clarified can regarded reliable, equation stated produced non-ionic compounds, suggesting compound ionogenic (weak acid/base) ionic.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"","code":"TSCF(log_Kow, method = c(\"briggs82\", \"dettenmaier09\"))"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"log_Kow decadic logarithm octanol-water partition constant method Short name estimation method.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"Dettenmaier equation given show views subject exist.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"FOCUS (2014) Generic Guidance Tier 1 FOCUS Ground Water Assessments. Version 2.2, May 2014 Dettenmaier EM, Doucette WJ Bugbee B (2009) Chemical hydrophobicity uptake plant roots. Environ. Sci. Technol 43, 324 - 329","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"","code":"plot(TSCF, -1, 5, xlab = \"log Kow\", ylab = \"TSCF\", ylim = c(0, 1.1)) TSCF_2 <- function(x) TSCF(x, method = \"dettenmaier09\") curve(TSCF_2, -1, 5, add = TRUE, lty = 2) legend(\"topright\", lty = 1:2, bty = \"n\", legend = c(\"Briggs et al. (1982)\", \"Dettenmaier et al. (2009)\"))"},{"path":"https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","title":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","text":"Create chemical compound object FOCUS Step 1 calculations","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","text":"","code":"chent_focus_sw( name, Koc, DT50_ws = NA, DT50_soil = NA, DT50_water = NA, DT50_sediment = NA, cwsat = 1000, mw = NA, max_soil = 1, max_ws = 1 )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","text":"name Length one character vector containing name Koc Partition coefficient organic carbon water L/kg. DT50_ws Half-life water/sediment systems days DT50_soil Half-life soil days DT50_water Half-life water days (Step 2) DT50_sediment Half-life sediment days (Step 2) cwsat Water solubility mg/L mw Molar weight g/mol. max_soil Maximum observed fraction (dimensionless) soil max_ws Maximum observed fraction (dimensionless) water/sediment systems","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","text":"list substance specific properties","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":null,"dir":"Reference","previous_headings":"","what":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","title":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","text":"Deposition spray drift expressed percent applied dose published German Julius-Kühn Institute (JKI).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","text":"","code":"drift_data_JKI"},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","text":"list currently containing matrices spray drift percentage data field crops (Ackerbau), Pome/stone fruit, early late (Obstbau frueh, spaet).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","text":"JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html 2015-06-11, present 2024-01-31 Rautmann, D., Streloke, M Winkler, R (2001) New basic drift values authorization procedure plant protection products Mitt. Biol. Bundesanst. Land- Forstwirtsch. 383, 133-141","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","text":"data extracted spreadsheet cited using R code given file data_generation/drift_data_JKI.R installed package. file included package, licence clear. Additional spray drift values taken publication Rautmann et al. (2001). Specifically, values early vines, values 3 m buffer incomplete spreadsheet. Note vegetables, ornamentals small fruit, values field crops used crops < 50 cm, vales late vines used crops > 50 cm. JKI spreadsheet, indicated values used spray applications handheld/knapsack equipment (tragbare Spritz- und Sprühgerate). Values non-professional use listed JKI spreadsheet included.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","text":"","code":"drift_data_JKI #> [[1]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 2.77 NA NA NA NA #> 3 0.95 29.20 15.73 2.70 8.02 #> 5 0.57 19.89 8.41 1.18 3.62 #> 10 0.29 11.81 3.60 0.39 1.23 #> 15 0.20 5.55 1.81 0.20 0.65 #> 20 0.15 2.77 1.09 0.13 0.42 #> 30 0.10 1.04 0.54 0.07 0.22 #> 40 0.07 0.52 0.32 0.04 0.14 #> 50 0.06 0.30 0.22 0.03 0.10 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 4.440 NA #> 3 19.33 NA 0.018721696 #> 5 11.57 0.180 0.014363896 #> 10 5.77 0.050 0.010026007 #> 15 3.84 0.020 0.008124366 #> 20 1.79 0.012 0.006998158 #> 30 0.56 0.005 0.005670811 #> 40 0.25 0.003 NA #> 50 0.13 0.002 0.004350831 #> #> [[2]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 2.38 NA NA NA NA #> 3 0.79 25.53 12.13 2.53 7.23 #> 5 0.47 16.87 6.81 1.09 3.22 #> 10 0.24 9.61 3.11 0.35 1.07 #> 15 0.16 5.61 1.58 0.18 0.56 #> 20 0.12 2.59 0.90 0.11 0.36 #> 30 0.08 0.87 0.40 0.06 0.19 #> 40 0.06 0.40 0.23 0.03 0.12 #> 50 0.05 0.22 0.15 0.02 0.08 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 3.780 NA #> 3 17.73 NA NA #> 5 9.60 0.160 NA #> 10 4.18 0.040 NA #> 15 2.57 0.020 NA #> 20 1.21 0.011 NA #> 30 0.38 0.005 NA #> 40 0.17 0.003 NA #> 50 0.09 0.002 NA #> #> [[3]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 2.01 NA NA NA NA #> 3 0.68 23.96 11.01 2.49 6.90 #> 5 0.41 15.79 6.04 1.04 3.07 #> 10 0.20 8.96 2.67 0.32 1.02 #> 15 0.14 4.24 1.39 0.16 0.54 #> 20 0.10 2.01 0.80 0.10 0.34 #> 30 0.07 0.70 0.36 0.05 0.18 #> 40 0.05 0.33 0.21 0.03 0.11 #> 50 0.04 0.19 0.13 0.02 0.08 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 3.420 NA #> 3 15.93 NA NA #> 5 8.57 0.150 NA #> 10 3.70 0.040 NA #> 15 2.26 0.020 NA #> 20 1.05 0.010 NA #> 30 0.34 0.004 NA #> 40 0.15 0.003 NA #> 50 0.08 0.002 NA #> #> [[4]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.85 NA NA NA NA #> 3 0.62 23.61 10.12 2.44 6.71 #> 5 0.38 15.42 5.60 1.02 2.99 #> 10 0.19 8.66 2.50 0.31 0.99 #> 15 0.13 4.01 1.28 0.16 0.52 #> 20 0.10 1.89 0.75 0.10 0.33 #> 30 0.06 0.66 0.35 0.05 0.17 #> 40 0.05 0.31 0.20 0.03 0.11 #> 50 0.04 0.17 0.13 0.02 0.08 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 2.290 NA #> 3 15.38 NA NA #> 5 8.26 0.120 NA #> 10 3.55 0.030 NA #> 15 2.17 0.020 NA #> 20 0.93 0.009 NA #> 30 0.31 0.004 NA #> 40 0.14 0.002 NA #> 50 0.08 0.002 NA #> #> [[5]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.75 NA NA NA NA #> 3 0.59 23.12 9.74 2.37 6.59 #> 5 0.36 15.06 5.41 1.00 2.93 #> 10 0.18 8.42 2.43 0.31 0.98 #> 15 0.12 3.83 1.24 0.15 0.51 #> 20 0.09 1.81 0.72 0.09 0.33 #> 30 0.06 0.63 0.34 0.05 0.17 #> 40 0.05 0.30 0.20 0.03 0.11 #> 50 0.04 0.17 0.13 0.02 0.08 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 2.120 NA #> 3 15.12 NA NA #> 5 7.99 0.110 NA #> 10 3.36 0.030 NA #> 15 2.03 0.010 NA #> 20 0.88 0.008 NA #> 30 0.29 0.004 NA #> 40 0.14 0.002 NA #> 50 0.07 0.002 NA #> #> [[6]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.64 NA NA NA NA #> 3 0.56 22.76 9.21 2.29 6.41 #> 5 0.34 14.64 5.18 0.97 2.85 #> 10 0.17 8.04 2.38 0.30 0.95 #> 15 0.11 3.71 1.20 0.15 0.50 #> 20 0.09 1.75 0.68 0.09 0.32 #> 30 0.06 0.61 0.31 0.05 0.17 #> 40 0.04 0.29 0.17 0.03 0.11 #> 50 0.03 0.16 0.11 0.02 0.07 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 1.980 NA #> 3 14.90 NA NA #> 5 7.79 0.100 NA #> 10 3.23 0.030 NA #> 15 1.93 0.010 NA #> 20 0.83 0.008 NA #> 30 0.28 0.004 NA #> 40 0.13 0.002 NA #> 50 0.07 0.001 NA #> #> [[7]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.61 NA NA NA NA #> 3 0.55 22.69 9.10 2.24 6.33 #> 5 0.33 14.45 5.11 0.94 2.81 #> 10 0.17 7.83 2.33 0.29 0.94 #> 15 0.11 3.62 1.20 0.15 0.49 #> 20 0.08 1.71 0.67 0.09 0.31 #> 30 0.06 0.60 0.30 0.05 0.16 #> 40 0.04 0.28 0.17 0.03 0.10 #> 50 0.03 0.16 0.11 0.02 0.07 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 1.930 NA #> 3 14.63 NA NA #> 5 7.60 0.100 NA #> 10 3.13 0.030 NA #> 15 1.86 0.010 NA #> 20 0.81 0.008 NA #> 30 0.26 0.004 NA #> 40 0.12 0.002 NA #> 50 0.06 0.001 NA #> #> [[8]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.52 NA NA NA NA #> 3 0.52 22.24 8.66 2.16 6.26 #> 5 0.31 14.09 4.92 0.91 2.78 #> 10 0.16 7.58 2.29 0.28 0.93 #> 15 0.11 3.48 1.14 0.14 0.49 #> 20 0.08 1.65 0.65 0.09 0.31 #> 30 0.05 0.57 0.29 0.04 0.16 #> 40 0.04 0.27 0.16 0.03 0.10 #> 50 0.03 0.15 0.11 0.02 0.07 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 1.640 NA #> 3 13.53 NA NA #> 5 7.15 0.090 NA #> 10 3.01 0.020 NA #> 15 1.82 0.010 NA #> 20 0.78 0.007 NA #> 30 0.25 0.003 NA #> 40 0.12 0.002 NA #> 50 0.06 0.001 NA #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":null,"dir":"Reference","previous_headings":"","what":"Regression parameters for the Rautmann drift data — drift_parameters_focus","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"parameters extracted Appendix B FOCUS surface water guidance using R code given file data_generation/drift_parameters_focus.R installed package. appendix included package, licence clear.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"","code":"drift_parameters_focus"},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"tibble::tibble.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"hinge distance, Inf substituted cases hinge distance given data, way parameters C D never used distance B used case distance smaller hinge distance.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"FOCUS (2014) Generic guidance Surface Water Scenarios (version 1.4). FOrum Co-ordination pesticde fate models USe. http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf FOCUS (2001) FOCUS Surface Water Scenarios EU Evaluation Process 91/414/EEC. Report FOCUS Working Group Surface Water Scenarios, EC Document Reference SANCO/4802/2001-rev.2. 245, Appendix B. https://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/FOCUS_SWS_APPENDIX_B.doc Rautmann, D., Streloke, M Winkler, R (2001) New basic drift values authorization procedure plant protection products Mitt. Biol. Bundesanst. Land- Forstwirtsch. 383, 133-141","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"","code":"drift_parameters_focus #> # A tibble: 49 × 8 #> crop_group n_apps percentile A B C D hinge #> <chr> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 arable 1 90 2.76 -0.978 NA NA Inf #> 2 arable 2 82 2.44 -1.01 NA NA Inf #> 3 arable 3 77 2.02 -0.996 NA NA Inf #> 4 arable 4 74 1.86 -0.986 NA NA Inf #> 5 arable 5 72 1.79 -0.994 NA NA Inf #> 6 arable 6 70 1.63 -0.986 NA NA Inf #> 7 arable 7 69 1.58 -0.981 NA NA Inf #> 8 arable 8 67 1.51 -0.983 NA NA Inf #> 9 hops 1 90 58.2 -1.00 8655. -2.84 15.3 #> 10 hops 2 82 66.2 -1.20 5555. -2.82 15.3 #> # ℹ 39 more rows unique(drift_parameters_focus$crop_group) #> [1] \"arable\" \"hops\" \"vines, late\" \"vines, early\" \"fruit, late\" #> [6] \"fruit, early\" \"aerial\""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"Calculate drift percentages based Rautmann data","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"","code":"drift_percentages_rautmann( distances, applications = 1, crop_group_RF = \"arable\", formula = c(\"Rautmann\", \"FOCUS\"), widths = 1 )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"distances distances m get PEC values applications Number applications selection drift percentile crop_group_RF Crop group(s) used drift_parameters_focus, .e. \"arable\", \"hops\", \"vines, late\", \"vines, early\", \"fruit, late\", \"fruit, early\" \"aerial\". formula default, original Rautmann formula used. specify \"FOCUS\", mean drift input width water body calculated described Chapter 5.4.5 FOCUS surface water guidance widths widths water bodies (used FOCUS formula)","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"FOCUS (2014) Generic guidance Surface Water Scenarios (version 1.4). FOrum Co-ordination pesticde fate models USe. http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"","code":"# Compare JKI data with Rautmann and FOCUS formulas for arable crops (default) # One application on field crops, for 1 m, 3 m and 5 m distance drift_data_JKI[[1]][as.character(c(1, 3, 5)), \"Ackerbau\"] #> 1 3 5 #> 2.77 0.95 0.57 drift_percentages_rautmann(c(1, 3, 5)) #> [1] 2.7593000 0.9424748 0.5719342 drift_percentages_rautmann(c(1, 3, 5), formula = \"FOCUS\") #> [1] 1.9273922 0.8160023 0.5224362 # Since pfm 0.6.5, the function can also take a vector of crop groups drift_percentages_rautmann( distances = c(1, 5, 5), crop_group_RF = c(\"fruit, early\", \"fruit, early\", \"fruit, late\")) #> [1] 66.702000 19.884442 8.410849 # Two applications, all else equal drift_data_JKI[[2]][as.character(c(1, 3, 5)), \"Ackerbau\"] #> 1 3 5 #> 2.38 0.79 0.47 drift_percentages_rautmann(c(1, 3, 5), applications = 2) #> [1] 2.4376000 0.8036556 0.4797365 drift_percentages_rautmann(c(1, 3, 5), formula = \"FOCUS\", app = 2) #> [1] 1.6837733 0.6925952 0.4369331 # One application to early or late fruit crops drift_data_JKI[[1]][as.character(c(3, 5, 20, 50)), \"Obstbau frueh\"] #> 3 5 20 50 #> 29.20 19.89 2.77 0.30 drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = \"fruit, early\") #> [1] 29.1973659 19.8844422 2.7618138 0.3012008 drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = \"fruit, early\", formula = \"FOCUS\") #> [1] 26.1193421 18.5428680 2.6038558 0.2940792 drift_data_JKI[[1]][as.character(c(3, 5, 20, 50)), \"Obstbau spaet\"] #> 3 5 20 50 #> 15.73 8.41 1.09 0.22 drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = \"fruit, late\") #> [1] 15.7246994 8.4108487 1.0813887 0.2155992 drift_percentages_rautmann(c(3, 5, 20, 50), crop_group_RF = \"fruit, late\", formula = \"FOCUS\") #> [1] 13.1414350 7.5123244 1.0359007 0.2118734 # We get a continuum if the waterbody covers the hinge distance # (11.4 m for 1 early app to fruit) x <- seq(3, 30, by = 0.1) d <- drift_percentages_rautmann(x, crop_group_RF = \"fruit, early\", formula = \"FOCUS\") plot(x, d, type = \"l\", xlab = \"Distance of near edge [m]\", ylab = \"Mean drift percentage over waterbody width\", main = \"One application to fruit, early\") abline(v = 11.4, lty = 2)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"R6 class objects class chent represent chemical entities can hold list information loaded chemical yaml file chyaml field. information extracted optionally aggregated function.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"","code":"endpoint( chent, medium = \"soil\", type = c(\"degradation\", \"sorption\"), lab_field = c(NA, \"laboratory\", \"field\"), redox = c(NA, \"aerobic\", \"anaerobic\"), value = c(\"DT50ref\", \"Kfoc\", \"N\"), aggregator = geomean, raw = FALSE, signif = 3 ) soil_DT50( chent, aggregator = geomean, signif = 3, lab_field = \"laboratory\", value = \"DT50ref\", redox = \"aerobic\", raw = FALSE ) soil_Kfoc(chent, aggregator = geomean, signif = 3, value = \"Kfoc\", raw = FALSE) soil_N(chent, aggregator = mean, signif = 3, raw = FALSE) soil_sorption( chent, values = c(\"Kfoc\", \"N\"), aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3), raw = FALSE )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"chent chent object get information medium medium information sought type information type lab_field NA, want laboratory field endpoints redox NA, looking aerobic anaerobic data value name value want. list given usage section exclusive aggregator aggregator function. Can mean, geomean, identity, example. raw number(s) returned stored chent object (character value) retain original information precision? signif many significant digits want values values returned aggregators named vector aggregator functions used","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"result applying aggregator function values converted numeric vector, rounded given number significant digits, , raw = TRUE, values character value, retaining implicit information precision may present.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"functions soil_* functions extract soil specific endpoints. Freundlich exponent, capital letter N used order facilitate dealing data R. pesticide fate modelling, exponent often called 1/n.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the geometric mean — geomean","title":"Calculate the geometric mean — geomean","text":"Based posts thread Stackoverflow http://stackoverflow.com/questions/2602583/geometric-mean----built-function returns NA NA values present na.rm = FALSE (default). negative values present, gives error message. least one element vector 0, returns 0.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the geometric mean — geomean","text":"","code":"geomean(x, na.rm = FALSE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the geometric mean — geomean","text":"x Vector numbers na.rm NA values omitted?","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate the geometric mean — geomean","text":"geometric mean","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate the geometric mean — geomean","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the geometric mean — geomean","text":"","code":"geomean(c(1, 3, 9)) #> [1] 3 geomean(c(1, 3, NA, 9)) #> [1] NA geomean(c(1, -3, 9)) # returns an error #> Error in geomean(c(1, -3, 9)): Only defined for positive numbers"},{"path":"https://pkgdown.jrwb.de/pfm/reference/get_vertex.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a parabola through three points — get_vertex","title":"Fit a parabola through three points — get_vertex","text":"inspired answer stackoverflow https://stackoverflow.com//717791","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/get_vertex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a parabola through three points — get_vertex","text":"","code":"get_vertex(x, y)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/get_vertex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a parabola through three points — get_vertex","text":"x Three x coordinates y Three y coordinates","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":null,"dir":"Reference","previous_headings":"","what":"The maximum time weighted average concentration for a moving window — max_twa","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"generate time series using sawtooth, need make sure length time series allows finding maximum. therefore recommended check using plot.one_box using window size argument max_twa.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"","code":"max_twa(x, window = 21)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"x object type one_box window size moving window","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"method working directly fitted mkinfit objects uses equations given PEC soil section FOCUS guidance restricted SFO, FOMC DFOP models parent compound","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"","code":"pred <- sawtooth(one_box(10), applications = data.frame(time = c(0, 7), amount = c(1, 1))) max_twa(pred) #> $max #> parent #> 0.9537545 #> #> $window_start #> parent #> 0 #> #> $window_end #> parent #> 21 #> pred_FOMC <- mkinfit(\"FOMC\", FOCUS_2006_C, quiet = TRUE) max_twa(pred_FOMC) #> 21 #> 18.22124"},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a time series of decline data — one_box","title":"Create a time series of decline data — one_box","text":"Create time series decline data","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a time series of decline data — one_box","text":"","code":"one_box(x, ini, ..., t_end = 100, res = 0.01) # S3 method for class 'numeric' one_box(x, ini = 1, ..., t_end = 100, res = 0.01) # S3 method for class 'character' one_box(x, ini = 1, parms, ..., t_end = 100, res = 0.01) # S3 method for class 'mkinfit' one_box(x, ini = \"model\", ..., t_end = 100, res = 0.01)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a time series of decline data — one_box","text":"x numeric, half-life used exponential decline. character string specifying parent decline model given e.g. FOMC, parms must contain corresponding parameters. x mkinfit object, decline calculated object. ini initial amount. x mkinfit object, ini 'model', fitted initial concentrations used. Otherwise, ini must numeric. length one, used parent initial values metabolites zero, otherwise, must give values observed variables. ... arguments passed methods t_end End time series res Resolution time series parms named numeric vector containing model parameters","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a time series of decline data — one_box","text":"object class one_box, inheriting ts.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a time series of decline data — one_box","text":"","code":"# Only use a half-life pred_0 <- one_box(10) plot(pred_0) # Use a fitted mkinfit model require(mkin) fit <- mkinfit(\"FOMC\", FOCUS_2006_C, quiet = TRUE) pred_1 <- one_box(fit) plot(pred_1) # Use a model with more than one observed variable m_2 <- mkinmod(parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data pred_2 <- one_box(fit_2, ini = \"model\") plot(pred_2)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":null,"dir":"Reference","previous_headings":"","what":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"table loss percentages used Exposit 3 twelve different Koc classes","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"","code":"perc_runoff_exposit"},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"data frame percentage values dissolved fraction fraction bound eroding particles, Koc classes used row names Koc_lower_bound lower bound Koc class dissolved percentage applied substance transferred adjacent water body dissolved phase bound percentage applied substance transferred adjacent water body bound eroding particles","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"Excel 3.02 spreadsheet available https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"","code":"print(perc_runoff_exposit) #> Koc_lower_bound dissolved bound #> 0-20 0 [L/kg] 0.110 0.000 #> >20-50 20 [L/kg] 0.151 0.000 #> >50-100 50 [L/kg] 0.197 0.000 #> >100-200 100 [L/kg] 0.248 0.001 #> >200-500 200 [L/kg] 0.224 0.004 #> >500-1000 500 [L/kg] 0.184 0.020 #> >1000-2000 1000 [L/kg] 0.133 0.042 #> >2000-5000 2000 [L/kg] 0.084 0.091 #> >5000-10000 5000 [L/kg] 0.037 0.159 #> >10000-20000 10000 [L/kg] 0.031 0.192 #> >20000-50000 20000 [L/kg] 0.014 0.291 #> >50000 50000 [L/kg] 0.001 0.451"},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":null,"dir":"Reference","previous_headings":"","what":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"table runoff reduction percentages used Exposit 3 different vegetated buffer widths","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"","code":"perc_runoff_reduction_exposit"},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"named list data frames reduction percentage values dissolved fraction fraction bound eroding particles, vegetated buffer widths row names. names list items Exposit versions values taken. dissolved reduction percentage dissolved phase bound reduction percentage particulate phase","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"Excel 3.02 spreadsheet available https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html Agroscope version 3.01a additional runoff factors 3 m 6 m buffer zones received Muris Korkaric (published). variant 3.01a2 introduced consistency previous calculations performed Agroscope 3 m buffer zone.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"","code":"print(perc_runoff_reduction_exposit) #> $`3.02` #> dissolved bound #> No buffer 0 0 #> 5 m 40 40 #> 10 m 60 85 #> 20 m 80 95 #> #> $`3.01a` #> dissolved bound #> No buffer 0 0 #> 3 m 25 30 #> 5 m 40 40 #> 6 m 45 55 #> 10 m 60 85 #> 20 m 80 95 #> #> $`3.01a2` #> dissolved bound #> No buffer 0 0 #> 3 m 25 25 #> #> $`2.0` #> dissolved bound #> No buffer 0.0 0.0 #> 20 m 97.5 97.5 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"Calculate time course relative concentrations based mkinmod model","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"","code":"pfm_degradation( model = \"SFO\", DT50 = 1000, parms = c(k_parent = log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, by = step_days) )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"model degradation model used. Either parent model like 'SFO' 'FOMC', mkinmod object DT50 half-life. used simple exponential decline calculated (SFO model). parms parameters used degradation model years many years degradation predicted? step_days step size days output ? times output times","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"","code":"head(pfm_degradation(\"SFO\", DT50 = 10)) #> time parent #> 0 0 1.0000000 #> 1 1 0.9330330 #> 2 2 0.8705506 #> 3 3 0.8122524 #> 4 4 0.7578583 #> 5 5 0.7071068"},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"Plot TOXSWA hourly concentrations chemical substance specific segment TOXSWA surface water body.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"","code":"# S3 method for class 'TOXSWA_cwa' plot( x, time_column = c(\"datetime\", \"t\", \"t_firstjan\", \"t_rel_to_max\"), xlab = \"default\", ylab = \"default\", add = FALSE, threshold_factor = 1000, thin_low = 1, total = FALSE, LC_TIME = \"C\", ... )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"x TOXSWA_cwa object plotted. time_column used time axis. \"t_firstjan\" chosen, time given days relative first January first year. xlab, ylab Labels x y axis. add add existing plot? threshold_factor factor data lower maximum order get thinned plotting (see next argument). thin_low integer greater 1, data close zero (smaller 1/threshold_factor maximum) series thinned factor order decrease amount data included plots total total concentration water plotted, including substance sorbed suspended matter? LC_TIME Specification locale used format dates ... arguments passed plot adding existing plot","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"","code":"H_sw_D4_pond <- read.TOXSWA_cwa(\"00001p_pa.cwa\", basedir = \"SwashProjects/project_H_sw/TOXSWA\", zipfile = system.file(\"testdata/SwashProjects.zip\", package = \"pfm\")) plot(H_sw_D4_pond) plot(H_sw_D4_pond, time_column = \"t\") plot(H_sw_D4_pond, time_column = \"t_firstjan\") plot(H_sw_D4_pond, time_column = \"t_rel_to_max\") H_sw_R1_stream <- read.TOXSWA_cwa(\"00003s_pa.cwa\", basedir = \"SwashProjects/project_H_sw/TOXSWA\", zipfile = system.file(\"testdata/SwashProjects.zip\", package = \"pfm\")) plot(H_sw_R1_stream, time_column = \"t_rel_to_max\")"},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.one_box.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot time series of decline data — plot.one_box","title":"Plot time series of decline data — plot.one_box","text":"Plot time series decline data","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.one_box.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot time series of decline data — plot.one_box","text":"","code":"# S3 method for class 'one_box' plot( x, xlim = range(time(x)), ylim = c(0, max(x)), xlab = \"Time\", ylab = \"Residue\", max_twa = NULL, max_twa_var = dimnames(x)[[2]][1], ... )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.one_box.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot time series of decline data — plot.one_box","text":"x object type one_box plotted xlim Limits x axis ylim Limits y axis xlab Label x axis ylab Label y axis max_twa numeric value given, maximum time weighted average concentration(s) /shown graph. max_twa_var Variable maximum time weighted average shown max_twa NULL. ... arguments passed methods","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.one_box.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot time series of decline data — plot.one_box","text":"","code":"dfop_pred <- one_box(\"DFOP\", parms = c(k1 = 0.2, k2 = 0.02, g = 0.7)) plot(dfop_pred) plot(sawtooth(dfop_pred, 3, 7), max_twa = 21) # Use a fitted mkinfit model m_2 <- mkinmod(parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data pred_2 <- one_box(fit_2, ini = 1) pred_2_saw <- sawtooth(pred_2, 2, 7) plot(pred_2_saw) plot(pred_2_saw, max_twa = 21, max_twa_var = \"m1\")"},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":null,"dir":"Reference","previous_headings":"","what":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"Read TOXSWA hourly concentrations chemical substance specific segment TOXSWA surface water body. Per default, data last segment imported. TOXSWA 4 reports values end hour (ConLiqWatLayCur) summary file, use value well instead hourly averages (ConLiqWatLay). TOXSWA 5.5.3 variable renamed ConLiqWatLay file.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"","code":"read.TOXSWA_cwa( filename, basedir = \".\", zipfile = NULL, segment = \"last\", substance = \"parent\", total = FALSE, windows = NULL, thresholds = NULL )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"filename filename cwa file (TOXSWA 2.x.y similar) file using FOCUS TOXSWA 4 (.e. TOXSWA 4.4.2) higher. basedir path directory cwa file resides. zipfile Optional path zip file containing cwa file. segment segment data read. Either \"last\", segment number. substance .files, default value \"parent\" leads reading concentrations parent compound. Alternatively, substance interested can selected code name. total Set TRUE order read total concentrations well. necessary .files generated TOXSWA 4.4.2 similar, .cwa files. .cwa files, total concentration always read well. windows Numeric vector width moving windows days, calculating maximum time weighted average concentrations areas curve. thresholds Numeric vector threshold concentrations µg/L generating event statistics.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"instance R6 object class TOXSWA_cwa.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"","code":"H_sw_D4_pond <- read.TOXSWA_cwa(\"00001p_pa.cwa\", basedir = \"SwashProjects/project_H_sw/TOXSWA\", zipfile = system.file(\"testdata/SwashProjects.zip\", package = \"pfm\"))"},{"path":"https://pkgdown.jrwb.de/pfm/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. mkin set_nd_nq(), set_nd_nq_focus()","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/sawtooth.html","id":null,"dir":"Reference","previous_headings":"","what":"Create decline time series for multiple applications — sawtooth","title":"Create decline time series for multiple applications — sawtooth","text":"application pattern specified applications, n disregarded.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/sawtooth.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create decline time series for multiple applications — sawtooth","text":"","code":"sawtooth( x, n = 1, i = 365, applications = data.frame(time = seq(0, (n - 1) * i, length.out = n), amount = 1) )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/sawtooth.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create decline time series for multiple applications — sawtooth","text":"x one_box object n number applications. applications specified, n ignored interval applications. applications specified, ignored applications data frame holding application times first column corresponding amounts applied second column.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/sawtooth.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create decline time series for multiple applications — sawtooth","text":"","code":"applications = data.frame(time = seq(0, 14, by = 7), amount = c(1, 2, 3)) pred <- one_box(10) plot(sawtooth(pred, applications = applications)) m_2 <- mkinmod(parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data pred_2 <- one_box(fit_2, ini = 1) pred_2_saw <- sawtooth(pred_2, 2, 7) plot(pred_2_saw, max_twa = 21, max_twa_var = \"m1\") max_twa(pred_2_saw) #> $max #> parent m1 #> 0.7834481 0.8617049 #> #> $window_start #> parent m1 #> 0.00 26.85 #> #> $window_end #> parent m1 #> 21.00 47.85 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":null,"dir":"Reference","previous_headings":"","what":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"Properties predefined scenarios used Tier 1, Tier 2A Tier 3A concentration soil given EFSA guidance (2015, p. 13/14). Also, scenario model adjustment factors p. 15 p. 17 included.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"","code":"soil_scenario_data_EFSA_2015"},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"data frame one row scenario. Row names scenario codes, e.g. CTN Northern scenario total concentration soil. Columns mostly self-explanatory. rho dry bulk density top soil.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"EFSA (European Food Safety Authority) (2015) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 13(4) 4093 doi:10.2903/j.efsa.2015.4093","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"","code":"soil_scenario_data_EFSA_2015 #> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce #> CTN North Estonia 4.7 7.0 Coarse 0.118 0.244 0.95 3.0 #> CTC Central Germany 8.0 10.1 Coarse 0.086 0.244 1.05 2.0 #> CTS South France 11.0 12.3 Medium fine 0.048 0.385 1.22 2.0 #> CLN North Denmark 8.2 9.8 Medium 0.023 0.347 1.39 2.0 #> CLC Central Czech Republik 9.1 11.2 Medium 0.018 0.347 1.43 1.5 #> CLS South Spain 12.8 14.7 Medium 0.011 0.347 1.51 1.5 #> f_mod #> CTN 2 #> CTC 2 #> CTS 2 #> CLN 4 #> CLC 4 #> CLS 4"},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":null,"dir":"Reference","previous_headings":"","what":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"Properties predefined scenarios used Tier 1, Tier 2A Tier 3A concentration soil given EFSA guidance (2017, p. 14/15). Also, scenario model adjustment factors p. 16 p. 18 included.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"","code":"soil_scenario_data_EFSA_2017"},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"data frame one row scenario. Row names scenario codes, e.g. CTN Northern scenario total concentration soil. Columns mostly self-explanatory. rho dry bulk density top soil.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"EFSA (European Food Safety Authority) (2017) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 15(10) 4982 doi:10.2903/j.efsa.2017.4982","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"","code":"soil_scenario_data_EFSA_2017 #> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce f_mod #> CTN North Estonia 5.7 7.6 Coarse 0.220 0.244 0.707 1.4 3 #> CTC Central Poland 7.4 9.3 Coarse 0.122 0.244 0.934 1.4 3 #> CTS South France 10.2 11.7 Medium 0.070 0.349 1.117 1.4 3 #> CLN North Denmark 8.0 9.2 Medium 0.025 0.349 1.371 1.6 4 #> CLC Central Austria 9.3 11.3 Medium 0.018 0.349 1.432 1.6 4 #> CLS South Spain 15.4 16.7 Medium 0.010 0.349 1.521 1.6 4 #> FOCUS_zone prec #> CTN Hamburg 639 #> CTC Hamburg 617 #> CTS Hamburg 667 #> CLN Hamburg 602 #> CLC Châteaudun 589 #> CLS Sevilla 526 waldo::compare(soil_scenario_data_EFSA_2017, soil_scenario_data_EFSA_2015) #> `old` is length 12 #> `new` is length 10 #> #> `names(old)[8:12]`: \"rho\" \"f_sce\" \"f_mod\" \"FOCUS_zone\" \"prec\" #> `names(new)[8:10]`: \"rho\" \"f_sce\" \"f_mod\" #> #> `old$Country`: \"Estonia\" \"Poland\" \"France\" \"Denmark\" \"Austria\" \"Spain\" #> `new$Country`: \"Estonia\" \"Germany\" \"France\" \"Denmark\" \"Czech Republik\" \"Spain\" #> #> `old$T_arit`: 5.70 7.40 10.20 8.00 9.30 15.40 #> `new$T_arit`: 4.70 8.00 11.00 8.20 9.10 12.80 #> #> `old$T_arr`: 7.60 9.30 11.70 9.20 11.30 16.70 #> `new$T_arr`: 7.00 10.10 12.30 9.80 11.20 14.70 #> #> `old$Texture`: \"Coarse\" \"Coarse\" \"Medium\" \"Medium\" \"Medium\" \"Medium\" #> `new$Texture`: \"Coarse\" \"Coarse\" \"Medium fine\" \"Medium\" \"Medium\" \"Medium\" #> #> `old$f_om`: 0.2200 0.1220 0.0700 0.0250 0.0180 0.0100 #> `new$f_om`: 0.1180 0.0860 0.0480 0.0230 0.0180 0.0110 #> #> `old$theta_fc`: 0.2440 0.2440 0.3490 0.3490 0.3490 0.3490 #> `new$theta_fc`: 0.2440 0.2440 0.3850 0.3470 0.3470 0.3470 #> #> `old$rho`: 0.7070 0.9340 1.1170 1.3710 1.4320 1.5210 #> `new$rho`: 0.9500 1.0500 1.2200 1.3900 1.4300 1.5100 #> #> `old$f_sce`: 1.40 1.40 1.40 1.60 1.60 1.60 #> `new$f_sce`: 3.00 2.00 2.00 2.00 1.50 1.50 #> #> And 3 more differences ..."},{"path":"https://pkgdown.jrwb.de/pfm/reference/twa.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate a time weighted average concentration — twa","title":"Calculate a time weighted average concentration — twa","text":"moving average built using values past, earliest possible time maximum time series returned one window passed.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/twa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate a time weighted average concentration — twa","text":"","code":"twa(x, window = 21) # S3 method for class 'one_box' twa(x, window = 21)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/twa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate a time weighted average concentration — twa","text":"x object type one_box window size moving window","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/twa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate a time weighted average concentration — twa","text":"","code":"pred <- sawtooth(one_box(10), applications = data.frame(time = c(0, 7), amount = c(1, 1))) max_twa(pred) #> $max #> parent #> 0.9537545 #> #> $window_start #> parent #> 0 #> #> $window_end #> parent #> 21 #>"},{"path":"https://pkgdown.jrwb.de/pfm/news/index.html","id":"version-065","dir":"Changelog","previous_headings":"","what":"version 0.6.5","title":"version 0.6.5","text":"R/PEC_sw_drift.R: Support specifying units distances widths using units package. R/TOXSWA_cwa.R: Adapt readr (>= 2.2.0) requiring wrap literal input used reading .files (). R/PEC_sw_drainage_UK.R: Create function drainage_date_UK respect beginning drainage period 1 October, also end drainage period 30 April, use determining degradation time. Applications early year 1 May now correctly calculated without degradation time. R/PEC_sw_drift.R: Vectorise function respect distances, rates water depths, also respect crop groups. Closes issue #2 reported Julian Klein (@juklei).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/news/index.html","id":"version-064","dir":"Changelog","previous_headings":"","what":"version 0.6.4","title":"version 0.6.4","text":"R/PEC_sw_drainage_uk.R: Fix bug preventing function work latest_application set 29 February. Also, make function correctly deal units. R/twa.R: Fix bug plotting one-box models class one_box affected plots displayed time weighted average. R/PEC_sw_drainage_uk.R: Fix bug leading increased PEC values case application date beginning drainage period soil_DT50 specified.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/news/index.html","id":"version-063","dir":"Changelog","previous_headings":"","what":"version 0.6.3","title":"version 0.6.3","text":"R/{PEC_sw_drift,PEC_sw_exposit_runoff,PEC_sw_sed}.R: Make use units package. R/PEC_sw_drift.R: Change argument name ‘crop_group_focus’ ‘crop_group_RF’, order make easier understand relation ‘drift_data’ argument.","code":""}] diff --git a/log/check.log b/log/check.log index 6b8ff0b..3c0c083 100644 --- a/log/check.log +++ b/log/check.log @@ -1,20 +1,18 @@ -* using log directory ‘/home/jranke/git/pfm/pfm.Rcheck’ -* using R version 4.5.2 (2025-10-31) +* using log directory ‘/home/f80868656/projects/pfm/pfm.Rcheck’ +* using R version 4.6.0 (2026-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by - gcc (Debian 14.2.0-19) 14.2.0 - GNU Fortran (Debian 14.2.0-19) 14.2.0 -* running under: Debian GNU/Linux 13 (trixie) + gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0 + GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0 +* running under: Ubuntu 24.04.4 LTS * using session charset: UTF-8 +* current time: 2026-06-22 16:48:14 UTC * using options ‘--no-tests --as-cran’ * checking for file ‘pfm/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘pfm’ version ‘0.6.5’ * package encoding: UTF-8 -* checking CRAN incoming feasibility ... NOTE -Maintainer: ‘Johannes Ranke <johannes.ranke@agroscope.admin.ch>’ - -Size of tarball: 8535898 bytes +* checking CRAN incoming feasibility ... OK * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK @@ -25,12 +23,11 @@ Size of tarball: 8535898 bytes * checking for sufficient/correct file permissions ... OK * checking whether package ‘pfm’ can be installed ... OK * checking installed package size ... INFO - installed size is 10.3Mb + installed size is 10.4Mb sub-directories of 1Mb or more: - testdata 9.9Mb + testdata 10.0Mb * checking package directory ... OK -* checking for future file timestamps ... NOTE -unable to verify current time +* checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK @@ -63,17 +60,20 @@ unable to verify current time * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK -* checking examples ... OK +* checking examples ... [11s/10s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking PDF version of manual ... OK -* checking HTML version of manual ... OK +* checking HTML version of manual ... NOTE +Skipping checking HTML validation: no command 'tidy' found. +Please obtain a recent version of HTML Tidy by downloading a binary +release or compiling the source code from <https://www.html-tidy.org/>. * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE -Status: 2 NOTEs +Status: 1 NOTE See - ‘/home/jranke/git/pfm/pfm.Rcheck/00check.log’ + ‘/home/f80868656/projects/pfm/pfm.Rcheck/00check.log’ for details. diff --git a/log/test.log b/log/test.log index c2a6fc7..30b8fa9 100644 --- a/log/test.log +++ b/log/test.log @@ -2,17 +2,17 @@ ✔ | F W S OK | Context ✔ | 7 | Exposit calculations ✔ | 6 | Geometric mean calculation -✔ | 1 | Check max_twa for parent mkinfit models against analytical solutions +✔ | 1 | Check max_twa for parent mkinfit models against analytical solutions [1.0s] ✔ | 1 | Simple PEC sediment calculations ✔ | 17 | Simple PEC soil calculations ✔ | 11 | Simple PEC surface water calculations with drift entry ✔ | 1 | Actual and time weighted average concentrations for SFO kinetics ✔ | 9 | FOCUS Step 1 calculations ✔ | 8 | FOCUS Steps 12 input files -✔ | 7 | Read and analyse TOXSWA cwa files [4.4s] +✔ | 7 | Read and analyse TOXSWA cwa files [4.6s] ✔ | 18 | UK drainage PEC calculations ══ Results ═════════════════════════════════════════════════════════════════════════════════════════ -Duration: 6.3 s +Duration: 6.5 s [ FAIL 0 | WARN 0 | SKIP 0 | PASS 86 ] @@ -73,8 +73,8 @@ A list with the DT50 and Koc used as well as the resulting score of class GUS_result } \description{ -The groundwater ubiquity score GUS is calculated according to -the following equation +The groundwater ubiquity score GUS is calculated according to the +equation \deqn{GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})}{GUS = log10 DT50soil * (4 - log10 Koc)} } \references{ diff --git a/man/PEC_sw_drift.Rd b/man/PEC_sw_drift.Rd index 89919bb..6774ba7 100644 --- a/man/PEC_sw_drift.Rd +++ b/man/PEC_sw_drift.Rd @@ -90,6 +90,10 @@ PEC_sw_drift(100, drift_data = "RF") # This makes it possible to also use different distances PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = "RF") +# We can also specify distance units explicitly +library(units) +PEC_sw_drift(100, distances = set_units(c(1, 3, 5, 6, 10, 20, 50, 100), "m"), drift_data = "RF") + # or consider aerial application PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = "RF", crop_group_RF = "aerial") |
