Authors • pfm

The R package pfm provides some utilities for fate modelling, including dealing with FOCUS pesticide fate modelling tools, (currently only TOXSWA cwa and out files), made available under the GNU public license. This means:

This program is free software: you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation, either version 3 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT
-ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
-details.
-
-You should have received a copy of the GNU General Public License along with
-this program. If not, see <http://www.gnu.org/licenses/>

Installation

The easiest way to install the package is probably to use drat:

install.packages("drat")
-drat::addRepo("jranke")
-install.packages("pfm")

install.packages("drat")
+drat::addRepo("jranke")
+install.packages("pfm")

Alternatively you can install the package using the devtools package. Using quick = TRUE skips docs, multiple-architecture builds, demos, and vignettes.

library(devtools)
-install_github("jranke/pfm", quick = TRUE)

library(devtools)
+install_github("jranke/pfm", quick = TRUE)

@@ -101,19 +90,16 @@

Examples

One recent 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.

Another, even more recent example shows how FOCUS PELMO can be run in parallel under Linux as shown here.

- diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 6ca2f37..c03fb08 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -58,9 +58,14 @@ img { max-width: 100%; } +/* Fix bug in bootstrap (only seen in firefox) */ +summary { + display: list-item; +} + /* Typographic tweaking ---------------------------------*/ -.contents h1.page-header { +.contents .page-header { margin-top: calc(-60px + 1em); } @@ -136,10 +141,9 @@ a.anchor { .ref-index th {font-weight: normal;} .ref-index td {vertical-align: top;} +.ref-index .icon {width: 40px;} .ref-index .alias {width: 40%;} -.ref-index .title {width: 60%;} - -.ref-index .alias {width: 40%;} +.ref-index-icons .alias {width: calc(40% - 40px);} .ref-index .title {width: 60%;} .ref-arguments th {text-align: right; padding-right: 10px;} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index de9bd72..eb7e83d 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -25,9 +25,13 @@ for (var i = 0; i < links.length; i++) { if (links[i].getAttribute("href") === "#") continue; - var path = paths(links[i].pathname); + // Ignore external links + if (links[i].host !== location.host) + continue; + + var nav_path = paths(links[i].pathname); - var length = prefix_length(cur_path, path); + var length = prefix_length(nav_path, cur_path); if (length > max_length) { max_length = length; pos = i; @@ -52,13 +56,14 @@ return(pieces); } + // Returns -1 if not found function prefix_length(needle, haystack) { if (needle.length > haystack.length) - return(0); + return(-1); // Special case for length-0 haystack, since for loop won't run if (haystack.length === 0) { - return(needle.length === 0 ? 1 : 0); + return(needle.length === 0 ? 0 : -1); } for (var i = 0; i < haystack.length; i++) { @@ -78,9 +83,9 @@ element.setAttribute('data-original-title', tooltipOriginalTitle); } - if(Clipboard.isSupported()) { + if(ClipboardJS.isSupported()) { $(document).ready(function() { - var copyButton = ""; + var copyButton = ""; $(".examples, div.sourceCode").addClass("hasCopyButton"); @@ -91,7 +96,7 @@ $('.btn-copy-ex').tooltip({container: 'body'}); // Initialize clipboard: - var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', { + var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', { text: function(trigger) { return trigger.parentNode.textContent; } diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 7908647..1dc6ec1 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ pandoc: 2.2.1 -pkgdown: 1.1.0 +pkgdown: 1.3.0 pkgdown_sha: ~ articles: [] diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html index 65a6df2..d60f44f 100644 --- a/docs/reference/FOCUS_GW_scenarios_2012.html +++ b/docs/reference/FOCUS_GW_scenarios_2012.html @@ -1,6 +1,6 @@ - + @@ -9,17 +9,17 @@ A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012 • pfm - + - - + + - + - + @@ -39,7 +39,8 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> - + + - + @@ -9,17 +9,17 @@ Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios • pfm - + - - + + - + - + @@ -39,7 +39,8 @@ The text file is not included in the package as its licence is not clear." /> - + + - + @@ -9,17 +9,17 @@ Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa • pfm - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Groundwater ubiquity score based on Gustafson (1989) — GUS • pfm - + - - + + - + - + @@ -40,7 +40,8 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> - + + - + @@ -9,17 +9,17 @@ Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel • pfm - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Calculate predicted environmental concentrations in soil — PEC_soil • pfm - + - - + + - + - + @@ -42,7 +42,8 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)." /> - + + + + + + + + + +Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets • pfm + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + +

+ +

Calculate initial and accumulation PEC soil for a set of metabolites

+ +

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 80dd7fa..b924c99 100644 --- a/docs/reference/PEC_sw_drainage_UK.html +++ b/docs/reference/PEC_sw_drainage_UK.html @@ -1,6 +1,6 @@ - + @@ -9,17 +9,17 @@ Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK • pfm - + - - + + - + - + @@ -39,7 +39,8 @@ published on the CRC website" /> - + + - + @@ -9,17 +9,17 @@ Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift • pfm - + - - + + - + - + @@ -40,7 +40,8 @@ with input via spray drift." /> - + + - + @@ -9,17 +9,17 @@ Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff • pfm - + - - + + - + - + @@ -39,7 +39,8 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values - + + - + @@ -9,17 +9,17 @@ Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • pfm - + - - + + - + - + @@ -44,7 +44,8 @@ to be used with the FOCUS calculator." /> - + + - + @@ -10,17 +10,17 @@ water concentrations — PEC_sw_sed • pfm - + - - + + - + - + @@ -41,7 +41,8 @@ PEC calculator" /> - + + - + @@ -9,17 +9,17 @@ Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa • pfm - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification • pfm - + - - + + - + - + @@ -39,7 +39,8 @@ checked against the spreadsheet published on the CRC website" /> - + + - + @@ -9,17 +9,17 @@ R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfm - + - - + + - + - + @@ -39,7 +39,8 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> - + + - + @@ -9,17 +9,17 @@ Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw • pfm - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -10,17 +10,17 @@ published by the JKI — drift_data_JKI • pfm - + - - + + - + - + @@ -41,7 +41,8 @@ published by the German Julius-Kühn Institute (JKI)." /> - + + - + @@ -9,17 +9,17 @@ Retrieve endpoint information from the chyaml field of a chent object — endpoint • pfm - + - - + + - + - + @@ -41,7 +41,8 @@ this function." /> - + + - + @@ -9,17 +9,17 @@ Calculate the geometric mean — geomean • pfm - + - - + + - + - + @@ -41,7 +41,8 @@ returns 0 if at least one element of the vector is 0." /> - + + - + @@ -9,17 +9,17 @@ Fit a parabola through three points — get_vertex • pfm - + - - + + - + - + @@ -39,7 +39,8 @@ https://stackoverflow.com/a/717791" /> - + + - + @@ -9,17 +9,17 @@ Function reference • pfm - + - - + + - + - + @@ -35,7 +35,8 @@ - + + - + @@ -9,17 +9,17 @@ The maximum time weighted average concentration for a moving window — max_twa • pfm - + - - + + - + - + @@ -42,7 +42,8 @@ max_twa." /> - + + - + @@ -9,17 +9,17 @@ Create a time series of decline data — one_box • pfm - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit • pfm - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit • pfm - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation • pfm - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa • pfm - + - - + + - + - + @@ -39,7 +39,8 @@ segment of a TOXSWA surface water body." /> - + + - + @@ -9,17 +9,17 @@ Plot time series of decline data — plot.one_box • pfm - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Read TOXSWA surface water concentrations — read.TOXSWA_cwa • pfm - + - - + + - + - + @@ -43,7 +43,8 @@ renamed to ConLiqWatLay in the out file." /> - + + - + @@ -9,17 +9,17 @@ Create decline time series for multiple applications — sawtooth • pfm - + - - + + - + - + @@ -40,7 +40,8 @@ times, with an interval i." /> - + + - + @@ -9,17 +9,17 @@ Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015 • pfm - + - - + + - + - + @@ -40,7 +40,8 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." /> - + + - + @@ -9,17 +9,17 @@ Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017 • pfm - + - - + + - + - + @@ -40,7 +40,8 @@ scenario and model adjustment factors from p. 16 and p. 18 are included." /> - + + - + @@ -9,17 +9,17 @@ Calculate a time weighted average concentration — twa • pfm - + - - + + - + - + @@ -40,7 +40,8 @@ is after one window has passed." /> - + +

pfm

Installation

@@ -101,19 +90,16 @@

Examples

Links

Developers

Calculate initial and accumulation PEC soil for a set of metabolites

Arguments

Contents