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| author | Ranke Johannes <johannes.ranke@agroscope.admin.ch> | 2026-06-22 18:01:11 +0200 |
|---|---|---|
| committer | Ranke Johannes <johannes.ranke@agroscope.admin.ch> | 2026-06-22 18:01:11 +0200 |
| commit | e0c130005ee7adbac9b832ea8157712419d51b7e (patch) | |
| tree | f5c188285ee3abd9edda16a6bb96b6142c80afba /docs | |
| parent | f8fdbc3237d12d5511058d2c0c40f3e99debe682 (diff) | |
Update static docs
Diffstat (limited to 'docs')
108 files changed, 4206 insertions, 210 deletions
diff --git a/docs/404.html b/docs/404.html index 074a3db..712b3c2 100644 --- a/docs/404.html +++ b/docs/404.html @@ -61,7 +61,7 @@ Content not found. Please use links in the navbar. </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer> diff --git a/docs/404.md b/docs/404.md new file mode 100644 index 0000000..5107f89 --- /dev/null +++ b/docs/404.md @@ -0,0 +1,3 @@ +Content not found. Please use links in the navbar. + +# Page not found (404) diff --git a/docs/authors.html b/docs/authors.html index 37a01ae..6c14ec6 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -70,7 +70,7 @@ R package version 0.6.5, <a href="https://pkgdown.jrwb.de/pfm">https://pkgdown.j </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/authors.md b/docs/authors.md new file mode 100644 index 0000000..100dbbc --- /dev/null +++ b/docs/authors.md @@ -0,0 +1,24 @@ +# Authors and Citation + +## Authors + +- **Johannes Ranke**. Author, maintainer. + [](https://orcid.org/0000-0003-4371-6538) + +- **Elisabeth Lutz**. Contributor. + +## Citation + +Source: +[`DESCRIPTION`](https://github.com/jranke/pfm/blob/HEAD/DESCRIPTION) + +Johannes Ranke (2026). *pfm: Utilities for Pesticide Fate Modelling*. R +package version 0.6.5, <https://pkgdown.jrwb.de/pfm>. + + @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}, + } diff --git a/docs/index.html b/docs/index.html index 26803d7..160afaa 100644 --- a/docs/index.html +++ b/docs/index.html @@ -140,7 +140,7 @@ Korkaric M, Hanke I, Grossar D, Neuweiler R, Christ B, Wirth J, Hochstrasser M, </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer> diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..62199a9 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,88 @@ +# 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) | diff --git a/docs/llms.txt b/docs/llms.txt new file mode 100644 index 0000000..fed8f27 --- /dev/null +++ b/docs/llms.txt @@ -0,0 +1,218 @@ +# 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 + diff --git a/docs/news/index.html b/docs/news/index.html index c86b3be..6b1dec0 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -57,7 +57,7 @@ </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/news/index.md b/docs/news/index.md new file mode 100644 index 0000000..1b86e03 --- /dev/null +++ b/docs/news/index.md @@ -0,0 +1,37 @@ +# Changelog + +## version 0.6.5 + +- 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](https://github.com/jranke/pfm/issues/2) + reported by Julian Klein ([@juklei](https://github.com/juklei)). + +## version 0.6.4 + +- R/PEC_sw_drainage_uk.R: Fix a bug preventing the function to work of + `latest_application` is set to 29 February. Also, make this function + correctly deal with units. + +- R/twa.R: Fix a bug in plotting one-box models of class `one_box` that + affected plots that displayed a time weighted average. + +- R/PEC_sw_drainage_uk.R: Fix a bug leading to increased PEC values in + the case the application date is after the beginning of the drainage + period and `soil_DT50` was specified. + +## version 0.6.3 + +- R/{PEC_sw_drift,PEC_sw_exposit_runoff,PEC_sw_sed}.R: Make use of the + `units` package. + +- R/PEC_sw_drift.R: Change argument name from ‘crop_group_focus’ to + ‘crop_group_RF’, in order to make it easier to understand the relation + to the ‘drift_data’ argument. diff --git a/docs/reference/EFSA_GW_interception_2014.html b/docs/reference/EFSA_GW_interception_2014.html index 97d9e3a..411533f 100644 --- a/docs/reference/EFSA_GW_interception_2014.html +++ b/docs/reference/EFSA_GW_interception_2014.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -78,7 +78,7 @@ products of these active substances in soil. <em>EFSA Journal</em> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/EFSA_GW_interception_2014.md b/docs/reference/EFSA_GW_interception_2014.md new file mode 100644 index 0000000..cca84b2 --- /dev/null +++ b/docs/reference/EFSA_GW_interception_2014.md @@ -0,0 +1,38 @@ +# Subset of EFSA crop interception default values for groundwater modelling + +Subset of EFSA crop interception default values for groundwater +modelling + +## Usage + +``` r +EFSA_GW_interception_2014 +``` + +## Format + +A matrix containing interception values, currently only for some +selected crops + +## Source + +European Food Safety Authority (2014) EFSA Guidance Document for +evaluating laboratory and field dissipation studies to obtain DegT50 +values of active substances of plant protection products and +transformation products of these active substances in soil. *EFSA +Journal* **12**(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662 + +## Examples + +``` r +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 +``` diff --git a/docs/reference/EFSA_washoff_2017.html b/docs/reference/EFSA_washoff_2017.html index 04ddd3f..bf8f767 100644 --- a/docs/reference/EFSA_washoff_2017.html +++ b/docs/reference/EFSA_washoff_2017.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -78,7 +78,7 @@ doi:10.2903/j.efsa.2017.4982</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/EFSA_washoff_2017.md b/docs/reference/EFSA_washoff_2017.md new file mode 100644 index 0000000..4dd90c5 --- /dev/null +++ b/docs/reference/EFSA_washoff_2017.md @@ -0,0 +1,37 @@ +# Subset of EFSA crop washoff default values + +Subset of EFSA crop washoff default values + +## Usage + +``` r +EFSA_washoff_2017 +``` + +## Format + +A matrix containing wash-off factors, currently only for some selected +crops + +## Source + +European Food Safety Authority (2017) EFSA guidance document for +predicting environmental concentrations of active substances of plant +protection products and transformation products of these active +substances in soil. *EFSA Journal* **15**(10) 4982 +doi:10.2903/j.efsa.2017.4982 + +## Examples + +``` r +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 +``` diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html index 8885e11..86bbc9b 100644 --- a/docs/reference/FOCUS_GW_scenarios_2012.html +++ b/docs/reference/FOCUS_GW_scenarios_2012.html @@ -9,7 +9,7 @@ soil definitions are from page 46ff. from FOCUS (2012)."></head><body> <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -46,10 +46,6 @@ soil definitions are from page 46ff. from FOCUS (2012).</p> </div> <div class="section level2"> - <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> - <p>An object of class <code>list</code> of length 2.</p> - </div> - <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. FOrum for the Co-ordination of pesticde fate models and their USe. @@ -130,7 +126,7 @@ http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/FOCUS_GW_scenarios_2012.md b/docs/reference/FOCUS_GW_scenarios_2012.md new file mode 100644 index 0000000..43d05e8 --- /dev/null +++ b/docs/reference/FOCUS_GW_scenarios_2012.md @@ -0,0 +1,84 @@ +# A very small subset of the FOCUS Groundwater scenario definitions + +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). + +## Usage + +``` r +FOCUS_GW_scenarios_2012 +``` + +## References + +FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. +Version 2.1. FOrum for the Co-ordination of pesticde fate models and +their USe. +http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf + +## Examples + +``` r +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 +#> +``` diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html index 434a6aa..1da0901 100644 --- a/docs/reference/FOCUS_Step_12_scenarios.html +++ b/docs/reference/FOCUS_Step_12_scenarios.html @@ -9,7 +9,7 @@ The text file is not included in the package as its licence is not clear."></hea <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -61,27 +61,27 @@ calculations in a matrix called 'rd'.</p> <span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="va">sce</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/utils/read.table.html" class="external-link">read.table</a></span><span class="op">(</span>text <span class="op">=</span> <span class="va">scenarios</span>, sep <span class="op">=</span> <span class="st">"\t"</span>, header <span class="op">=</span> <span class="cn">TRUE</span>, check.names <span class="op">=</span> <span class="cn">FALSE</span>,</span></span> <span class="r-in"><span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'scenarios' not found</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> object 'scenarios' not found</span> <span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">names</span> <span class="op">=</span> <span class="va">sce</span><span class="op">$</span><span class="va">Crop</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> object 'sce' not found</span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">sce</span><span class="op">)</span> <span class="op"><-</span> <span class="va">sce</span><span class="op">$</span><span class="va">Crop</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> object 'sce' not found</span> <span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">drift</span> <span class="op">=</span> <span class="va">sce</span><span class="op">[</span>, <span class="fl">3</span><span class="op">:</span><span class="fl">11</span><span class="op">]</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> object 'sce' not found</span> <span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">interception</span> <span class="op">=</span> <span class="va">sce</span><span class="op">[</span>, <span class="fl">12</span><span class="op">:</span><span class="fl">15</span><span class="op">]</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce' not found</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> object 'sce' not found</span> <span class="r-in"><span> <span class="va">sce_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readLines.html" class="external-link">readLines</a></span><span class="op">(</span><span class="va">scenario_path</span><span class="op">)</span><span class="op">[</span><span class="fl">41</span><span class="op">:</span><span class="fl">46</span><span class="op">]</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>cannot open file 'inst/extdata/FOCUS_Step_12_scenarios.txt': No such file or directory</span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in file(con, "r"):</span> cannot open the connection</span> <span class="r-in"><span> <span class="va">rd</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/utils/read.table.html" class="external-link">read.table</a></span><span class="op">(</span>text <span class="op">=</span> <span class="va">sce_2</span>, sep <span class="op">=</span> <span class="st">"\t"</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">]</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'sce_2' not found</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> object 'sce_2' not found</span> <span class="r-in"><span> <span class="va">rd_mat</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="va">rd</span><span class="op">$</span><span class="va">V2</span>, nrow <span class="op">=</span> <span class="fl">3</span>, byrow <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'rd' not found</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> object 'rd' not found</span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/dimnames.html" class="external-link">dimnames</a></span><span class="op">(</span><span class="va">rd_mat</span><span class="op">)</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>Time <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"Oct-Feb"</span>, <span class="st">"Mar-May"</span>, <span class="st">"Jun-Sep"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> Region <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"North"</span>, <span class="st">"South"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> object 'rd_mat' not found</span> <span class="r-in"><span> <span class="va">FOCUS_Step_12_scenarios</span><span class="op">$</span><span class="va">rd</span> <span class="op">=</span> <span class="va">rd_mat</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'rd_mat' not found</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> object 'rd_mat' not found</span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/save.html" class="external-link">save</a></span><span class="op">(</span><span class="va">FOCUS_Step_12_scenarios</span>, file <span class="op">=</span> <span class="st">"data/FOCUS_Step_12_scenarios.RData"</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>cannot open compressed file 'data/FOCUS_Step_12_scenarios.RData', probable reason 'No such file or directory'</span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in gzfile(file, "wb"):</span> cannot open the connection</span> @@ -101,7 +101,7 @@ calculations in a matrix called 'rd'.</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/FOCUS_Step_12_scenarios.md b/docs/reference/FOCUS_Step_12_scenarios.md new file mode 100644 index 0000000..3bf1ae2 --- /dev/null +++ b/docs/reference/FOCUS_Step_12_scenarios.md @@ -0,0 +1,56 @@ +# Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator + +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. + +## Format + +A list containing the scenario names in a character vector called +'names', the drift percentiles in a matrix called 'drift', interception +percentages in a matrix called 'interception' and the runoff/drainage +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" + 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() +``` diff --git a/docs/reference/FOMC_actual_twa.html b/docs/reference/FOMC_actual_twa.html index 54b45ed..98eac90 100644 --- a/docs/reference/FOMC_actual_twa.html +++ b/docs/reference/FOMC_actual_twa.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -99,7 +99,7 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/FOMC_actual_twa.md b/docs/reference/FOMC_actual_twa.md new file mode 100644 index 0000000..e49c1bb --- /dev/null +++ b/docs/reference/FOMC_actual_twa.md @@ -0,0 +1,57 @@ +# Actual and maximum moving window time average concentrations for FOMC kinetics + +Actual and maximum moving window time average concentrations for FOMC +kinetics + +## Usage + +``` r +FOMC_actual_twa( + alpha = 1.0001, + beta = 10, + times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100) +) +``` + +## Source + +FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation +Kinetics from Environmental Fate Studies on Pesticides in EU +Registration, Version 1.1, 18 December 2014, p. 251 + +## Arguments + +- alpha: + + Parameter of the FOMC model + +- beta: + + Parameter of the FOMC model + +- times: + + The output times, and window sizes for time weighted average + concentrations + +## Author + +Johannes Ranke + +## Examples + +``` r +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 +``` diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html index 06d6c48..b5a65e9 100644 --- a/docs/reference/GUS.html +++ b/docs/reference/GUS.html @@ -11,7 +11,7 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$"></head><body> <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -162,7 +162,7 @@ toxicology and chemistry</em> <b>8</b>(4) 339–57.</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/GUS.md b/docs/reference/GUS.md new file mode 100644 index 0000000..b81f464 --- /dev/null +++ b/docs/reference/GUS.md @@ -0,0 +1,113 @@ +# 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})\$\$ + +## Usage + +``` r +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) +``` + +## Arguments + +- ...: + + Included in the generic to allow for further arguments later. + Therefore this also had to be added to the specific methods. + +- DT50: + + Half-life of the chemical in soil. Should be a field half-life + according to Gustafson (1989). However, leaching to the sub-soil can + not completely be excluded in field dissipation experiments and + Gustafson did not refer to any normalisation procedure, but says the + field study should be conducted under use conditions. + +- Koc: + + The sorption constant normalised to organic carbon. Gustafson does not + mention the nonlinearity of the sorption constant commonly found and + usually described by Freundlich sorption, therefore it is unclear at + which reference concentration the Koc should be observed (and if the + reference concentration would be in soil or in porewater). + +- chent: + + If a chent is given with appropriate information present in its chyaml + field, this information is used, with defaults specified below. + +- degradation_value: + + Which of the available degradation values should be used? + +- lab_field: + + Should laboratory or field half-lives be used? This defaults to lab in + this implementation, in order to avoid double-accounting for mobility. + If comparability with the original GUS values given by + Gustafson (1989) is desired, non-normalised first-order field + half-lives obtained under actual use conditions should be used. + +- redox: + + Aerobic or anaerobic degradation data + +- sorption_value: + + Which of the available sorption values should be used? Defaults to + Kfoc as this is what is generally available from the European + pesticide peer review process. These values generally use a reference + concentration of 1 mg/L in porewater, that means they would be + expected to be Koc values at a concentration of 1 mg/L in the water + phase. + +- degradation_aggregator: + + Function for aggregating half-lives + +- sorption_aggregator: + + Function for aggregation Koc values + +- x: + + An object of class GUS_result to be printed + +- digits: + + The number of digits used in the print method + +## Value + +A list with the DT50 and Koc used as well as the resulting score of +class GUS_result + +## References + +Gustafson, David I. (1989) Groundwater ubiquity score: a simple method +for assessing pesticide leachability. *Environmental toxicology and +chemistry* **8**(4) 339–57. + +## Author + +Johannes Ranke diff --git a/docs/reference/PEC_FOMC_accu_rel.html b/docs/reference/PEC_FOMC_accu_rel.html index 47993c7..c9c7b6a 100644 --- a/docs/reference/PEC_FOMC_accu_rel.html +++ b/docs/reference/PEC_FOMC_accu_rel.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -72,7 +72,7 @@ </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/PEC_FOMC_accu_rel.md b/docs/reference/PEC_FOMC_accu_rel.md new file mode 100644 index 0000000..7ae2982 --- /dev/null +++ b/docs/reference/PEC_FOMC_accu_rel.md @@ -0,0 +1,29 @@ +# Get the relative accumulation of an FOMC model over multiples of an interval + +Get the relative accumulation of an FOMC model over multiples of an +interval + +## Usage + +``` r +PEC_FOMC_accu_rel(n, interval, FOMC) +``` + +## Arguments + +- n: + + number of applications + +- interval: + + Time between applications + +- FOMC: + + Named numeric vector containing the FOMC parameters alpha and beta + +## Value + +A numeric vector containing all n accumulation factors for the n +applications diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index e405bdf..b148280 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -15,7 +15,7 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)."></head><b <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -213,7 +213,7 @@ guidance (2017, p. 14/15) can easily be calculated.</p> <div class="section level2"> <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2> <p>While time weighted average (TWA) concentrations given in the examples -from the EFSA guidance from 2015 (p. 80) are be reproduced, this is not +from the EFSA guidance from 2015 (p. 80) can be reproduced, this is not true for the TWA concentrations given for the same example in the EFSA guidance from 2017 (p. 92).</p> <p>According to the EFSA guidance (EFSA, 2017, p. 43), leaching should be @@ -306,7 +306,7 @@ doi:10.2903/j.efsa.2015.4093</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/PEC_soil.md b/docs/reference/PEC_soil.md new file mode 100644 index 0000000..d7666dc --- /dev/null +++ b/docs/reference/PEC_soil.md @@ -0,0 +1,261 @@ +# Calculate predicted environmental concentrations in soil + +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 and +in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017). + +## Usage + +``` r +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 +) +``` + +## Arguments + +- rate: + + Application rate in units specified below + +- rate_units: + + Defaults to g/ha + +- interception: + + The fraction of the application rate that does not reach the soil + +- mixing_depth: + + Mixing depth in cm + +- PEC_units: + + Requested units for the calculated PEC. Only mg/kg currently supported + +- PEC_pw_units: + + Only mg/L currently supported + +- interval: + + Period of the deeper mixing. The default is NA, i.e. no deeper mixing. + For annual deeper mixing, set this to 365 when degradation units are + in days + +- n_periods: + + Number of periods to be considered for long term PEC calculations + +- tillage_depth: + + Periodic (see interval) deeper mixing in cm + +- leaching_depth: + + EFSA (2017) uses the mixing depth (ecotoxicological evaluation depth) + to calculate leaching for annual crops where tillage takes place. By + default, losses from the layer down to the tillage depth are taken + into account in this implementation. + +- crop: + + Ignored for scenarios other than EFSA_2017. Only annual crops are + supported when these scenarios are used. Only crops with a single + cropping cycle per year are currently supported. + +- cultivation: + + Does mechanical cultivation in the sense of EFSA (2017) take place, + i.e. twice a year to a depth of 5 cm? Ignored for scenarios other than + EFSA_2017 + +- chent: + + An optional chent object holding substance specific information. Can + also be a name for the substance as a character string + +- DT50: + + If specified, overrides soil DT50 endpoints from a chent object If + DT50 is not specified here and not available from the chent object, + zero degradation is assumed + +- FOMC: + + If specified, it should be a named numeric vector containing the FOMC + parameters alpha and beta. This overrides any other degradation + endpoints, and the degradation during the interval and after the + maximum PEC is calculated using these parameters without temperature + correction + +- Koc: + + If specified, overrides Koc endpoints from a chent object + +- Kom: + + Calculated from Koc by default, but can explicitly be specified as Kom + here + +- t_avg: + + Averaging times for time weighted average concentrations + +- t_act: + + Time series for actual concentrations + +- scenarios: + + If this is 'default', a soil bulk density of 1.5 kg/L will be used. + The DT50 will be used without correction and soil properties as + specified in the REACH guidance (R.16, Table R.16-9) are used for + porewater PEC calculations. If this is "EFSA_2015", the DT50 is taken + to be a modelling half-life at 20°C and pF2 (for when 'chent' is + specified, the DegT50 with destination 'PECgw' will be used), and + corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also + model and scenario adjustment factors from the EFSA guidance are used. + +- leaching: + + Should leaching be taken into account? The default is FALSE, except + when the EFSA_2017 scenarios are used. + +- porewater: + + Should equilibrium porewater concentrations be estimated based on Kom + and the organic carbon fraction of the soil instead of total soil + concentrations? Based on equation (7) given in the PPR panel opinion + (EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance + (2015, p. 13). + +## Value + +The predicted concentration in soil + +## Details + +This assumes that the complete load to soil during the time specified by +'interval' (typically 365 days) is dosed at once. As in the PPR panel +opinion cited below (EFSA PPR panel 2012), only temperature correction +using the Arrhenius equation is performed. + +Total soil and porewater PEC values for the scenarios as defined in the +EFSA guidance (2017, p. 14/15) can easily be calculated. + +## Note + +While time weighted average (TWA) concentrations given in the examples +from the EFSA guidance from 2015 (p. 80) can be reproduced, this is not +true for the TWA concentrations given for the same example in the EFSA +guidance from 2017 (p. 92). + +According to the EFSA guidance (EFSA, 2017, p. 43), leaching should be +taken into account for the EFSA 2017 scenarios, using the evaluation +depth (here mixing depth) as the depth of the layer from which leaching +takes place. However, as the amount leaching below the evaluation depth +(often 5 cm) will partly be mixed back during tillage, the default in +this function is to use the tillage depth for the calculation of the +leaching rate. + +If temperature information is available in the selected scenarios, as +e.g. in the EFSA scenarios, the DT50 for groundwater modelling +(destination 'PECgw') is taken from the chent object, otherwise the DT50 +with destination 'PECsoil'. + +## References + +EFSA Panel on Plant Protection Products and their Residues (2012) +Scientific Opinion on the science behind the guidance for scenario +selection and scenario parameterisation for predicting environmental +concentrations of plant protection products in soil. *EFSA Journal* +**10**(2) 2562, doi:10.2903/j.efsa.2012.2562 + +EFSA (European Food Safety Authority) 2017) EFSA guidance document for +predicting environmental concentrations of active substances of plant +protection products and transformation products of these active +substances in soil. *EFSA Journal* **15**(10) 4982 +doi:10.2903/j.efsa.2017.4982 + +EFSA (European Food Safety Authority) (2015) EFSA guidance document for +predicting environmental concentrations of active substances of plant +protection products and transformation products of these active +substances in soil. *EFSA Journal* **13**(4) 4093 +doi:10.2903/j.efsa.2015.4093 + +## Author + +Johannes Ranke + +## Examples + +``` r +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) +``` diff --git a/docs/reference/PEC_soil_mets.html b/docs/reference/PEC_soil_mets.html index f078454..d615c46 100644 --- a/docs/reference/PEC_soil_mets.html +++ b/docs/reference/PEC_soil_mets.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -78,7 +78,7 @@ maximum occurrence in soil and their soil DT50</p></dd> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/PEC_soil_mets.md b/docs/reference/PEC_soil_mets.md new file mode 100644 index 0000000..5811b9e --- /dev/null +++ b/docs/reference/PEC_soil_mets.md @@ -0,0 +1,33 @@ +# Calculate initial and accumulation PEC soil for a set of metabolites + +Calculate initial and accumulation PEC soil for a set of metabolites + +## Usage + +``` r +PEC_soil_mets(rate, mw_parent, mets, interval = 365, ...) +``` + +## Arguments + +- rate: + + Application rate in units specified below + +- mw_parent: + + The molecular weight of the parent compound + +- mets: + + A dataframe with metabolite identifiers as rownames and columns "mw", + "occ" and "DT50" holding their molecular weight, maximum occurrence in + soil and their soil DT50 + +- interval: + + The interval for accumulation calculations + +- ...: + + Further arguments are passed to PEC_soil diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html index c8667c4..8dbfc78 100644 --- a/docs/reference/PEC_sw_drainage_UK.html +++ b/docs/reference/PEC_sw_drainage_UK.html @@ -144,7 +144,7 @@ accessed 2026-02-13</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/PEC_sw_drainage_UK.md b/docs/reference/PEC_sw_drainage_UK.md new file mode 100644 index 0000000..c241a69 --- /dev/null +++ b/docs/reference/PEC_sw_drainage_UK.md @@ -0,0 +1,98 @@ +# Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method + +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`. + +## Usage + +``` r +PEC_sw_drainage_UK( + rate, + interception = 0, + Koc, + latest_application = NULL, + soil_DT50 = NULL, + model = NULL, + model_parms = NULL +) + +drainage_date_UK(application_date) +``` + +## Arguments + +- rate: + + Application rate in g/ha or with a compatible unit specified with the + units package + +- interception: + + The fraction of the application rate that does not reach the soil + +- Koc: + + The sorption coefficient normalised to organic carbon in L/kg or a + unit specified with the units package + +- latest_application: + + Latest application date, formatted as e.g. "01 July" + +- soil_DT50: + + Soil degradation half-life, if SFO kinetics are to be used, in days or + a time unit specified with the units package + +- model: + + The soil degradation model to be used. Either one of "FOMC", "DFOP", + "HS", or "IORE", or an mkinmod object + +- model_parms: + + A named numeric vector containing the model parameters + +- application_date: + + Application date + +## Value + +The predicted concentration in surface water in µg/L + +## References + +HSE's Chemicals Regulation Division (CRD) Active substance PECsw +calculations (for 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 and tier 1 drainflow calculator Version 2.1.1 +(2025) Spreadsheet published at +<https://www.hse.gov.uk/pesticides/assets/docs/PEC%20sw-sed%20(spraydrift).xlsx)> +accessed 2026-02-13 + +## Author + +Johannes Ranke + +## Examples + +``` r +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" +``` diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html index 033e805..ee2f973 100644 --- a/docs/reference/PEC_sw_drift.html +++ b/docs/reference/PEC_sw_drift.html @@ -265,7 +265,7 @@ applications, water depth, crop groups and distances</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/PEC_sw_drift.md b/docs/reference/PEC_sw_drift.md new file mode 100644 index 0000000..c16a02a --- /dev/null +++ b/docs/reference/PEC_sw_drift.md @@ -0,0 +1,227 @@ +# Calculate predicted environmental concentrations in surface water due to drift + +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. + +## Usage + +``` r +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" +) +``` + +## Arguments + +- rate: + + Application rate in units specified below, or with units defined via + the `units` package. + +- applications: + + Number of applications for selection of drift percentile + +- water_depth: + + Depth of the water body in cm + +- drift_percentages: + + Percentage drift values for which to calculate PECsw. Overrides + 'drift_data', 'distances', 'applications', crop group and formula + arguments if not NULL. + +- drift_data: + + Source of drift percentage data. If 'JKI', the + [drift_data_JKI](https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.md) + included in the package is used. If 'RF', the Rautmann drift data are + calculated either in the original form or integrated over the width of + the water body, depending on the 'formula' argument. + +- crop_group_JKI: + + When using the 'JKI' drift data, one of the German names as used in + [drift_data_JKI](https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.md). + Will only be used if drift_data is 'JKI'. Available crop groups are + "Ackerbau", "Obstbau frueh", "Obstbau spaet", "Weinbau frueh", + "Weinbau spaet", "Hopfenbau", "Flaechenkulturen \> 900 l/ha" and + "Gleisanlagen". + +- crop_group_RF: + + Crop group(s) as used in + [drift_parameters_focus](https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.md), + i.e. "arable", "hops", "vines, late", "vines, early", "fruit, late", + "fruit, early" or "aerial". + +- distances: + + The distances in m for which to get PEC values + +- formula: + + By default, the original Rautmann formula is used. If you specify + "FOCUS", mean drift input over the width of the water body is + calculated as described in Chapter 5.4.5 of the FOCUS surface water + guidance + +- water_width: + + Width of the water body in cm + +- side_angle: + + The angle of the side of the water relative to the bottom which is + assumed to be horizontal, in degrees. The SYNOPS model assumes 45 + degrees here. + +- rate_units: + + Defaults to g/ha. For backwards compatibility, only used if the + specified rate does not have + [units::units](https://r-quantities.github.io/units/reference/units.html)\]. + +- PEC_units: + + Requested units for the calculated PEC. Only µg/L currently supported + +## Value + +A numeric vector with the predicted concentration in surface water. 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. + +## Details + +It is recommened to specify the arguments `rate`, `water_depth` and +`water_width` using +[units::units](https://r-quantities.github.io/units/reference/units.html) +from the `units` package. + +Since pfm version 0.6.5, the function is vectorised with respect to +rates, applications, water depth, crop groups and distances + +## See also + +[drift_parameters_focus](https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.md), +[drift_percentages_rautmann](https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.md) + +## Author + +Johannes Ranke + +## Examples + +``` r +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 +``` diff --git a/docs/reference/PEC_sw_exposit_drainage.html b/docs/reference/PEC_sw_exposit_drainage.html index ebcf7d1..792e774 100644 --- a/docs/reference/PEC_sw_exposit_drainage.html +++ b/docs/reference/PEC_sw_exposit_drainage.html @@ -23,7 +23,7 @@ V_ditch and V_drainage using units::units from the units package.'></head><body> <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -169,7 +169,7 @@ scenarios. If the rate was given in g/ha, the PECsw are in microg/L.</p></dd> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/PEC_sw_exposit_drainage.md b/docs/reference/PEC_sw_exposit_drainage.md new file mode 100644 index 0000000..cc626d9 --- /dev/null +++ b/docs/reference/PEC_sw_exposit_drainage.md @@ -0,0 +1,119 @@ +# Calculate PEC surface water due to drainage as in Exposit 3 + +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 with modest to high mobility (groups 2, +3 and 4). In this implementation, the group is derived only from the +Koc, if not given explicitly. For details, see the discussion of the +function arguments below. It is recommened to specify the arguments +`rate`, `Koc`, `DT50`, `t_drainage`, `V_ditch` and `V_drainage` using +[units::units](https://r-quantities.github.io/units/reference/units.html) +from the `units` package. + +## Usage + +``` r +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 +) +``` + +## Source + +Excel 3.02 spreadsheet available from +<https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html> + +## Arguments + +- rate: + + The application rate in g/ha + +- interception: + + The fraction intercepted by the crop + +- Koc: + + The sorption coefficient to soil organic carbon used to determine the + mobility. A trigger value of 550 L/kg is used in order to decide if + Koc \>\> 500. + +- mobility: + + Overrides what is determined from the Koc. + +- DT50: + + The soil half-life in days + +- t_drainage: + + The time between application and the drainage event, where degradation + occurs, in days + +- V_ditch: + + The volume of the ditch is assumed to be 1 m \* 100 m \* 30 cm = 30 m3 + +- V_drainage: + + The drainage volume, equivalent to 1 mm precipitation on 1 ha for + spring/summer or 10 mm for autumn/winter/early spring. + +- dilution: + + The dilution factor + +## Value + +A list containing the following components + +- perc_drainage_total: + + Gesamtaustrag (total fraction of the residue drained) + +- perc_peak: + + Stoßbelastung (fraction drained at event) + +- PEC_sw_drainage: + + A matrix containing PEC values for the spring and autumn scenarios. If + the rate was given in g/ha, the PECsw are in microg/L. + +## See also + +[`perc_runoff_exposit`](https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.md) +for runoff loss percentages and +[`perc_runoff_reduction_exposit`](https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.md) +for runoff reduction percentages used + +## Examples + +``` r + 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 +#> +``` diff --git a/docs/reference/PEC_sw_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html index 5fbdfd9..8104913 100644 --- a/docs/reference/PEC_sw_exposit_runoff.html +++ b/docs/reference/PEC_sw_exposit_runoff.html @@ -184,7 +184,7 @@ using <a href="https://r-quantities.github.io/units/reference/units.html" class= </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/PEC_sw_exposit_runoff.md b/docs/reference/PEC_sw_exposit_runoff.md new file mode 100644 index 0000000..d5bcda2 --- /dev/null +++ b/docs/reference/PEC_sw_exposit_runoff.md @@ -0,0 +1,150 @@ +# Calculate PEC surface water due to runoff and erosion as in Exposit 3 + +This is a reimplementation of the calculation described in the Exposit +3.02 spreadsheet file, in the worksheet "Konzept Runoff". + +## Usage + +``` r +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 +) +``` + +## Source + +Excel 3.02 spreadsheet available from +<https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html> + +## Arguments + +- rate: + + Application rate in g/ha or with a compatible unit specified with the + units package + +- interception: + + The fraction intercepted by the crop + +- Koc: + + The sorption coefficient to soil organic carbon + +- DT50: + + The soil half-life in days + +- t_runoff: + + The time between application and the runoff event, where degradation + occurs, in days + +- exposit_reduction_version: + + The version of the reduction factors to be used. "3.02" is the current + version used in Germany, "3.01a" is the version with additional + percentages for 3 m and 6 m buffer zones used in Switzerland. "3.01a2" + is a version introduced for consistency with previous calculations + performed for a 3 m buffer zone in Switzerland, with the same + reduction being applied to the dissolved and the bound fraction. + +- V_ditch: + + The volume of the ditch is assumed to be 1 m \* 100 m \* 30 cm = 30 m3 + +- V_event: + + The unreduced runoff volume, equivalent to 10 mm precipitation on 1 ha + +- dilution: + + The dilution factor + +## Value + +A list containing the following components + +- perc_runoff: + + The runoff percentages for dissolved and bound substance + +- runoff: + + A matrix containing dissolved and bound input for the different + distances + +- PEC_sw_runoff: + + A dataframe containing PEC values for dissolved and bound substance + for the different distances. If the rate was given in g/ha, the PECsw + are in microg/L. + +## Details + +It is recommened to specify the arguments `rate`, `Koc`, `DT50`, +`t_runoff`, `V_ditch` and `V_event` using +[units::units](https://r-quantities.github.io/units/reference/units.html) +from the `units` package. + +## See also + +[`perc_runoff_exposit`](https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.md) +for runoff loss percentages and +[`perc_runoff_reduction_exposit`](https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.md) +for runoff reduction percentages used + +## Examples + +``` r + 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] +#> +``` diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html index 9f8fc6c..a315bdc 100644 --- a/docs/reference/PEC_sw_focus.html +++ b/docs/reference/PEC_sw_focus.html @@ -19,7 +19,7 @@ the FOCUS calculator."></head><body> <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -296,7 +296,7 @@ http://esdac.jrc.ec.europa.eu/projects/stepsonetwo</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/PEC_sw_focus.md b/docs/reference/PEC_sw_focus.md new file mode 100644 index 0000000..aa87968 --- /dev/null +++ b/docs/reference/PEC_sw_focus.md @@ -0,0 +1,241 @@ +# Calculate PEC surface water at FOCUS Step 1 + +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 this +implementation. Only Step 1 PECs are calculated. However, input files +can be generated that are suitable as input for the FOCUS calculator. + +## Usage + +``` r +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 +) +``` + +## Arguments + +- parent: + + A list containing substance specific parameters, e.g. conveniently + generated by + [chent_focus_sw](https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.md). + +- rate: + + The application rate in g/ha. Overriden when applications are given + explicitly + +- n: + + The number of applications + +- i: + + The application interval + +- comment: + + A comment for the input file + +- met: + + A list containing metabolite specific parameters. e.g. conveniently + generated by + [chent_focus_sw](https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.md). + If not NULL, the PEC is calculated for this compound, not the parent. + +- f_drift: + + The fraction of the application rate reaching the waterbody via drift. + If NA, this is derived from the scenario name and the number of + applications via the drift data defined by the + [FOCUS_Step_12_scenarios](https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.md) + +- f_rd: + + The fraction of the amount applied reaching the waterbody via + runoff/drainage. At Step 1, it is assumed to be 10%, be it the parent + or a metabolite + +- scenario: + + The name of the scenario. Must be one of the scenario names given in + [FOCUS_Step_12_scenarios](https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.md) + +- region: + + 'n' for Northern Europe or 's' for Southern Europe. If NA, only Step 1 + PECsw are calculated + +- season: + + 'of' for October to February, 'mm' for March to May, and 'js' for June + to September. If NA, only step 1 PECsw are calculated + +- interception: + + One of 'no interception' (default), 'minimal crop cover', 'average + crop cover' or 'full canopy' + +- met_form_water: + + Should the metabolite formation in water be taken into account? This + can be switched off to check the influence and to compare with + previous versions of the Steps 12 calculator + +- txt_file: + + the name, and potentially the full path to the Steps.12 input text + file to which the specification of the run(s) should be written + +- overwrite: + + Should an existing file a the location specified in `txt_file` be + overwritten? Only takes effect if append is FALSE. + +- append: + + Should the input text file be appended, if it exists? + +## Note + +The formulas for input to the waterbody via runoff/drainage of the +parent and subsequent formation of the metabolite in water is not +documented in the model description coming with the calculator. As one +would expect, this appears to be (as we get the same results) calculated +by multiplying the application rate with the molar weight correction and +the formation fraction in water/sediment systems. + +Step 2 is not implemented. + +## References + +FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4). +FOrum for the Co-ordination of pesticde fate models and their USe. +http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf + +Website of the Steps 1 and 2 calculator at the Joint Research Center of +the European Union: http://esdac.jrc.ec.europa.eu/projects/stepsonetwo + +## Examples + +``` r +# 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 +#> +``` diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html index b826c2c..8346564 100644 --- a/docs/reference/PEC_sw_sed.html +++ b/docs/reference/PEC_sw_sed.html @@ -9,7 +9,7 @@ PEC calculator"></head><body> <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -114,7 +114,7 @@ g/cm3)</p></dd> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/PEC_sw_sed.md b/docs/reference/PEC_sw_sed.md new file mode 100644 index 0000000..21d9748 --- /dev/null +++ b/docs/reference/PEC_sw_sed.md @@ -0,0 +1,67 @@ +# Calculate predicted environmental concentrations in sediment from surface water concentrations + +The method 'percentage' is equivalent to what is used in the CRD +spreadsheet PEC calculator + +## Usage + +``` r +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") +) +``` + +## Arguments + +- PEC_sw: + + Numeric vector or matrix of surface water concentrations in µg/L for + which the corresponding sediment concentration is to be estimated + +- percentage: + + The percentage in sediment, used for the percentage method + +- method: + + The method used for the calculation + +- sediment_depth: + + Depth of the sediment layer + +- water_depth: + + Depth of the water body in cm + +- sediment_density: + + The density of the sediment in kg/L (equivalent to g/cm3) + +- PEC_sed_units: + + The units of the estimated sediment PEC value + +## Value + +The predicted concentration in sediment + +## Author + +Johannes Ranke + +## Examples + +``` 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 5b82810..bcfeb05 100644 --- a/docs/reference/SFO_actual_twa.html +++ b/docs/reference/SFO_actual_twa.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -91,7 +91,7 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/SFO_actual_twa.md b/docs/reference/SFO_actual_twa.md new file mode 100644 index 0000000..52eaef5 --- /dev/null +++ b/docs/reference/SFO_actual_twa.md @@ -0,0 +1,49 @@ +# Actual and maximum moving window time average concentrations for SFO kinetics + +Actual and maximum moving window time average concentrations for SFO +kinetics + +## Usage + +``` r +SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100)) +``` + +## Source + +FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation +Kinetics from Environmental Fate Studies on Pesticides in EU +Registration, Version 1.1, 18 December 2014, p. 251 + +## Arguments + +- DT50: + + The half-life. + +- times: + + The output times, and window sizes for time weighted average + concentrations + +## Author + +Johannes Ranke + +## Examples + +``` r +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 +``` diff --git a/docs/reference/SSLRC_mobility_classification.html b/docs/reference/SSLRC_mobility_classification.html index f554693..5dd600c 100644 --- a/docs/reference/SSLRC_mobility_classification.html +++ b/docs/reference/SSLRC_mobility_classification.html @@ -9,7 +9,7 @@ checked against the spreadsheet published on the CRD website"></head><body> <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -100,7 +100,7 @@ accessed 2019-09-27</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/SSLRC_mobility_classification.md b/docs/reference/SSLRC_mobility_classification.md new file mode 100644 index 0000000..4793d6f --- /dev/null +++ b/docs/reference/SSLRC_mobility_classification.md @@ -0,0 +1,56 @@ +# Determine the SSLRC mobility classification for a chemical substance from its Koc + +This implements the method specified in the UK data requirements +handbook and was checked against the spreadsheet published on the CRD +website + +## Usage + +``` r +SSLRC_mobility_classification(Koc) +``` + +## Arguments + +- Koc: + + The sorption coefficient normalised to organic carbon in L/kg + +## Value + +A list containing the classification and the percentage of the compound +transported per 10 mm drain water + +## References + +HSE's Chemicals Regulation Division (CRD) Active substance PECsw +calculations (for 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 at +<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 + +## Author + +Johannes Ranke + +## Examples + +``` r +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 +#> +``` diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index 234c89a..2087177 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -15,7 +15,7 @@ by read.TOXSWA_cwa."></head><body> <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -46,13 +46,13 @@ by read.TOXSWA_cwa."></head><body> and some associated statistics. like maximum moving window average concentrations, and dataframes holding the events exceeding specified thresholds. Usually, an instance of this class will be generated -by <code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></code>.</p> +by <a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a>.</p> </div> <div class="section level2"> <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> - <p>An <code><a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6Class</a></code> generator object.</p> + <p>An <a href="https://r6.r-lib.org/reference/R6Class.html" class="external-link">R6::R6Class</a> generator object.</p> </div> <div class="section level2"> <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></h2> @@ -60,31 +60,31 @@ by <code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></code>.</p> <dd><p>Length one character vector holding the filename.</p></dd> -<dt><code>basedir</code></dt> + <dt><code>basedir</code></dt> <dd><p>Length one character vector holding the directory where the file came from.</p></dd> -<dt><code>zipfile</code></dt> + <dt><code>zipfile</code></dt> <dd><p>If not null, giving the path to the zip file from which the file was read.</p></dd> -<dt><code>segment</code></dt> + <dt><code>segment</code></dt> <dd><p>Length one integer, specifying for which segment the cwa data were read.</p></dd> -<dt><code>substance</code></dt> + <dt><code>substance</code></dt> <dd><p>The TOXSWA name of the substance.</p></dd> -<dt><code>cwas</code></dt> + <dt><code>cwas</code></dt> <dd><p>Dataframe holding the concentrations.</p></dd> -<dt><code>events</code></dt> + <dt><code>events</code></dt> <dd><p>List of dataframes holding the event statistics for each threshold.</p></dd> -<dt><code>windows</code></dt> + <dt><code>windows</code></dt> <dd><p>Matrix of maximum time weighted average concentrations (TWAC_max) and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) for the requested moving window sizes in days.</p></dd> @@ -97,14 +97,13 @@ for the requested moving window sizes in days.</p></dd> <div class="section"> <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3> - -<ul><li><p><a href="#method-TOXSWA_cwa-new"><code>TOXSWA_cwa$new()</code></a></p></li> +<p></p><ul><li><p><a href="#method-TOXSWA_cwa-initialize"><code>TOXSWA_cwa$new()</code></a></p></li> <li><p><a href="#method-TOXSWA_cwa-moving_windows"><code>TOXSWA_cwa$moving_windows()</code></a></p></li> <li><p><a href="#method-TOXSWA_cwa-get_events"><code>TOXSWA_cwa$get_events()</code></a></p></li> <li><p><a href="#method-TOXSWA_cwa-print"><code>TOXSWA_cwa$print()</code></a></p></li> <li><p><a href="#method-TOXSWA_cwa-clone"><code>TOXSWA_cwa$clone()</code></a></p></li> -</ul></div><p></p><hr><a id="method-TOXSWA_cwa-new"></a><div class="section"> -<h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> +</ul></div><p></p><hr><a id="method-TOXSWA_cwa-initialize"></a><div class="section"> +<h3 id="toxswa-cwa-new-"><code>TOXSWA_cwa$new()</code><a class="anchor" aria-label="anchor" href="#toxswa-cwa-new-"></a></h3> <p>Create a TOXSWA_cwa object from a file</p><div class="section"> <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va"><a href="../reference/TOXSWA_cwa.html">TOXSWA_cwa</a></span><span class="op">$</span><span class="fu">new</span><span class="op">(</span></span> @@ -115,51 +114,43 @@ for the requested moving window sizes in days.</p></dd> <span> substance <span class="op">=</span> <span class="st">"parent"</span>,</span> <span> total <span class="op">=</span> <span class="cn">FALSE</span></span> <span><span class="op">)</span></span></code></pre></div><p></p></div> -</div> - -<div class="section"> +</div><p></p><div class="section"> <h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4> <p></p><div class="arguments"><dl><dt><code>filename</code></dt> <dd><p>The filename</p></dd> - -<dt><code>basedir</code></dt> + <dt><code>basedir</code></dt> <dd><p>The directory to look in</p></dd> - -<dt><code>zipfile</code></dt> + <dt><code>zipfile</code></dt> <dd><p>Optional path to a zipfile holding the file</p></dd> - -<dt><code>segment</code></dt> + <dt><code>segment</code></dt> <dd><p>Either "last" or the number of the segment for which to read the data</p></dd> - -<dt><code>substance</code></dt> + <dt><code>substance</code></dt> <dd><p>The TOXSWA substance name (for TOXSWA 4 or higher)</p></dd> - -<dt><code>total</code></dt> + <dt><code>total</code></dt> <dd><p>Should total concentrations be read in? If FALSE, free concentrations are read</p></dd> </dl><p></p></div> </div> -</div><p></p><hr><a id="method-TOXSWA_cwa-moving_windows"></a><div class="section"> -<h3 id="method-moving-windows-">Method <code>moving_windows()</code><a class="anchor" aria-label="anchor" href="#method-moving-windows-"></a></h3> +</div> + +<p></p><hr><a id="method-TOXSWA_cwa-moving_windows"></a><div class="section"> +<h3 id="toxswa-cwa-moving-windows-"><code>TOXSWA_cwa$moving_windows()</code><a class="anchor" aria-label="anchor" href="#toxswa-cwa-moving-windows-"></a></h3> <p>Add to the <code>windows</code> field described above.</p><div class="section"> <h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">moving_windows</span><span class="op">(</span><span class="va">windows</span>, total <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> -</div> - -<div class="section"> +</div><p></p><div class="section"> <h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4> <p></p><div class="arguments"><dl><dt><code>windows</code></dt> <dd><p>Window sizes in days</p></dd> - -<dt><code>total</code></dt> + <dt><code>total</code></dt> <dd><p>If TRUE, the total concentration including the amount adsorbed to suspended matter will be used.</p></dd> @@ -167,22 +158,21 @@ suspended matter will be used.</p></dd> </dl><p></p></div> </div> -</div><p></p><hr><a id="method-TOXSWA_cwa-get_events"></a><div class="section"> -<h3 id="method-get-events-">Method <code>get_events()</code><a class="anchor" aria-label="anchor" href="#method-get-events-"></a></h3> +</div> + +<p></p><hr><a id="method-TOXSWA_cwa-get_events"></a><div class="section"> +<h3 id="toxswa-cwa-get-events-"><code>TOXSWA_cwa$get_events()</code><a class="anchor" aria-label="anchor" href="#toxswa-cwa-get-events-"></a></h3> <p>Populate a datataframe with event information for the specified threshold value. The resulting dataframe is stored in the <code>events</code> field of the object.</p><div class="section"> <h4 id="usage-2">Usage<a class="anchor" aria-label="anchor" href="#usage-2"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">get_events</span><span class="op">(</span><span class="va">thresholds</span>, total <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> -</div> - -<div class="section"> +</div><p></p><div class="section"> <h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#arguments-2"></a></h4> <p></p><div class="arguments"><dl><dt><code>thresholds</code></dt> <dd><p>Threshold values in µg/L.</p></dd> - -<dt><code>total</code></dt> + <dt><code>total</code></dt> <dd><p>If TRUE, the total concentration including the amount adsorbed to suspended matter will be used.</p></dd> @@ -190,22 +180,23 @@ suspended matter will be used.</p></dd> </dl><p></p></div> </div> -</div><p></p><hr><a id="method-TOXSWA_cwa-print"></a><div class="section"> -<h3 id="method-print-">Method <code><a href="https://rdrr.io/r/base/print.html" class="external-link">print()</a></code><a class="anchor" aria-label="anchor" href="#method-print-"></a></h3> +</div> + +<p></p><hr><a id="method-TOXSWA_cwa-print"></a><div class="section"> +<h3 id="toxswa-cwa-print-"><code>TOXSWA_cwa$print()</code><a class="anchor" aria-label="anchor" href="#toxswa-cwa-print-"></a></h3> <p>Print a <code>TOXSWA_cwa</code> object</p><div class="section"> <h4 id="usage-3">Usage<a class="anchor" aria-label="anchor" href="#usage-3"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">print</span><span class="op">(</span><span class="op">)</span></span></code></pre></div><p></p></div> </div> +</div> -</div><p></p><hr><a id="method-TOXSWA_cwa-clone"></a><div class="section"> -<h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3> +<p></p><hr><a id="method-TOXSWA_cwa-clone"></a><div class="section"> +<h3 id="toxswa-cwa-clone-"><code>TOXSWA_cwa$clone()</code><a class="anchor" aria-label="anchor" href="#toxswa-cwa-clone-"></a></h3> <p>The objects of this class are cloneable with this method.</p><div class="section"> <h4 id="usage-4">Usage<a class="anchor" aria-label="anchor" href="#usage-4"></a></h4> <p></p><div class="r"><div class="sourceCode"><pre><code><span><span class="va">TOXSWA_cwa</span><span class="op">$</span><span class="fu">clone</span><span class="op">(</span>deep <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div><p></p></div> -</div> - -<div class="section"> +</div><p></p><div class="section"> <h4 id="arguments-3">Arguments<a class="anchor" aria-label="anchor" href="#arguments-3"></a></h4> <p></p><div class="arguments"><dl><dt><code>deep</code></dt> <dd><p>Whether to make a deep clone.</p></dd> @@ -216,6 +207,7 @@ suspended matter will be used.</p></dd> </div> + </div> <div class="section level2"> @@ -264,7 +256,7 @@ suspended matter will be used.</p></dd> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/TOXSWA_cwa.md b/docs/reference/TOXSWA_cwa.md new file mode 100644 index 0000000..3a362d8 --- /dev/null +++ b/docs/reference/TOXSWA_cwa.md @@ -0,0 +1,217 @@ +# R6 class for holding TOXSWA water concentration data and associated statistics + +An R6 class for holding TOXSWA water concentration (cwa) data and some +associated statistics. like maximum moving window average +concentrations, and dataframes holding the events exceeding specified +thresholds. Usually, an instance of this class will be generated by +[read.TOXSWA_cwa](https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.md). + +## Format + +An [R6::R6Class](https://r6.r-lib.org/reference/R6Class.html) generator +object. + +## Public fields + +- `filename`: + + Length one character vector holding the filename. + +- `basedir`: + + Length one character vector holding the directory where the file came + from. + +- `zipfile`: + + If not null, giving the path to the zip file from which the file was + read. + +- `segment`: + + Length one integer, specifying for which segment the cwa data were + read. + +- `substance`: + + The TOXSWA name of the substance. + +- `cwas`: + + Dataframe holding the concentrations. + +- `events`: + + List of dataframes holding the event statistics for each threshold. + +- `windows`: + + Matrix of maximum time weighted average concentrations (TWAC_max) and + areas under the curve in µg/day \* h (AUC_max_h) or µg/day \* d + (AUC_max_d) for the requested moving window sizes in days. + +## Methods + +### Public methods + +- [`TOXSWA_cwa$new()`](#method-TOXSWA_cwa-initialize) + +- [`TOXSWA_cwa$moving_windows()`](#method-TOXSWA_cwa-moving_windows) + +- [`TOXSWA_cwa$get_events()`](#method-TOXSWA_cwa-get_events) + +- [`TOXSWA_cwa$print()`](#method-TOXSWA_cwa-print) + +- [`TOXSWA_cwa$clone()`](#method-TOXSWA_cwa-clone) + +------------------------------------------------------------------------ + +### `TOXSWA_cwa$new()` + +Create a TOXSWA_cwa object from a file + +#### Usage + + TOXSWA_cwa$new( + filename, + basedir, + zipfile = NULL, + segment = "last", + substance = "parent", + total = FALSE + ) + +#### Arguments + +- `filename`: + + The filename + +- `basedir`: + + The directory to look in + +- `zipfile`: + + Optional path to a zipfile holding the file + +- `segment`: + + Either "last" or the number of the segment for which to read the data + +- `substance`: + + The TOXSWA substance name (for TOXSWA 4 or higher) + +- `total`: + + Should total concentrations be read in? If FALSE, free concentrations + are read + +------------------------------------------------------------------------ + +### `TOXSWA_cwa$moving_windows()` + +Add to the `windows` field described above. + +#### Usage + + TOXSWA_cwa$moving_windows(windows, total = FALSE) + +#### Arguments + +- `windows`: + + Window sizes in days + +- `total`: + + If TRUE, the total concentration including the amount adsorbed to + suspended matter will be used. + +------------------------------------------------------------------------ + +### `TOXSWA_cwa$get_events()` + +Populate a datataframe with event information for the specified +threshold value. The resulting dataframe is stored in the `events` field +of the object. + +#### Usage + + TOXSWA_cwa$get_events(thresholds, total = FALSE) + +#### Arguments + +- `thresholds`: + + Threshold values in µg/L. + +- `total`: + + If TRUE, the total concentration including the amount adsorbed to + suspended matter will be used. + +------------------------------------------------------------------------ + +### `TOXSWA_cwa$print()` + +Print a `TOXSWA_cwa` object + +#### Usage + + TOXSWA_cwa$print() + +------------------------------------------------------------------------ + +### `TOXSWA_cwa$clone()` + +The objects of this class are cloneable with this method. + +#### Usage + + TOXSWA_cwa$clone(deep = FALSE) + +#### Arguments + +- `deep`: + + Whether to make a deep clone. + +## Examples + +``` r +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 +``` diff --git a/docs/reference/TSCF-1.png b/docs/reference/TSCF-1.png Binary files differindex 788f4d3..71b1825 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 92fec23..4ad4475 100644 --- a/docs/reference/TSCF.html +++ b/docs/reference/TSCF.html @@ -17,7 +17,7 @@ or ionic."></head><body> <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -100,7 +100,7 @@ by plant roots. Environ. Sci. Technol 43, 324 - 329</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/TSCF.md b/docs/reference/TSCF.md new file mode 100644 index 0000000..6d33759 --- /dev/null +++ b/docs/reference/TSCF.md @@ -0,0 +1,46 @@ +# Estimation of the transpiration stream concentration factor + +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 the compound should not be ionogenic (weak +acid/base) or ionic. + +## Usage + +``` r +TSCF(log_Kow, method = c("briggs82", "dettenmaier09")) +``` + +## Arguments + +- log_Kow: + + The decadic logarithm of the octanol-water partition constant + +- method: + + Short name of the estimation method. + +## Details + +The Dettenmaier equation is given to show that other views on the +subject exist. + +## References + +FOCUS (2014) Generic Guidance for Tier 1 FOCUS Ground Water Assessments. +Version 2.2, May 2014 Dettenmaier EM, Doucette WJ and Bugbee B (2009) +Chemical hydrophobicity and uptake by plant roots. Environ. Sci. Technol +43, 324 - 329 + +## Examples + +``` r +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)")) +``` diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html index 5f6fe6c..4fe4400 100644 --- a/docs/reference/chent_focus_sw.html +++ b/docs/reference/chent_focus_sw.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -113,7 +113,7 @@ systems</p></dd> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/chent_focus_sw.md b/docs/reference/chent_focus_sw.md new file mode 100644 index 0000000..b4ed108 --- /dev/null +++ b/docs/reference/chent_focus_sw.md @@ -0,0 +1,66 @@ +# Create a chemical compound object for FOCUS Step 1 calculations + +Create a chemical compound object for FOCUS Step 1 calculations + +## Usage + +``` r +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 +) +``` + +## Arguments + +- name: + + Length one character vector containing the name + +- Koc: + + Partition coefficient between organic carbon and water in L/kg. + +- DT50_ws: + + Half-life in water/sediment systems in days + +- DT50_soil: + + Half-life in soil in days + +- DT50_water: + + Half-life in water in days (Step 2) + +- DT50_sediment: + + Half-life in sediment in days (Step 2) + +- cwsat: + + Water solubility in mg/L + +- mw: + + Molar weight in g/mol. + +- max_soil: + + Maximum observed fraction (dimensionless) in soil + +- max_ws: + + Maximum observed fraction (dimensionless) in water/sediment systems + +## Value + +A list with the substance specific properties diff --git a/docs/reference/drift_data_JKI.html b/docs/reference/drift_data_JKI.html index c8a2d1d..ff1fd5a 100644 --- a/docs/reference/drift_data_JKI.html +++ b/docs/reference/drift_data_JKI.html @@ -9,7 +9,7 @@ published by the German Julius-Kühn Institute (JKI)."></head><body> <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -285,7 +285,7 @@ included.</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/drift_data_JKI.md b/docs/reference/drift_data_JKI.md new file mode 100644 index 0000000..c9dd92a --- /dev/null +++ b/docs/reference/drift_data_JKI.md @@ -0,0 +1,245 @@ +# Deposition from spray drift expressed as percent of the applied dose as published by the JKI + +Deposition from spray drift expressed as percent of the applied dose as +published by the German Julius-Kühn Institute (JKI). + +## Usage + +``` r +drift_data_JKI +``` + +## Format + +A list currently containing matrices with spray drift percentage data +for field crops (Ackerbau), and Pome/stone fruit, early and late +(Obstbau frueh, spaet). + +## Source + +JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved from +http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html +on 2015-06-11, not present any more 2024-01-31 + +Rautmann, D., Streloke, M and Winkler, R (2001) New basic drift values +in the authorization procedure for plant protection products Mitt. Biol. +Bundesanst. Land- Forstwirtsch. 383, 133-141 + +## Details + +The data were extracted from the spreadsheet cited below using the R +code given in the file `data_generation/drift_data_JKI.R` installed with +this package. The file itself is not included in the package, as its +licence is not clear. + +Additional spray drift values were taken from the publication by +Rautmann et al. (2001). Specifically, these are the values for early +vines, and the values for a 3 m buffer which are incomplete in the +spreadsheet. + +Note that for vegetables, ornamentals and small fruit, the values for +field crops are used for crops \< 50 cm, and the vales for late vines +are used for crops \> 50 cm. In the JKI spreadsheet, it is indicated +that these values are used for spray applications with handheld/knapsack +equipment (tragbare Spritz- und Sprühgerate). + +Values for non-professional use listed in the JKI spreadsheet were not +included. + +## Examples + +``` r +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 +#> +``` diff --git a/docs/reference/drift_parameters_focus.html b/docs/reference/drift_parameters_focus.html index e794b3d..0915b00 100644 --- a/docs/reference/drift_parameters_focus.html +++ b/docs/reference/drift_parameters_focus.html @@ -13,7 +13,7 @@ as its licence is not clear."></head><body> <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -111,7 +111,7 @@ Bundesanst. Land- Forstwirtsch. 383, 133-141</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/drift_parameters_focus.md b/docs/reference/drift_parameters_focus.md new file mode 100644 index 0000000..c83841e --- /dev/null +++ b/docs/reference/drift_parameters_focus.md @@ -0,0 +1,67 @@ +# Regression parameters for the Rautmann drift data + +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. + +## Usage + +``` r +drift_parameters_focus +``` + +## Format + +A [tibble::tibble](https://tibble.tidyverse.org/reference/tibble.html). + +## Details + +For the hinge distance, `Inf` was substituted for the cases where no +hinge distance is given in the data, in this way parameters C and D are +never used for any distance if A and B are used for the case that the +distance is smaller than the hinge distance. + +## References + +FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4). +FOrum for the Co-ordination of pesticde fate models and their 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 in the EU Evaluation Process +under 91/414/EEC. Report of the FOCUS Working Group on 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 and Winkler, R (2001) New basic drift values +in the authorization procedure for plant protection products Mitt. Biol. +Bundesanst. Land- Forstwirtsch. 383, 133-141 + +## See also + +[drift_percentages_rautmann](https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.md), +[PEC_sw_drift](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.md) + +## Examples + +``` r +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" +``` diff --git a/docs/reference/drift_percentages_rautmann-1.png b/docs/reference/drift_percentages_rautmann-1.png Binary files differindex f046ca0..8e40b84 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 cf630e8..96dfebf 100644 --- a/docs/reference/drift_percentages_rautmann.html +++ b/docs/reference/drift_percentages_rautmann.html @@ -153,7 +153,7 @@ FOrum for the Co-ordination of pesticde fate models and their USe. </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/drift_percentages_rautmann.md b/docs/reference/drift_percentages_rautmann.md new file mode 100644 index 0000000..cd323a3 --- /dev/null +++ b/docs/reference/drift_percentages_rautmann.md @@ -0,0 +1,111 @@ +# Calculate drift percentages based on Rautmann data + +Calculate drift percentages based on Rautmann data + +## Usage + +``` r +drift_percentages_rautmann( + distances, + applications = 1, + crop_group_RF = "arable", + formula = c("Rautmann", "FOCUS"), + widths = 1 +) +``` + +## Arguments + +- distances: + + The distances in m for which to get PEC values + +- applications: + + Number of applications for selection of drift percentile + +- crop_group_RF: + + Crop group(s) as used in + [drift_parameters_focus](https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.md), + i.e. "arable", "hops", "vines, late", "vines, early", "fruit, late", + "fruit, early" or "aerial". + +- formula: + + By default, the original Rautmann formula is used. If you specify + "FOCUS", mean drift input over the width of the water body is + calculated as described in Chapter 5.4.5 of the FOCUS surface water + guidance + +- widths: + + The widths of the water bodies (only used in the FOCUS formula) + +## References + +FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4). +FOrum for the Co-ordination of pesticde fate models and their USe. +<http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf> + +## See also + +[drift_parameters_focus](https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.md), +[PEC_sw_drift](https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.md) + +## Examples + +``` r +# 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) +``` diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html index 5ccb59a..cbcb9f4 100644 --- a/docs/reference/endpoint.html +++ b/docs/reference/endpoint.html @@ -13,7 +13,7 @@ this function."></head><body> <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -160,7 +160,7 @@ exponent is often called 1/n.</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/endpoint.md b/docs/reference/endpoint.md new file mode 100644 index 0000000..62eea9d --- /dev/null +++ b/docs/reference/endpoint.md @@ -0,0 +1,108 @@ +# Retrieve endpoint information from the chyaml field of a chent object + +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. + +## Usage + +``` r +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 +) +``` + +## Arguments + +- chent: + + The chent object to get the information from + +- medium: + + The medium for which information is sought + +- type: + + The information type + +- lab_field: + + If not NA, do we want laboratory or field endpoints + +- redox: + + If not NA, are we looking for aerobic or anaerobic data + +- value: + + The name of the value we want. The list given in the usage section is + not exclusive + +- aggregator: + + The aggregator function. Can be mean, + [`geomean`](https://pkgdown.jrwb.de/pfm/reference/geomean.md), or + identity, for example. + +- raw: + + Should the number(s) be returned as stored in the chent object (could + be a character value) to retain original information about precision? + +- signif: + + How many significant digits do we want + +- values: + + The values to be returned + +- aggregators: + + A named vector of aggregator functions to be used + +## Value + +The result from applying the aggregator function to the values converted +to a numeric vector, rounded to the given number of significant digits, +or, if raw = TRUE, the values as a character value, retaining any +implicit information on precision that may be present. + +## Details + +The functions `soil_*` are functions to extract soil specific endpoints. +For the Freundlich exponent, the capital letter `N` is used in order to +facilitate dealing with such data in R. In pesticide fate modelling, +this exponent is often called 1/n. diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html index 1307a93..76a309d 100644 --- a/docs/reference/geomean.html +++ b/docs/reference/geomean.html @@ -15,7 +15,7 @@ If at least one element of the vector is 0, it returns 0."></head><body> <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -94,7 +94,7 @@ If at least one element of the vector is 0, it returns 0.</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/geomean.md b/docs/reference/geomean.md new file mode 100644 index 0000000..9567bdb --- /dev/null +++ b/docs/reference/geomean.md @@ -0,0 +1,42 @@ +# Calculate the geometric mean + +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. If +at least one element of the vector is 0, it returns 0. + +## Usage + +``` r +geomean(x, na.rm = FALSE) +``` + +## Arguments + +- x: + + Vector of numbers + +- na.rm: + + Should NA values be omitted? + +## Value + +The geometric mean + +## Author + +Johannes Ranke + +## Examples + +``` r +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 +``` diff --git a/docs/reference/get_vertex.html b/docs/reference/get_vertex.html index 45a3408..d721667 100644 --- a/docs/reference/get_vertex.html +++ b/docs/reference/get_vertex.html @@ -9,7 +9,7 @@ https://stackoverflow.com/a/717791"></head><body> <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -67,7 +67,7 @@ https://stackoverflow.com/a/717791</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/get_vertex.md b/docs/reference/get_vertex.md new file mode 100644 index 0000000..5f2b18b --- /dev/null +++ b/docs/reference/get_vertex.md @@ -0,0 +1,20 @@ +# Fit a parabola through three points + +This was inspired by an answer on stackoverflow +https://stackoverflow.com/a/717791 + +## Usage + +``` r +get_vertex(x, y) +``` + +## Arguments + +- x: + + Three x coordinates + +- y: + + Three y coordinates diff --git a/docs/reference/index.html b/docs/reference/index.html index b88b64a..6d7b495 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -36,8 +36,7 @@ <div class="section-desc"><p>Functions that are independent of specific fate modelling areas</p></div> - - </div><div class="section level2"> + <dl></dl></div><div class="section level2"> @@ -48,61 +47,71 @@ </dt> <dd>Calculate the geometric mean</dd> - </dl><dl><dt> + + <dt> <code><a href="one_box.html">one_box()</a></code> </dt> <dd>Create a time series of decline data</dd> - </dl><dl><dt> + + <dt> <code><a href="plot.one_box.html">plot(<i><one_box></i>)</a></code> </dt> <dd>Plot time series of decline data</dd> - </dl><dl><dt> + + <dt> <code><a href="sawtooth.html">sawtooth()</a></code> </dt> <dd>Create decline time series for multiple applications</dd> - </dl><dl><dt> + + <dt> <code><a href="twa.html">twa()</a></code> </dt> <dd>Calculate a time weighted average concentration</dd> - </dl><dl><dt> + + <dt> <code><a href="max_twa.html">max_twa()</a></code> </dt> <dd>The maximum time weighted average concentration for a moving window</dd> - </dl><dl><dt> + + <dt> <code><a href="pfm_degradation.html">pfm_degradation()</a></code> </dt> <dd>Calculate a time course of relative concentrations based on an mkinmod model</dd> - </dl><dl><dt> + + <dt> <code><a href="SFO_actual_twa.html">SFO_actual_twa()</a></code> </dt> <dd>Actual and maximum moving window time average concentrations for SFO kinetics</dd> - </dl><dl><dt> + + <dt> <code><a href="FOMC_actual_twa.html">FOMC_actual_twa()</a></code> </dt> <dd>Actual and maximum moving window time average concentrations for FOMC kinetics</dd> - </dl><dl><dt> + + <dt> <code><a href="reexports.html">reexports</a></code> <code><a href="reexports.html">set_nd_nq</a></code> <code><a href="reexports.html">set_nd_nq_focus</a></code> </dt> <dd>Objects exported from other packages</dd> - </dl><dl><dt> + + <dt> <code><a href="TSCF.html">TSCF()</a></code> @@ -113,8 +122,7 @@ - - </div><div class="section level2"> + <dl></dl></div><div class="section level2"> @@ -125,31 +133,36 @@ </dt> <dd>Calculate predicted environmental concentrations in soil</dd> - </dl><dl><dt> + + <dt> <code><a href="PEC_soil_mets.html">PEC_soil_mets()</a></code> </dt> <dd>Calculate initial and accumulation PEC soil for a set of metabolites</dd> - </dl><dl><dt> + + <dt> <code><a href="soil_scenario_data_EFSA_2015.html">soil_scenario_data_EFSA_2015</a></code> </dt> <dd>Properties of the predefined scenarios from the EFSA guidance from 2015</dd> - </dl><dl><dt> + + <dt> <code><a href="soil_scenario_data_EFSA_2017.html">soil_scenario_data_EFSA_2017</a></code> </dt> <dd>Properties of the predefined scenarios from the EFSA guidance from 2017</dd> - </dl><dl><dt> + + <dt> <code><a href="PEC_FOMC_accu_rel.html">PEC_FOMC_accu_rel()</a></code> </dt> <dd>Get the relative accumulation of an FOMC model over multiples of an interval</dd> - </dl><dl><dt> + + <dt> <code><a href="EFSA_washoff_2017.html">EFSA_washoff_2017</a></code> @@ -160,8 +173,7 @@ - - </div><div class="section level2"> + <dl></dl></div><div class="section level2"> @@ -172,7 +184,8 @@ </dt> <dd>A very small subset of the FOCUS Groundwater scenario definitions</dd> - </dl><dl><dt> + + <dt> <code><a href="EFSA_GW_interception_2014.html">EFSA_GW_interception_2014</a></code> @@ -183,8 +196,7 @@ - - </div><div class="section level2"> + <dl></dl></div><div class="section level2"> @@ -195,91 +207,106 @@ </dt> <dd>Calculate predicted environmental concentrations in surface water due to drift</dd> - </dl><dl><dt> + + <dt> <code><a href="drift_data_JKI.html">drift_data_JKI</a></code> </dt> <dd>Deposition from spray drift expressed as percent of the applied dose as published by the JKI</dd> - </dl><dl><dt> + + <dt> <code><a href="drift_parameters_focus.html">drift_parameters_focus</a></code> </dt> <dd>Regression parameters for the Rautmann drift data</dd> - </dl><dl><dt> + + <dt> <code><a href="drift_percentages_rautmann.html">drift_percentages_rautmann()</a></code> </dt> <dd>Calculate drift percentages based on Rautmann data</dd> - </dl><dl><dt> + + <dt> <code><a href="PEC_sw_drainage_UK.html">PEC_sw_drainage_UK()</a></code> <code><a href="PEC_sw_drainage_UK.html">drainage_date_UK()</a></code> </dt> <dd>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</dd> - </dl><dl><dt> + + <dt> <code><a href="PEC_sw_sed.html">PEC_sw_sed()</a></code> </dt> <dd>Calculate predicted environmental concentrations in sediment from surface water concentrations</dd> - </dl><dl><dt> + + <dt> <code><a href="PEC_sw_focus.html">PEC_sw_focus()</a></code> </dt> <dd>Calculate PEC surface water at FOCUS Step 1</dd> - </dl><dl><dt> + + <dt> <code><a href="chent_focus_sw.html">chent_focus_sw()</a></code> </dt> <dd>Create a chemical compound object for FOCUS Step 1 calculations</dd> - </dl><dl><dt> + + <dt> <code><a href="FOCUS_Step_12_scenarios.html">FOCUS_Step_12_scenarios</a></code> </dt> <dd>Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator</dd> - </dl><dl><dt> + + <dt> <code><a href="PEC_sw_exposit_drainage.html">PEC_sw_exposit_drainage()</a></code> </dt> <dd>Calculate PEC surface water due to drainage as in Exposit 3</dd> - </dl><dl><dt> + + <dt> <code><a href="PEC_sw_exposit_runoff.html">PEC_sw_exposit_runoff()</a></code> </dt> <dd>Calculate PEC surface water due to runoff and erosion as in Exposit 3</dd> - </dl><dl><dt> + + <dt> <code><a href="perc_runoff_exposit.html">perc_runoff_exposit</a></code> </dt> <dd>Runoff loss percentages as used in Exposit 3</dd> - </dl><dl><dt> + + <dt> <code><a href="perc_runoff_reduction_exposit.html">perc_runoff_reduction_exposit</a></code> </dt> <dd>Runoff reduction percentages as used in Exposit</dd> - </dl><dl><dt> + + <dt> <code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code> </dt> <dd>R6 class for holding TOXSWA water concentration data and associated statistics</dd> - </dl><dl><dt> + + <dt> <code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa()</a></code> </dt> <dd>Read TOXSWA surface water concentrations</dd> - </dl><dl><dt> + + <dt> <code><a href="plot.TOXSWA_cwa.html">plot(<i><TOXSWA_cwa></i>)</a></code> @@ -290,8 +317,7 @@ <div class="section-desc"><p>Evaluating environmental fate properties</p></div> - - </div><div class="section level2"> + <dl></dl></div><div class="section level2"> @@ -302,7 +328,8 @@ </dt> <dd>Determine the SSLRC mobility classification for a chemical substance from its Koc</dd> - </dl><dl><dt> + + <dt> <code><a href="GUS.html">GUS()</a></code> <code><a href="GUS.html">print(<i><GUS_result></i>)</a></code> @@ -313,8 +340,7 @@ - - </div><div class="section level2"> + <dl></dl></div><div class="section level2"> @@ -330,8 +356,7 @@ - - </div><div class="section level2"> + <dl></dl></div><div class="section level2"> @@ -352,7 +377,7 @@ </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/index.md b/docs/reference/index.md new file mode 100644 index 0000000..089bd81 --- /dev/null +++ b/docs/reference/index.md @@ -0,0 +1,128 @@ +# 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 diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html index 02c8320..f1ebfeb 100644 --- a/docs/reference/max_twa.html +++ b/docs/reference/max_twa.html @@ -15,7 +15,7 @@ max_twa."></head><body> <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -59,7 +59,7 @@ for finding the maximum. It is therefore recommended to check this using <dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> -<dd><p>An object of type <code><a href="one_box.html">one_box</a></code></p></dd> +<dd><p>An object of type <a href="one_box.html">one_box</a></p></dd> <dt id="arg-window">window<a class="anchor" aria-label="anchor" href="#arg-window"></a></dt> @@ -68,7 +68,7 @@ for finding the maximum. It is therefore recommended to check this using </dl></div> <div class="section level2"> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> - <p>The method working directly on fitted <code><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></code> objects uses the + <p>The method working directly on fitted <a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a> objects uses the equations given in the PEC soil section of the FOCUS guidance and is restricted SFO, FOMC and DFOP models and to the parent compound</p> </div> @@ -117,7 +117,7 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/max_twa.md b/docs/reference/max_twa.md new file mode 100644 index 0000000..fc9fe56 --- /dev/null +++ b/docs/reference/max_twa.md @@ -0,0 +1,68 @@ +# The maximum time weighted average concentration for a moving window + +If you generate your time series using +[`sawtooth`](https://pkgdown.jrwb.de/pfm/reference/sawtooth.md), 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`](https://pkgdown.jrwb.de/pfm/reference/plot.one_box.md) +using the window size for the argument `max_twa`. + +## Usage + +``` r +max_twa(x, window = 21) +``` + +## Arguments + +- x: + + An object of type + [one_box](https://pkgdown.jrwb.de/pfm/reference/one_box.md) + +- window: + + The size of the moving window + +## Details + +The method working directly on fitted +[mkinfit](https://pkgdown.jrwb.de/mkin/reference/mkinfit.html) objects +uses the equations given in the PEC soil section of the FOCUS guidance +and is restricted SFO, FOMC and DFOP models and to the parent compound + +## References + +FOCUS (2006) “Guidance Document on Estimating Persistence and +Degradation Kinetics from Environmental Fate Studies on Pesticides in EU +Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC +Document Reference Sanco/10058/2005 version 2.0, 434 pp, +<http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics> + +## See also + +[`twa`](https://pkgdown.jrwb.de/pfm/reference/twa.md) + +## Examples + +``` r +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 +``` diff --git a/docs/reference/one_box-1.png b/docs/reference/one_box-1.png Binary files differindex b280532..62ed361 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 8c8188c..9cf9480 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 3d77b8e..59943e5 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 a61ce62..7b73a42 100644 --- a/docs/reference/one_box.html +++ b/docs/reference/one_box.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -59,12 +59,12 @@ <dd><p>When numeric, this is the half-life to be used for an exponential decline. When a character string specifying a parent decline model is given e.g. <code>FOMC</code>, <code>parms</code> must contain the corresponding parameters. -If x is an <code><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></code> object, the decline is calculated from this +If x is an <a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a> object, the decline is calculated from this object.</p></dd> <dt id="arg-ini">ini<a class="anchor" aria-label="anchor" href="#arg-ini"></a></dt> -<dd><p>The initial amount. If x is an <code><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></code> object, and +<dd><p>The initial amount. If x is an <a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a> object, and ini is 'model', the fitted initial concentrations are used. Otherwise, ini must be numeric. If it has length one, it is used for the parent and initial values of metabolites are zero, otherwise, it must give values for @@ -89,7 +89,7 @@ all observed variables.</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - <p>An object of class <code>one_box</code>, inheriting from <code><a href="https://rdrr.io/r/stats/ts.html" class="external-link">ts</a></code>.</p> + <p>An object of class <code>one_box</code>, inheriting from <a href="https://rdrr.io/r/stats/ts.html" class="external-link">ts</a>.</p> </div> <div class="section level2"> @@ -125,7 +125,7 @@ all observed variables.</p></dd> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/one_box.md b/docs/reference/one_box.md new file mode 100644 index 0000000..0c93346 --- /dev/null +++ b/docs/reference/one_box.md @@ -0,0 +1,83 @@ +# Create a time series of decline data + +Create a time series of decline data + +## Usage + +``` r +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) +``` + +## Arguments + +- x: + + When numeric, this is the half-life to be used for an exponential + decline. When a character string specifying a parent decline model is + given e.g. `FOMC`, `parms` must contain the corresponding parameters. + If x is an + [mkinfit](https://pkgdown.jrwb.de/mkin/reference/mkinfit.html) object, + the decline is calculated from this object. + +- ini: + + The initial amount. If x is an + [mkinfit](https://pkgdown.jrwb.de/mkin/reference/mkinfit.html) object, + and ini is 'model', the fitted initial concentrations are used. + Otherwise, ini must be numeric. If it has length one, it is used for + the parent and initial values of metabolites are zero, otherwise, it + must give values for all observed variables. + +- ...: + + Further arguments passed to methods + +- t_end: + + End of the time series + +- res: + + Resolution of the time series + +- parms: + + A named numeric vector containing the model parameters + +## Value + +An object of class `one_box`, inheriting from +[ts](https://rdrr.io/r/stats/ts.html). + +## Examples + +``` r +# 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) +``` diff --git a/docs/reference/perc_runoff_exposit.html b/docs/reference/perc_runoff_exposit.html index 5fdc1ba..ee5dda0 100644 --- a/docs/reference/perc_runoff_exposit.html +++ b/docs/reference/perc_runoff_exposit.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -91,7 +91,7 @@ adjacent water body bound to eroding particles</p></dd> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/perc_runoff_exposit.md b/docs/reference/perc_runoff_exposit.md new file mode 100644 index 0000000..9166e2c --- /dev/null +++ b/docs/reference/perc_runoff_exposit.md @@ -0,0 +1,53 @@ +# Runoff loss percentages as used in Exposit 3 + +A table of the loss percentages used in Exposit 3 for the twelve +different Koc classes + +## Usage + +``` r +perc_runoff_exposit +``` + +## Format + +A data frame with percentage values for the dissolved fraction and the +fraction bound to eroding particles, with Koc classes used as row names + +- Koc_lower_bound: + + The lower bound of the Koc class + +- dissolved: + + The percentage of the applied substance transferred to an adjacent + water body in the dissolved phase + +- bound: + + The percentage of the applied substance transferred to an adjacent + water body bound to eroding particles + +## Source + +Excel 3.02 spreadsheet available from +<https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html> + +## Examples + +``` r +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 +``` diff --git a/docs/reference/perc_runoff_reduction_exposit.html b/docs/reference/perc_runoff_reduction_exposit.html index 3547a64..a264847 100644 --- a/docs/reference/perc_runoff_reduction_exposit.html +++ b/docs/reference/perc_runoff_reduction_exposit.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -103,7 +103,7 @@ The variant 3.01a2 was introduced for consistency with previous calculations per </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/perc_runoff_reduction_exposit.md b/docs/reference/perc_runoff_reduction_exposit.md new file mode 100644 index 0000000..7757223 --- /dev/null +++ b/docs/reference/perc_runoff_reduction_exposit.md @@ -0,0 +1,67 @@ +# Runoff reduction percentages as used in Exposit + +A table of the runoff reduction percentages used in Exposit 3 for +different vegetated buffer widths + +## Usage + +``` r +perc_runoff_reduction_exposit +``` + +## Format + +A named list of data frames with reduction percentage values for the +dissolved fraction and the fraction bound to eroding particles, with +vegetated buffer widths as row names. The names of the list items are +the Exposit versions from which the values were taken. + +- dissolved: + + The reduction percentage for the dissolved phase + +- bound: + + The reduction percentage for the particulate phase + +## Source + +Excel 3.02 spreadsheet available from +<https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html> + +Agroscope version 3.01a with additional runoff factors for 3 m and 6 m +buffer zones received from Muris Korkaric (not published). The variant +3.01a2 was introduced for consistency with previous calculations +performed by Agroscope for a 3 m buffer zone. + +## Examples + +``` r +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 +#> +``` diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html index 2540333..5fed8c1 100644 --- a/docs/reference/pfm_degradation.html +++ b/docs/reference/pfm_degradation.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -105,7 +105,7 @@ is calculated (SFO model).</p></dd> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/pfm_degradation.md b/docs/reference/pfm_degradation.md new file mode 100644 index 0000000..fb241ff --- /dev/null +++ b/docs/reference/pfm_degradation.md @@ -0,0 +1,62 @@ +# Calculate a time course of relative concentrations based on an mkinmod model + +Calculate a time course of relative concentrations based on an mkinmod +model + +## Usage + +``` r +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) +) +``` + +## Arguments + +- model: + + The degradation model to be used. Either a parent only model like + 'SFO' or 'FOMC', or an mkinmod object + +- DT50: + + The half-life. This is only used when simple exponential decline is + calculated (SFO model). + +- parms: + + The parameters used for the degradation model + +- years: + + For how many years should the degradation be predicted? + +- step_days: + + What step size in days should the output have? + +- times: + + The output times + +## Author + +Johannes Ranke + +## Examples + +``` r +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 +``` diff --git a/docs/reference/plot.TOXSWA_cwa-1.png b/docs/reference/plot.TOXSWA_cwa-1.png Binary files differindex 19dfbe6..6051d11 100644 --- a/docs/reference/plot.TOXSWA_cwa-1.png +++ b/docs/reference/plot.TOXSWA_cwa-1.png diff --git a/docs/reference/plot.TOXSWA_cwa-2.png b/docs/reference/plot.TOXSWA_cwa-2.png Binary files differindex 85ffe4b..de0bac4 100644 --- a/docs/reference/plot.TOXSWA_cwa-2.png +++ b/docs/reference/plot.TOXSWA_cwa-2.png diff --git a/docs/reference/plot.TOXSWA_cwa-3.png b/docs/reference/plot.TOXSWA_cwa-3.png Binary files differindex f2bb9cf..30603a5 100644 --- a/docs/reference/plot.TOXSWA_cwa-3.png +++ b/docs/reference/plot.TOXSWA_cwa-3.png diff --git a/docs/reference/plot.TOXSWA_cwa-4.png b/docs/reference/plot.TOXSWA_cwa-4.png Binary files differindex 6ee8f66..814e78c 100644 --- a/docs/reference/plot.TOXSWA_cwa-4.png +++ b/docs/reference/plot.TOXSWA_cwa-4.png diff --git a/docs/reference/plot.TOXSWA_cwa-5.png b/docs/reference/plot.TOXSWA_cwa-5.png Binary files differindex 989f777..dbffb7e 100644 --- a/docs/reference/plot.TOXSWA_cwa-5.png +++ b/docs/reference/plot.TOXSWA_cwa-5.png diff --git a/docs/reference/plot.TOXSWA_cwa.html b/docs/reference/plot.TOXSWA_cwa.html index 51b589c..dcfb565 100644 --- a/docs/reference/plot.TOXSWA_cwa.html +++ b/docs/reference/plot.TOXSWA_cwa.html @@ -9,7 +9,7 @@ segment of a TOXSWA surface water body."></head><body> <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -137,7 +137,7 @@ to suspended matter?</p></dd> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/plot.TOXSWA_cwa.md b/docs/reference/plot.TOXSWA_cwa.md new file mode 100644 index 0000000..1f5f07f --- /dev/null +++ b/docs/reference/plot.TOXSWA_cwa.md @@ -0,0 +1,93 @@ +# Plot TOXSWA surface water concentrations + +Plot TOXSWA hourly concentrations of a chemical substance in a specific +segment of a TOXSWA surface water body. + +## Usage + +``` r +# 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", + ... +) +``` + +## Arguments + +- x: + + The TOXSWA_cwa object to be plotted. + +- time_column: + + What should be used for the time axis. If "t_firstjan" is chosen, the + time is given in days relative to the first of January in the first + year. + +- xlab, ylab: + + Labels for x and y axis. + +- add: + + Should we add to an existing plot? + +- threshold_factor: + + The factor by which the data have to be lower than the maximum in + order to get thinned for plotting (see next argument). + +- thin_low: + + If an integer greater than 1, the data close to zero (smaller than + 1/threshold_factor of the maximum) in the series will be thinned by + this factor in order to decrease the amount of data that is included + in the plots + +- total: + + Should the total concentration in water be plotted, including + substance sorbed to suspended matter? + +- LC_TIME: + + Specification of the locale used to format dates + +- ...: + + Further arguments passed to `plot` if we are not adding to an existing + plot + +## Author + +Johannes Ranke + +## Examples + +``` r +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") +``` diff --git a/docs/reference/plot.one_box-1.png b/docs/reference/plot.one_box-1.png Binary files differindex 5149343..7ee0e8a 100644 --- a/docs/reference/plot.one_box-1.png +++ b/docs/reference/plot.one_box-1.png diff --git a/docs/reference/plot.one_box-2.png b/docs/reference/plot.one_box-2.png Binary files differindex e6ea438..f8f8450 100644 --- a/docs/reference/plot.one_box-2.png +++ b/docs/reference/plot.one_box-2.png diff --git a/docs/reference/plot.one_box-3.png b/docs/reference/plot.one_box-3.png Binary files differindex 33a9f43..45c84f0 100644 --- a/docs/reference/plot.one_box-3.png +++ b/docs/reference/plot.one_box-3.png diff --git a/docs/reference/plot.one_box-4.png b/docs/reference/plot.one_box-4.png Binary files differindex 3a4e7a2..d4e93f7 100644 --- a/docs/reference/plot.one_box-4.png +++ b/docs/reference/plot.one_box-4.png diff --git a/docs/reference/plot.one_box-5.png b/docs/reference/plot.one_box-5.png Binary files differindex 77e8eed..338feef 100644 --- a/docs/reference/plot.one_box-5.png +++ b/docs/reference/plot.one_box-5.png diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html index 8e25c06..34632ac 100644 --- a/docs/reference/plot.one_box.html +++ b/docs/reference/plot.one_box.html @@ -7,7 +7,7 @@ <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -57,7 +57,7 @@ <dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> -<dd><p>The object of type <code><a href="one_box.html">one_box</a></code> to be plotted</p></dd> +<dd><p>The object of type <a href="one_box.html">one_box</a> to be plotted</p></dd> <dt id="arg-xlim">xlim<a class="anchor" aria-label="anchor" href="#arg-xlim"></a></dt> @@ -92,7 +92,7 @@ be shown if max_twa is not NULL.</p></dd> </dl></div> <div class="section level2"> <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> - <div class="dont-index"><p><code><a href="sawtooth.html">sawtooth</a></code></p></div> + <div class="dont-index"><p><a href="sawtooth.html">sawtooth</a></p></div> </div> <div class="section level2"> @@ -126,7 +126,7 @@ be shown if max_twa is not NULL.</p></dd> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/plot.one_box.md b/docs/reference/plot.one_box.md new file mode 100644 index 0000000..cc20b94 --- /dev/null +++ b/docs/reference/plot.one_box.md @@ -0,0 +1,83 @@ +# Plot time series of decline data + +Plot time series of decline data + +## Usage + +``` r +# 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], + ... +) +``` + +## Arguments + +- x: + + The object of type + [one_box](https://pkgdown.jrwb.de/pfm/reference/one_box.md) to be + plotted + +- xlim: + + Limits for the x axis + +- ylim: + + Limits for the y axis + +- xlab: + + Label for the x axis + +- ylab: + + Label for the y axis + +- max_twa: + + If a numeric value is given, the maximum time weighted average + concentration(s) is/are shown in the graph. + +- max_twa_var: + + Variable for which the maximum time weighted average should be shown + if max_twa is not NULL. + +- ...: + + Further arguments passed to methods + +## See also + +[sawtooth](https://pkgdown.jrwb.de/pfm/reference/sawtooth.md) + +## Examples + +``` r +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") + +``` diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html index 04aaa02..44aa6f5 100644 --- a/docs/reference/read.TOXSWA_cwa.html +++ b/docs/reference/read.TOXSWA_cwa.html @@ -17,7 +17,7 @@ renamed to ConLiqWatLay in the out file."></head><body> <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -137,7 +137,7 @@ generating event statistics.</p></dd> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/read.TOXSWA_cwa.md b/docs/reference/read.TOXSWA_cwa.md new file mode 100644 index 0000000..5cd59f2 --- /dev/null +++ b/docs/reference/read.TOXSWA_cwa.md @@ -0,0 +1,85 @@ +# Read TOXSWA surface water concentrations + +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 of the hourly averages (ConLiqWatLay). In TOXSWA 5.5.3 this +variable was renamed to ConLiqWatLay in the out file. + +## Usage + +``` r +read.TOXSWA_cwa( + filename, + basedir = ".", + zipfile = NULL, + segment = "last", + substance = "parent", + total = FALSE, + windows = NULL, + thresholds = NULL +) +``` + +## Arguments + +- filename: + + The filename of the cwa file (TOXSWA 2.x.y or similar) or the out file + when using FOCUS TOXSWA 4 (i.e. TOXSWA 4.4.2) or higher. + +- basedir: + + The path to the directory where the cwa file resides. + +- zipfile: + + Optional path to a zip file containing the cwa file. + +- segment: + + The segment for which the data should be read. Either "last", or the + segment number. + +- substance: + + For .out files, the default value "parent" leads to reading + concentrations of the parent compound. Alternatively, the substance of + interested can be selected by its code name. + +- total: + + Set this to TRUE in order to read total concentrations as well. This + is only necessary for .out files as generated by TOXSWA 4.4.2 or + similar, not for .cwa files. For .cwa files, the total concentration + is always read as well. + +- windows: + + Numeric vector of width of moving windows in days, for calculating + maximum time weighted average concentrations and areas under the + curve. + +- thresholds: + + Numeric vector of threshold concentrations in µg/L for generating + event statistics. + +## Value + +An instance of an R6 object of class +[`TOXSWA_cwa`](https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.md). + +## Author + +Johannes Ranke + +## Examples + +``` r +H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", + basedir = "SwashProjects/project_H_sw/TOXSWA", + zipfile = system.file("testdata/SwashProjects.zip", + package = "pfm")) +``` diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 82d8303..bbd10af 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -3,14 +3,14 @@ below to see their documentation. mkin -set_nd_nq, set_nd_nq_focus +set_nd_nq(), set_nd_nq_focus() "><meta property="og:description" content="These objects are imported from other packages. Follow the links below to see their documentation. mkin -set_nd_nq, set_nd_nq_focus +set_nd_nq(), set_nd_nq_focus() "></head><body> @@ -21,7 +21,7 @@ set_nd_nq, set_nd_nq_focus <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -51,7 +51,7 @@ set_nd_nq, set_nd_nq_focus <p>These objects are imported from other packages. Follow the links below to see their documentation.</p> <dl><dt>mkin</dt> -<dd><p><code><a href="https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html" class="external-link">set_nd_nq</a></code>, <code><a href="https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html" class="external-link">set_nd_nq_focus</a></code></p></dd> +<dd><p><code><a href="https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html" class="external-link">set_nd_nq()</a></code>, <code><a href="https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html" class="external-link">set_nd_nq_focus()</a></code></p></dd> </dl></div> @@ -66,7 +66,7 @@ below to see their documentation.</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/reexports.md b/docs/reference/reexports.md new file mode 100644 index 0000000..a7a71c8 --- /dev/null +++ b/docs/reference/reexports.md @@ -0,0 +1,9 @@ +# Objects exported from other packages + +These objects are imported from other packages. Follow the links below +to see their documentation. + +- mkin: + + [`set_nd_nq()`](https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html), + [`set_nd_nq_focus()`](https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html) diff --git a/docs/reference/sawtooth-1.png b/docs/reference/sawtooth-1.png Binary files differindex 6cf67ed..b6fca96 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 3a4e7a2..d4e93f7 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 77e8eed..338feef 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 36fbb77..57467f0 100644 --- a/docs/reference/sawtooth.html +++ b/docs/reference/sawtooth.html @@ -9,7 +9,7 @@ n and i are disregarded."></head><body> <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -55,7 +55,7 @@ n and i are disregarded."></head><body> <dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> -<dd><p>A <code><a href="one_box.html">one_box</a></code> object</p></dd> +<dd><p>A <a href="one_box.html">one_box</a> object</p></dd> <dt id="arg-n">n<a class="anchor" aria-label="anchor" href="#arg-n"></a></dt> @@ -114,7 +114,7 @@ the corresponding amounts applied in the second column.</p></dd> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/sawtooth.md b/docs/reference/sawtooth.md new file mode 100644 index 0000000..4d1c9e1 --- /dev/null +++ b/docs/reference/sawtooth.md @@ -0,0 +1,69 @@ +# Create decline time series for multiple applications + +If the application pattern is specified in `applications`, `n` and `i` +are disregarded. + +## Usage + +``` r +sawtooth( + x, + n = 1, + i = 365, + applications = data.frame(time = seq(0, (n - 1) * i, length.out = n), amount = 1) +) +``` + +## Arguments + +- x: + + A [one_box](https://pkgdown.jrwb.de/pfm/reference/one_box.md) object + +- n: + + The number of applications. If `applications` is specified, `n` is + ignored + +- i: + + The interval between applications. If `applications` is specified, `i` + is ignored + +- applications: + + A data frame holding the application times in the first column and the + corresponding amounts applied in the second column. + +## Examples + +``` r +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 +#> +``` diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html index 22e30e5..f6900f3 100644 --- a/docs/reference/soil_scenario_data_EFSA_2015.html +++ b/docs/reference/soil_scenario_data_EFSA_2015.html @@ -11,7 +11,7 @@ scenario and model adjustment factors from p. 15 and p. 17 are included."></head <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -91,7 +91,7 @@ active substances in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093 </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/soil_scenario_data_EFSA_2015.md b/docs/reference/soil_scenario_data_EFSA_2015.md new file mode 100644 index 0000000..cf86bec --- /dev/null +++ b/docs/reference/soil_scenario_data_EFSA_2015.md @@ -0,0 +1,47 @@ +# Properties of the predefined scenarios from the EFSA guidance from 2015 + +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. + +## Usage + +``` r +soil_scenario_data_EFSA_2015 +``` + +## Format + +A data frame with one row for each scenario. Row names are the scenario +codes, e.g. CTN for the Northern scenario for the total concentration in +soil. Columns are mostly self-explanatory. `rho` is the dry bulk density +of the top soil. + +## Source + +EFSA (European Food Safety Authority) (2015) EFSA guidance document for +predicting environmental concentrations of active substances of plant +protection products and transformation products of these active +substances in soil. *EFSA Journal* **13**(4) 4093 +[doi:10.2903/j.efsa.2015.4093](https://doi.org/10.2903/j.efsa.2015.4093) + +## Examples + +``` r +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 +``` diff --git a/docs/reference/soil_scenario_data_EFSA_2017.html b/docs/reference/soil_scenario_data_EFSA_2017.html index fb866b9..60dfed5 100644 --- a/docs/reference/soil_scenario_data_EFSA_2017.html +++ b/docs/reference/soil_scenario_data_EFSA_2017.html @@ -11,7 +11,7 @@ scenario and model adjustment factors from p. 16 and p. 18 are included."></head <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -91,26 +91,26 @@ active substances in soil. <em>EFSA Journal</em> <b>15</b>(10) 4982 <span class="r-out co"><span class="r-pr">#></span> `old$Country`: <span style="color: #555555;">"Estonia"</span> <span style="color: #00BB00;">"Poland"</span> <span style="color: #555555;">"France"</span> <span style="color: #555555;">"Denmark"</span> <span style="color: #00BB00;">"Austria"</span> <span style="color: #555555;">"Spain"</span></span> <span class="r-out co"><span class="r-pr">#></span> `new$Country`: <span style="color: #555555;">"Estonia"</span> <span style="color: #00BB00;">"Germany"</span> <span style="color: #555555;">"France"</span> <span style="color: #555555;">"Denmark"</span> <span style="color: #00BB00;">"Czech Republik"</span> <span style="color: #555555;">"Spain"</span></span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> `old$T_arit`: <span style="color: #00BB00;">5.7</span> <span style="color: #00BB00;">7.4</span> <span style="color: #00BB00;">10.2</span> <span style="color: #00BB00;">8.0</span> <span style="color: #00BB00;">9.3</span> <span style="color: #00BB00;">15.4</span></span> -<span class="r-out co"><span class="r-pr">#></span> `new$T_arit`: <span style="color: #00BB00;">4.7</span> <span style="color: #00BB00;">8.0</span> <span style="color: #00BB00;">11.0</span> <span style="color: #00BB00;">8.2</span> <span style="color: #00BB00;">9.1</span> <span style="color: #00BB00;">12.8</span></span> +<span class="r-out co"><span class="r-pr">#></span> `old$T_arit`: <span style="color: #00BB00;">5.70</span> <span style="color: #00BB00;">7.40</span> <span style="color: #00BB00;">10.20</span> <span style="color: #00BB00;">8.00</span> <span style="color: #00BB00;">9.30</span> <span style="color: #00BB00;">15.40</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$T_arit`: <span style="color: #00BB00;">4.70</span> <span style="color: #00BB00;">8.00</span> <span style="color: #00BB00;">11.00</span> <span style="color: #00BB00;">8.20</span> <span style="color: #00BB00;">9.10</span> <span style="color: #00BB00;">12.80</span></span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> `old$T_arr`: <span style="color: #00BB00;">7.6</span> <span style="color: #00BB00;">9.3</span> <span style="color: #00BB00;">11.7</span> <span style="color: #00BB00;">9.2</span> <span style="color: #00BB00;">11.3</span> <span style="color: #00BB00;">16.7</span></span> -<span class="r-out co"><span class="r-pr">#></span> `new$T_arr`: <span style="color: #00BB00;">7.0</span> <span style="color: #00BB00;">10.1</span> <span style="color: #00BB00;">12.3</span> <span style="color: #00BB00;">9.8</span> <span style="color: #00BB00;">11.2</span> <span style="color: #00BB00;">14.7</span></span> +<span class="r-out co"><span class="r-pr">#></span> `old$T_arr`: <span style="color: #00BB00;">7.60</span> <span style="color: #00BB00;">9.30</span> <span style="color: #00BB00;">11.70</span> <span style="color: #00BB00;">9.20</span> <span style="color: #00BB00;">11.30</span> <span style="color: #00BB00;">16.70</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$T_arr`: <span style="color: #00BB00;">7.00</span> <span style="color: #00BB00;">10.10</span> <span style="color: #00BB00;">12.30</span> <span style="color: #00BB00;">9.80</span> <span style="color: #00BB00;">11.20</span> <span style="color: #00BB00;">14.70</span></span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> `old$Texture`: <span style="color: #555555;">"Coarse"</span> <span style="color: #555555;">"Coarse"</span> <span style="color: #00BB00;">"Medium"</span> <span style="color: #555555;">"Medium"</span> <span style="color: #555555;">"Medium"</span> <span style="color: #555555;">"Medium"</span></span> <span class="r-out co"><span class="r-pr">#></span> `new$Texture`: <span style="color: #555555;">"Coarse"</span> <span style="color: #555555;">"Coarse"</span> <span style="color: #00BB00;">"Medium fine"</span> <span style="color: #555555;">"Medium"</span> <span style="color: #555555;">"Medium"</span> <span style="color: #555555;">"Medium"</span></span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> `old$f_om`: <span style="color: #00BB00;">0.220</span> <span style="color: #00BB00;">0.122</span> <span style="color: #00BB00;">0.070</span> <span style="color: #00BB00;">0.025</span> <span style="color: #555555;">0.018</span> <span style="color: #00BB00;">0.010</span></span> -<span class="r-out co"><span class="r-pr">#></span> `new$f_om`: <span style="color: #00BB00;">0.118</span> <span style="color: #00BB00;">0.086</span> <span style="color: #00BB00;">0.048</span> <span style="color: #00BB00;">0.023</span> <span style="color: #555555;">0.018</span> <span style="color: #00BB00;">0.011</span></span> +<span class="r-out co"><span class="r-pr">#></span> `old$f_om`: <span style="color: #00BB00;">0.2200</span> <span style="color: #00BB00;">0.1220</span> <span style="color: #00BB00;">0.0700</span> <span style="color: #00BB00;">0.0250</span> <span style="color: #555555;">0.0180</span> <span style="color: #00BB00;">0.0100</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$f_om`: <span style="color: #00BB00;">0.1180</span> <span style="color: #00BB00;">0.0860</span> <span style="color: #00BB00;">0.0480</span> <span style="color: #00BB00;">0.0230</span> <span style="color: #555555;">0.0180</span> <span style="color: #00BB00;">0.0110</span></span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> `old$theta_fc`: <span style="color: #555555;">0.244</span> <span style="color: #555555;">0.244</span> <span style="color: #00BB00;">0.349</span> <span style="color: #00BB00;">0.349</span> <span style="color: #00BB00;">0.349</span> <span style="color: #00BB00;">0.349</span></span> -<span class="r-out co"><span class="r-pr">#></span> `new$theta_fc`: <span style="color: #555555;">0.244</span> <span style="color: #555555;">0.244</span> <span style="color: #00BB00;">0.385</span> <span style="color: #00BB00;">0.347</span> <span style="color: #00BB00;">0.347</span> <span style="color: #00BB00;">0.347</span></span> +<span class="r-out co"><span class="r-pr">#></span> `old$theta_fc`: <span style="color: #555555;">0.2440</span> <span style="color: #555555;">0.2440</span> <span style="color: #00BB00;">0.3490</span> <span style="color: #00BB00;">0.3490</span> <span style="color: #00BB00;">0.3490</span> <span style="color: #00BB00;">0.3490</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$theta_fc`: <span style="color: #555555;">0.2440</span> <span style="color: #555555;">0.2440</span> <span style="color: #00BB00;">0.3850</span> <span style="color: #00BB00;">0.3470</span> <span style="color: #00BB00;">0.3470</span> <span style="color: #00BB00;">0.3470</span></span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> `old$rho`: <span style="color: #00BB00;">0.707</span> <span style="color: #00BB00;">0.934</span> <span style="color: #00BB00;">1.117</span> <span style="color: #00BB00;">1.371</span> <span style="color: #00BB00;">1.432</span> <span style="color: #00BB00;">1.521</span></span> -<span class="r-out co"><span class="r-pr">#></span> `new$rho`: <span style="color: #00BB00;">0.950</span> <span style="color: #00BB00;">1.050</span> <span style="color: #00BB00;">1.220</span> <span style="color: #00BB00;">1.390</span> <span style="color: #00BB00;">1.430</span> <span style="color: #00BB00;">1.510</span></span> +<span class="r-out co"><span class="r-pr">#></span> `old$rho`: <span style="color: #00BB00;">0.7070</span> <span style="color: #00BB00;">0.9340</span> <span style="color: #00BB00;">1.1170</span> <span style="color: #00BB00;">1.3710</span> <span style="color: #00BB00;">1.4320</span> <span style="color: #00BB00;">1.5210</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$rho`: <span style="color: #00BB00;">0.9500</span> <span style="color: #00BB00;">1.0500</span> <span style="color: #00BB00;">1.2200</span> <span style="color: #00BB00;">1.3900</span> <span style="color: #00BB00;">1.4300</span> <span style="color: #00BB00;">1.5100</span></span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> `old$f_sce`: <span style="color: #00BB00;">1.4</span> <span style="color: #00BB00;">1.4</span> <span style="color: #00BB00;">1.4</span> <span style="color: #00BB00;">1.6</span> <span style="color: #00BB00;">1.6</span> <span style="color: #00BB00;">1.6</span></span> -<span class="r-out co"><span class="r-pr">#></span> `new$f_sce`: <span style="color: #00BB00;">3.0</span> <span style="color: #00BB00;">2.0</span> <span style="color: #00BB00;">2.0</span> <span style="color: #00BB00;">2.0</span> <span style="color: #00BB00;">1.5</span> <span style="color: #00BB00;">1.5</span></span> +<span class="r-out co"><span class="r-pr">#></span> `old$f_sce`: <span style="color: #00BB00;">1.40</span> <span style="color: #00BB00;">1.40</span> <span style="color: #00BB00;">1.40</span> <span style="color: #00BB00;">1.60</span> <span style="color: #00BB00;">1.60</span> <span style="color: #00BB00;">1.60</span></span> +<span class="r-out co"><span class="r-pr">#></span> `new$f_sce`: <span style="color: #00BB00;">3.00</span> <span style="color: #00BB00;">2.00</span> <span style="color: #00BB00;">2.00</span> <span style="color: #00BB00;">2.00</span> <span style="color: #00BB00;">1.50</span> <span style="color: #00BB00;">1.50</span></span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> And 3 more differences ...</span> </code></pre></div> @@ -124,7 +124,7 @@ active substances in soil. <em>EFSA Journal</em> <b>15</b>(10) 4982 </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/soil_scenario_data_EFSA_2017.md b/docs/reference/soil_scenario_data_EFSA_2017.md new file mode 100644 index 0000000..5e3c769 --- /dev/null +++ b/docs/reference/soil_scenario_data_EFSA_2017.md @@ -0,0 +1,80 @@ +# Properties of the predefined scenarios from the EFSA guidance from 2017 + +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. + +## Usage + +``` r +soil_scenario_data_EFSA_2017 +``` + +## Format + +A data frame with one row for each scenario. Row names are the scenario +codes, e.g. CTN for the Northern scenario for the total concentration in +soil. Columns are mostly self-explanatory. `rho` is the dry bulk density +of the top soil. + +## Source + +EFSA (European Food Safety Authority) (2017) EFSA guidance document for +predicting environmental concentrations of active substances of plant +protection products and transformation products of these active +substances in soil. *EFSA Journal* **15**(10) 4982 +[doi:10.2903/j.efsa.2017.4982](https://doi.org/10.2903/j.efsa.2017.4982) + +## Examples + +``` r +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 ... +``` diff --git a/docs/reference/twa.html b/docs/reference/twa.html index b8d97f1..ca6d605 100644 --- a/docs/reference/twa.html +++ b/docs/reference/twa.html @@ -11,7 +11,7 @@ is after one window has passed."></head><body> <a class="navbar-brand me-2" href="../index.html">pfm</a> - <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.4</small> + <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.6.5</small> <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> @@ -56,7 +56,7 @@ is after one window has passed.</p> <dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> -<dd><p>An object of type <code><a href="one_box.html">one_box</a></code></p></dd> +<dd><p>An object of type <a href="one_box.html">one_box</a></p></dd> <dt id="arg-window">window<a class="anchor" aria-label="anchor" href="#arg-window"></a></dt> @@ -96,7 +96,7 @@ is after one window has passed.</p> </div> <div class="pkgdown-footer-right"> - <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.2.0.</p> </div> </footer></div> diff --git a/docs/reference/twa.md b/docs/reference/twa.md new file mode 100644 index 0000000..5c3a4ea --- /dev/null +++ b/docs/reference/twa.md @@ -0,0 +1,49 @@ +# Calculate a time weighted average concentration + +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. + +## Usage + +``` r +twa(x, window = 21) + +# S3 method for class 'one_box' +twa(x, window = 21) +``` + +## Arguments + +- x: + + An object of type + [one_box](https://pkgdown.jrwb.de/pfm/reference/one_box.md) + +- window: + + The size of the moving window + +## See also + +[`max_twa`](https://pkgdown.jrwb.de/pfm/reference/max_twa.md) + +## Examples + +``` r +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 +#> +``` diff --git a/docs/search.json b/docs/search.json index 662c6df..097f74a 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":"format","dir":"Reference","previous_headings":"","what":"Format","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"object class list length 2.","code":""},{"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 in eval(expr, envir, enclos): object 'scenarios' not found FOCUS_Step_12_scenarios$names = sce$Crop #> Error in eval(expr, envir, enclos): object 'sce' not found rownames(sce) <- sce$Crop #> Error in eval(expr, envir, enclos): object 'sce' not found FOCUS_Step_12_scenarios$drift = sce[, 3:11] #> Error in eval(expr, envir, enclos): object 'sce' not found FOCUS_Step_12_scenarios$interception = sce[, 12:15] #> Error in eval(expr, envir, enclos): 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 in eval(expr, envir, enclos): object 'sce_2' not found rd_mat <- matrix(rd$V2, nrow = 3, byrow = FALSE) #> Error in eval(expr, envir, enclos): object 'rd' not found dimnames(rd_mat) = list(Time = c(\"Oct-Feb\", \"Mar-May\", \"Jun-Sep\"), Region = c(\"North\", \"South\")) #> Error: object 'rd_mat' not found FOCUS_Step_12_scenarios$rd = rd_mat #> Error in eval(expr, envir, enclos): 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) 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":"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":"method-new-","dir":"Reference","previous_headings":"","what":"Method 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$new( filename, basedir, zipfile = NULL, segment = \"last\", substance = \"parent\", total = FALSE )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"filename filename basedir directory look zipfile Optional path zipfile holding file segment Either \"last\" number segment read data substance TOXSWA substance name (TOXSWA 4 higher) total total concentrations read ? FALSE, free concentrations read","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"method-moving-windows-","dir":"Reference","previous_headings":"","what":"Method moving_windows()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"Add windows field described .","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$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":"method-get-events-","dir":"Reference","previous_headings":"","what":"Method 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$get_events(thresholds, total = FALSE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"thresholds Threshold values µg/L. total TRUE, total concentration including amount adsorbed suspended matter used.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"Print TOXSWA_cwa object","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$print()"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method 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`: 5.7 7.4 10.2 8.0 9.3 15.4 #> `new$T_arit`: 4.7 8.0 11.0 8.2 9.1 12.8 #> #> `old$T_arr`: 7.6 9.3 11.7 9.2 11.3 16.7 #> `new$T_arr`: 7.0 10.1 12.3 9.8 11.2 14.7 #> #> `old$Texture`: \"Coarse\" \"Coarse\" \"Medium\" \"Medium\" \"Medium\" \"Medium\" #> `new$Texture`: \"Coarse\" \"Coarse\" \"Medium fine\" \"Medium\" \"Medium\" \"Medium\" #> #> `old$f_om`: 0.220 0.122 0.070 0.025 0.018 0.010 #> `new$f_om`: 0.118 0.086 0.048 0.023 0.018 0.011 #> #> `old$theta_fc`: 0.244 0.244 0.349 0.349 0.349 0.349 #> `new$theta_fc`: 0.244 0.244 0.385 0.347 0.347 0.347 #> #> `old$rho`: 0.707 0.934 1.117 1.371 1.432 1.521 #> `new$rho`: 0.950 1.050 1.220 1.390 1.430 1.510 #> #> `old$f_sce`: 1.4 1.4 1.4 1.6 1.6 1.6 #> `new$f_sce`: 3.0 2.0 2.0 2.0 1.5 1.5 #> #> 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 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":""}] |
