# pfm
[](https://pkgdown.jrwb.de/pfm/)
[](https://jranke.r-universe.dev/ui/#package:pfm)
[](https://app.travis-ci.com/jranke/pfm)
[](https://codecov.io/github/jranke/pfm)
The R package **pfm** provides some utilities for fate modelling,
including simple routines for calculating predicted environmental
concentrations (PEC) and some routines for dealing with FOCUS pesticide
fate modelling tools made available under the GNU public license.
More specifically, **pfm** includes facilities for simple one-box
modelling of the
[saw-tooth](https://pkgdown.jrwb.de/pfm/reference/sawtooth.html)-like
curves resulting from multiple repeated applications, for calculation of
[PEC soil](https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html) based on
the 1997 SANCO guidance and the first tiers of the EFSA PEC soil
guidance from 2012 and 2015, as well as some functions for calculating
[PEC surface
water](https://pkgdown.jrwb.de/pfm/reference/sawtooth.html). The [PEC
drift](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html)
calculations can be based on the Rautmann drift percentiles published by
JKI, the exponential formulas published by Rautmann to inter- or
extrapolate to arbitrary distances, or on the integrated Rautmann
formulas (integrated over the width of the surface water body) used in
FOCUS drift calculations.
For PEC drainage calculations, the methods used by the [UK at tier
1](https://pkgdown.jrwb.de/pfm/reference/PEC_drainage_UK.html) and by
[Germany](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html)
are implemented. For runoff, the
[German](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html)
method used at tier 1 is available.
The output of FOCUS TOXSWA calculations can be read in, plotted, and
evaluated using the [TOXSWA
cwa](https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html) class giving
maximum time weighted average concentrations and peak statistics way as
available when using the
[EPAT](https://www.rifcon.com/en/downloads/software-2/) tool.
## Installation
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"))
```
The packages at R-universe are provided with a slight delay.
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")
```
## Use
Please refer to the
[reference](http://pkgdown.jrwb.de/pfm/reference/index.md).
## Examples
One nice example of the usage of this package is the visualisation of a
time weighted average for a sawtooth curve obtained from several
overlays of mkinfit predictions as shown
[here](http://pkgdown.jrwb.de/pfm/reference/plot.one_box.md).
## Applications
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, 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
## General utility functions
Functions that are independent of specific fate modelling areas
- [`geomean()`](https://pkgdown.jrwb.de/pfm/reference/geomean.md) :
Calculate the geometric mean
- [`one_box()`](https://pkgdown.jrwb.de/pfm/reference/one_box.md) :
Create a time series of decline data
- [`plot(`*`<one_box>`*`)`](https://pkgdown.jrwb.de/pfm/reference/plot.one_box.md)
: Plot time series of decline data
- [`sawtooth()`](https://pkgdown.jrwb.de/pfm/reference/sawtooth.md) :
Create decline time series for multiple applications
- [`twa()`](https://pkgdown.jrwb.de/pfm/reference/twa.md) : Calculate a
time weighted average concentration
- [`max_twa()`](https://pkgdown.jrwb.de/pfm/reference/max_twa.md) : The
maximum time weighted average concentration for a moving window
- [`pfm_degradation()`](https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.md)
: Calculate a time course of relative concentrations based on an
mkinmod model
- [`SFO_actual_twa()`](https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.md)
: Actual and maximum moving window time average concentrations for SFO
kinetics
- [`FOMC_actual_twa()`](https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.md)
: Actual and maximum moving window time average concentrations for
FOMC kinetics
- [`reexports`](https://pkgdown.jrwb.de/pfm/reference/reexports.md)
[`set_nd_nq`](https://pkgdown.jrwb.de/pfm/reference/reexports.md)
[`set_nd_nq_focus`](https://pkgdown.jrwb.de/pfm/reference/reexports.md)
: Objects exported from other packages
- [`TSCF()`](https://pkgdown.jrwb.de/pfm/reference/TSCF.md) : Estimation
of the transpiration stream concentration factor
## Predicted environmental concentrations in soil
- [`PEC_soil()`](https://pkgdown.jrwb.de/pfm/reference/PEC_soil.md) :
Calculate predicted environmental concentrations in soil
- [`PEC_soil_mets()`](https://pkgdown.jrwb.de/pfm/reference/PEC_soil_mets.md)
: Calculate initial and accumulation PEC soil for a set of metabolites
- [`soil_scenario_data_EFSA_2015`](https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.md)
: Properties of the predefined scenarios from the EFSA guidance from
2015
- [`soil_scenario_data_EFSA_2017`](https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.md)
: Properties of the predefined scenarios from the EFSA guidance from
2017
- [`PEC_FOMC_accu_rel()`](https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.md)
: Get the relative accumulation of an FOMC model over multiples of an
interval
- [`EFSA_washoff_2017`](https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.md)
: Subset of EFSA crop washoff default values
## Predicted environmental concentrations in groundwater
- [`FOCUS_GW_scenarios_2012`](https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.md)
: A very small subset of the FOCUS Groundwater scenario definitions
- [`EFSA_GW_interception_2014`](https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.md)
: Subset of EFSA crop interception default values for groundwater
modelling
## Predicted environmental concentrations in surface water
- [`PEC_sw_drift()`](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.md)
: Calculate predicted environmental concentrations in surface water
due to drift
- [`drift_data_JKI`](https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.md)
: Deposition from spray drift expressed as percent of the applied dose
as published by the JKI
- [`drift_parameters_focus`](https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.md)
: Regression parameters for the Rautmann drift data
- [`drift_percentages_rautmann()`](https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.md)
: Calculate drift percentages based on Rautmann data
- [`PEC_sw_drainage_UK()`](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.md)
[`drainage_date_UK()`](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.md)
: Calculate initial predicted environmental concentrations in surface
water due to drainage using the UK method
- [`PEC_sw_sed()`](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.md)
: Calculate predicted environmental concentrations in sediment from
surface water concentrations
- [`PEC_sw_focus()`](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.md)
: Calculate PEC surface water at FOCUS Step 1
- [`chent_focus_sw()`](https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.md)
: Create a chemical compound object for FOCUS Step 1 calculations
- [`FOCUS_Step_12_scenarios`](https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.md)
: Step 1/2 scenario data as distributed with the FOCUS Step 1/2
calculator
- [`PEC_sw_exposit_drainage()`](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.md)
: Calculate PEC surface water due to drainage as in Exposit 3
- [`PEC_sw_exposit_runoff()`](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.md)
: Calculate PEC surface water due to runoff and erosion as in Exposit
3
- [`perc_runoff_exposit`](https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.md)
: Runoff loss percentages as used in Exposit 3
- [`perc_runoff_reduction_exposit`](https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.md)
: Runoff reduction percentages as used in Exposit
- [`TOXSWA_cwa`](https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.md) :
R6 class for holding TOXSWA water concentration data and associated
statistics
- [`read.TOXSWA_cwa()`](https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.md)
: Read TOXSWA surface water concentrations
- [`plot(`*`<TOXSWA_cwa>`*`)`](https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.md)
: Plot TOXSWA surface water concentrations
## Classifications and indicators
Evaluating environmental fate properties
- [`SSLRC_mobility_classification()`](https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.md)
: Determine the SSLRC mobility classification for a chemical substance
from its Koc
- [`GUS()`](https://pkgdown.jrwb.de/pfm/reference/GUS.md)
[`print(`*`<GUS_result>`*`)`](https://pkgdown.jrwb.de/pfm/reference/GUS.md)
: Groundwater ubiquity score based on Gustafson (1989)
## Work with chent objects containing relevant information
- [`endpoint()`](https://pkgdown.jrwb.de/pfm/reference/endpoint.md)
[`soil_DT50()`](https://pkgdown.jrwb.de/pfm/reference/endpoint.md)
[`soil_Kfoc()`](https://pkgdown.jrwb.de/pfm/reference/endpoint.md)
[`soil_N()`](https://pkgdown.jrwb.de/pfm/reference/endpoint.md)
[`soil_sorption()`](https://pkgdown.jrwb.de/pfm/reference/endpoint.md)
: Retrieve endpoint information from the chyaml field of a chent
object
## Utilities
- [`get_vertex()`](https://pkgdown.jrwb.de/pfm/reference/get_vertex.md)
: Fit a parabola through three points
