diff options
| -rw-r--r-- | DESCRIPTION | 2 | ||||
| -rw-r--r-- | NEWS.md | 2 | ||||
| -rw-r--r-- | R/PEC_sw_drift.R | 25 | ||||
| -rw-r--r-- | log/check.log | 34 | ||||
| -rw-r--r-- | log/test.log | 6 | ||||
| -rw-r--r-- | man/PEC_sw_drift.Rd | 4 |
6 files changed, 44 insertions, 29 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). 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/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 ] 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") |