diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-09-27 10:00:15 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-09-27 11:08:53 +0200 |
| commit | 435e07a6f7fd2599d783fd306ee6d9e08acc0c6b (patch) | |
| tree | bd47fa18a307349eabf4ecfff7ea8da81f5bb654 | |
| parent | 803fe13e505960fddccdbd4dcb524715f5eb068d (diff) | |
Fix for UK drainage, some EFSA interception and washoff
- PEC_sw_drainage_UK() gave results that were a little bit too high
for the substances with the highest Koc (>4000), as I used 0.01% instead
of 0.008% for them. This must have come from an old vesion of the UK
data requirements handbook, at least I do not have another explanation
- Add EFSA interception (from 2014 DegT50 guidance) and tier 1
crop wash-off factors (from 2017 PEC soil guidance) for some major
arable crops
- Update docs
77 files changed, 758 insertions, 2042 deletions
@@ -1,3 +1,44 @@ +commit d28c33cfea96654a883ca869020671346c23568e +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2019-09-27 10:00:15 +0200 + + Fix for UK drainage, add some EFSA interception and washoff + + - PEC_sw_drainage_UK() gave results that were a little bit too high + for the substances with the highest Koc (>4000), as I used 0.01% instead + of 0.008% for them. This must have come from an old vesion of the UK + data requirements handbook, at least I do not have another explanation + + - Added EFSA interception (from 2014 DegT50 guidance) and tier 1 + crop wash-off factors (from 2017 PEC soil guidance) for some major + arable crops + + - Updated docs + +commit 803fe13e505960fddccdbd4dcb524715f5eb068d +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2019-09-18 18:18:40 +0200 + + Add url: tag to _pkgdown.yml, typo, update docs + +commit 8deaa29a659630a40e8b11df1fa3ebbbd9ca9e68 +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2019-07-01 08:04:40 +0200 + + Typo + +commit 37a1513d73201dbacc71af3c33a2a2a4e798583c +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2019-06-12 18:15:46 +0200 + + Update of static docs + +commit 5c9dd5c269acc4a6e6e32a7e599afb8f98d8ca36 +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2019-06-12 18:14:46 +0200 + + Documentation fix + commit 069824057caf8e57507852b858a7ecfd8e13e49a Author: Johannes Ranke <jranke@uni-bremen.de> Date: 2019-05-14 12:41:16 +0200 diff --git a/DESCRIPTION b/DESCRIPTION index db3d51d..1589b14 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling -Version: 0.5.6 -Date: 2019-09-18 +Version: 0.5.7 +Date: 2019-09-27 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0003-4371-6538")) diff --git a/GNUmakefile b/GNUmakefile index 76d369e..0d3f38e 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -34,7 +34,7 @@ README.html: README.md pd: roxygen @echo "Building static documentation..." # suppressWarnings to get rid of mbcsToSbcs warnings when plotting the 'µ' character - "$(R_HOME)/bin/Rscript" -e 'suppressWarnings(pkgdown::build_site())' + "$(R_HOME)/bin/Rscript" -e 'suppressWarnings(pkgdown::build_site(lazy=TRUE))' @echo "DONE." $(TGZ): $(pkgfiles) diff --git a/R/EFSA_GW_interception_2014.R b/R/EFSA_GW_interception_2014.R new file mode 100644 index 0000000..15d7835 --- /dev/null +++ b/R/EFSA_GW_interception_2014.R @@ -0,0 +1,41 @@ +#' Subset of EFSA crop interception default values for groundwater modelling +#' +#' @name EFSA_GW_interception_2014 +#' @docType data +#' @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. \emph{EFSA Journal} +#' \bold{12}(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662 +#' @format A matrix containing interception values, currently only for some selected crops +#' @examples +#' \dontrun{ +#' # This is the code that was used to define the data +#' bbch <- paste0(0:9, "x") +#' crops <- c( +#' "Beans (field + vegetable)", +#' "Peas", +#' "Summer oilseed rape", "Winter oilseed rape", +#' "Tomatoes", +#' "Spring cereals", "Winter cereals") +#' EFSA_GW_interception_2014 <- matrix(NA, length(crops), length(bbch), +#' dimnames = list(Crop = crops, BBCH = bbch)) +#' EFSA_GW_interception_2014["Beans (field + vegetable)", ] <- +#' c(0, 0.25, rep(0.4, 2), rep(0.7, 5), 0.8) +#' EFSA_GW_interception_2014["Peas", ] <- +#' c(0, 0.35, rep(0.55, 2), rep(0.85, 5), 0.85) +#' EFSA_GW_interception_2014["Summer oilseed rape", ] <- +#' c(0, 0.4, rep(0.8, 2), rep(0.8, 5), 0.9) +#' EFSA_GW_interception_2014["Winter oilseed rape", ] <- +#' c(0, 0.4, rep(0.8, 2), rep(0.8, 5), 0.9) +#' EFSA_GW_interception_2014["Tomatoes", ] <- +#' c(0, 0.5, rep(0.7, 2), rep(0.8, 5), 0.5) +#' EFSA_GW_interception_2014["Spring cereals", ] <- +#' c(0, 0, 0.2, 0.8, rep(0.9, 3), rep(0.8, 2), 0.8) +#' EFSA_GW_interception_2014["Winter cereals", ] <- +#' c(0, 0, 0.2, 0.8, rep(0.9, 3), rep(0.8, 2), 0.8) +#' save(EFSA_GW_interception_2014, +#' file = "../data/EFSA_GW_interception_2014.RData") +#' } +#' EFSA_GW_interception_2014 +NULL diff --git a/R/EFSA_washoff_2017.R b/R/EFSA_washoff_2017.R new file mode 100644 index 0000000..450c12e --- /dev/null +++ b/R/EFSA_washoff_2017.R @@ -0,0 +1,42 @@ +#' Subset of EFSA crop washoff default values +#' +#' @name EFSA_washoff_2017 +#' @docType data +#' @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. \emph{EFSA Journal} \bold{15}(10) 4982 +#' doi:10.2903/j.efsa.2017.4982 +#' @format A matrix containing wash-off factors, currently only for some selected crops +#' @examples +#' \dontrun{ +#' # This is the code that was used to define the data +#' bbch <- paste0(0:9, "x") +#' crops <- c( +#' "Beans (field + vegetable)", +#' "Peas", +#' "Summer oilseed rape", "Winter oilseed rape", +#' "Tomatoes", +#' "Spring cereals", "Winter cereals") +#' EFSA_washoff_2017 <- matrix(NA, length(crops), length(bbch), +#' dimnames = list(Crop = crops, BBCH = bbch)) +#' EFSA_washoff_2017["Beans (field + vegetable)", ] <- +#' c(NA, 0.6, rep(0.75, 2), rep(0.8, 5), 0.35) +#' EFSA_washoff_2017["Peas", ] <- +#' c(NA, 0.4, rep(0.6, 2), rep(0.65, 5), 0.35) +#' EFSA_washoff_2017["Summer oilseed rape", ] <- +#' c(NA, 0.4, rep(0.5, 2), rep(0.6, 5), 0.5) +#' EFSA_washoff_2017["Winter oilseed rape", ] <- +#' c(NA, 0.1, rep(0.4, 2), rep(0.55, 5), 0.3) +#' EFSA_washoff_2017["Tomatoes", ] <- +#' c(NA, 0.55, rep(0.75, 2), rep(0.7, 5), 0.35) +#' EFSA_washoff_2017["Spring cereals", ] <- +#' c(NA, 0.4, 0.5, 0.5, rep(0.65, 3), rep(0.65, 2), 0.55) +#' EFSA_washoff_2017["Winter cereals", ] <- +#' c(NA, 0.1, 0.4, 0.6, rep(0.55, 3), rep(0.6, 2), 0.4) +#' save(EFSA_washoff_2017, +#' file = "../data/EFSA_washoff_2017.RData") +#' } +#' EFSA_washoff_2017 +NULL diff --git a/R/PEC_sw_drainage_UK.R b/R/PEC_sw_drainage_UK.R index e53f179..3be4c97 100644 --- a/R/PEC_sw_drainage_UK.R +++ b/R/PEC_sw_drainage_UK.R @@ -29,6 +29,14 @@ #' "DFOP", "HS", or "IORE", or an mkinmod object #' @param model_parms A named numeric vector containing the model parameters #' @return 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) +#' \url{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 +#' \url{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 #' @export #' @author Johannes Ranke #' @examples diff --git a/R/SSLRC_mobility_classification.R b/R/SSLRC_mobility_classification.R index 2f8fb34..602f166 100644 --- a/R/SSLRC_mobility_classification.R +++ b/R/SSLRC_mobility_classification.R @@ -1,4 +1,4 @@ -# Copyright (C) 2015,2018 Johannes Ranke +# Copyright (C) 2015,2018,2019 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package pfm @@ -17,30 +17,39 @@ #' 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 +#' This implements the method specified in the UK data requirements handbook and was #' checked against the spreadsheet published on the CRC website #' #' @param Koc The sorption coefficient normalised to organic carbon in L/kg #' @return 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) +#' \url{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 +#' \url{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 #' @export #' @author Johannes Ranke #' @examples #' SSLRC_mobility_classification(100) +#' SSLRC_mobility_classification(10000) SSLRC_mobility_classification <- function(Koc) { if (!is.numeric(Koc) | length(Koc) != 1) stop("Please give a single number") if (is.na(Koc)) { result <- list(NA, NA) } else { - result <- list("Non mobile", 0.01) + result <- list("Non mobile", 0.008) if (Koc < 4000) result <- list("Slightly mobile", 0.02) if (Koc < 1000) result <- list("Slightly mobile", 0.5) if (Koc < 500) result <- list("Moderately mobile", 0.7) if (Koc < 75) result <- list("Mobile", 1.9) if (Koc < 15) result <- list("Very mobile", 1.9) } - names(result) <- c("Mobility classification", + names(result) <- c("Mobility classification", "Percentage drained per mm of drain water") return(result) } diff --git a/_pkgdown.yml b/_pkgdown.yml index b5f7ae7..bec5bf7 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -25,9 +25,11 @@ reference: - soil_scenario_data_EFSA_2015 - soil_scenario_data_EFSA_2017 - PEC_FOMC_accu_rel + - EFSA_washoff_2017 - title: Predicted environmental concentrations in groundwater contents: - FOCUS_GW_scenarios_2012 + - EFSA_GW_interception_2014 - title: Predicted environmental concentrations in surface water contents: - PEC_sw_drift @@ -7,5 +7,7 @@ Removed empty directory ‘pfm/inst/testdata/SwashProjects/Project_1/MACRO’ Removed empty directory ‘pfm/inst/testdata/SwashProjects/Project_1’ Removed empty directory ‘pfm/inst/testdata/SwashProjects’ * looking to see if a ‘data/datalist’ file should be added -* building ‘pfm_0.5.6.tar.gz’ + NB: this package now depends on R (>= 3.5.0) + WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: 'pfm/data/EFSA_GW_interception_2014.RData' WARNING: Added dependency on R >= 3.5.0 because serialized objects in serialize/load version 3 cannot be read in older versions of R. File(s) containing such objects: 'pfm/data/EFSA_washoff_2017.RData' +* building 'pfm_0.5.7.tar.gz' diff --git a/data/EFSA_GW_interception_2014.RData b/data/EFSA_GW_interception_2014.RData Binary files differnew file mode 100644 index 0000000..14fded6 --- /dev/null +++ b/data/EFSA_GW_interception_2014.RData diff --git a/data/EFSA_washoff_2017.RData b/data/EFSA_washoff_2017.RData Binary files differnew file mode 100644 index 0000000..699c0c0 --- /dev/null +++ b/data/EFSA_washoff_2017.RData diff --git a/docs/404.html b/docs/404.html index d665a2e..8e5e550 100644 --- a/docs/404.html +++ b/docs/404.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="https://pkgdown.jrwb.de/pfm/index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/README.html b/docs/README.html deleted file mode 100644 index efdf51f..0000000 --- a/docs/README.html +++ /dev/null @@ -1,144 +0,0 @@ -<!-- Generated by pkgdown: do not edit by hand --> -<!DOCTYPE html> -<html> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>/home/jranke/git/pfm/README.md • pfm</title> - -<!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> -<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> - -<!-- Font Awesome icons --> -<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> - -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> - -<!-- pkgdown --> -<link href="pkgdown.css" rel="stylesheet"> -<script src="jquery.sticky-kit.min.js"></script> -<script src="pkgdown.js"></script> - - -<meta property="og:title" content="/home/jranke/git/pfm/README.md" /> -<!-- mathjax --> -<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> - -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - </head> - - <body> - <div class="container template-title-body"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <a class="navbar-brand" href="index.html">pfm</a> - </div> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="index.html"> - <span class="fa fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="reference/index.html">Reference</a> -</li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/pfm"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul> - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - </header> - - <div class="row"> - <div class="contents col-md-12"> - <div class="page-header"> - <h1>/home/jranke/git/pfm/README.md</h1> - </div> - -<div id="pfm" class="section level1"> -<h1 class="hasAnchor"> -<a href="#pfm" class="anchor"></a>pfm</h1> -<p>The R package <strong>pfm</strong> 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:</p> -<div class="sourceCode"><pre class="sourceCode R"><code class="sourceCode r">This program is free software<span class="op">:</span><span class="st"> </span>you can redistribute it and<span class="op">/</span>or modify it under -the terms of the GNU General Public License as published by the Free Software -Foundation, either version <span class="dv">3</span> of the License, <span class="kw">or</span> (at your option) any later -version. - -This program is distributed <span class="cf">in</span> 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 <span class="cf">for</span> more -details. - -You should have received a copy of the GNU General Public License along with -this program. If not, see <span class="op"><</span>http<span class="op">:</span><span class="er">//</span>www.gnu.org<span class="op">/</span>licenses<span class="op">/</span><span class="er">></span></code></pre></div> -<div id="installation" class="section level2"> -<h2 class="hasAnchor"> -<a href="#installation" class="anchor"></a>Installation</h2> -<p>You can install the package from <a href="http://github.com/jranke/pfm">github</a>, e.g. using the <code>devtools</code> package. Using <code>quick = TRUE</code> skips docs, multiple-architecture builds, demos, and vignettes, to make installation as fast and painless as possible.</p> -<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(devtools) -<span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"jranke/pfm"</span>, <span class="dt">quick =</span> <span class="ot">TRUE</span>)</code></pre></div> -</div> -<div id="use" class="section level2"> -<h2 class="hasAnchor"> -<a href="#use" class="anchor"></a>Use</h2> -<p>Please refer to the <a href="http://pkgdown.jrwb.de/pfm/reference/index.html">reference</a>.</p> -</div> -<div id="examples" class="section level2"> -<h2 class="hasAnchor"> -<a href="#examples" class="anchor"></a>Examples</h2> -<p>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 <a href="http://pkgdown.jrwb.de/pfm/reference/plot.one_box.html">here</a>.</p> -<p>Another, even more recent example shows how FOCUS PELMO can be run in parallel under Linux as shown <a href="http://pkgdown.jrwb.de/pfm/reference/PELMO_runs.html">here</a>.</p> -</div> -</div> - - </div> - -</div> - - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> -</div> - - </footer> - </div> - - </body> -</html> - diff --git a/docs/authors.html b/docs/authors.html index 44d9236..ea71b72 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" 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+<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Subset of EFSA crop interception default values for groundwater modelling</h1> + + <div class="hidden name"><code>EFSA_GW_interception_2014.Rd</code></div> + </div> + + <div class="ref-description"> + + <p>Subset of EFSA crop interception default values for groundwater modelling</p> + + </div> + + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + + <p>A matrix containing interception values, currently only for some selected crops</p> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + + <p>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. <em>EFSA Journal</em> +<b>12</b>(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) { + <span class='co'># This is the code that was used to define the data</span> + <span class='no'>bbch</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='fl'>0</span>:<span class='fl'>9</span>, <span class='st'>"x"</span>) + <span class='no'>crops</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>( + <span class='st'>"Beans (field + vegetable)"</span>, + <span class='st'>"Peas"</span>, + <span class='st'>"Summer oilseed rape"</span>, <span class='st'>"Winter oilseed rape"</span>, + <span class='st'>"Tomatoes"</span>, + <span class='st'>"Spring cereals"</span>, <span class='st'>"Winter cereals"</span>) + <span class='no'>EFSA_GW_interception_2014</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fl'>NA</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>crops</span>), <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>bbch</span>), + <span class='kw'>dimnames</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Crop</span> <span class='kw'>=</span> <span class='no'>crops</span>, <span class='kw'>BBCH</span> <span class='kw'>=</span> <span class='no'>bbch</span>)) + <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Beans (field + vegetable)"</span>, ] <span class='kw'><-</span> + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.25</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.4</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.7</span>, <span class='fl'>5</span>), <span class='fl'>0.8</span>) + <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Peas"</span>, ] <span class='kw'><-</span> + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.35</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.55</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.85</span>, <span class='fl'>5</span>), <span class='fl'>0.85</span>) + <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Summer oilseed rape"</span>, ] <span class='kw'><-</span> + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.4</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>5</span>), <span class='fl'>0.9</span>) + <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Winter oilseed rape"</span>, ] <span class='kw'><-</span> + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.4</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>5</span>), <span class='fl'>0.9</span>) + <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Tomatoes"</span>, ] <span class='kw'><-</span> + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0.5</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.7</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>5</span>), <span class='fl'>0.5</span>) + <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Spring cereals"</span>, ] <span class='kw'><-</span> + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0</span>, <span class='fl'>0.2</span>, <span class='fl'>0.8</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.9</span>, <span class='fl'>3</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>2</span>), <span class='fl'>0.8</span>) + <span class='no'>EFSA_GW_interception_2014</span>[<span class='st'>"Winter cereals"</span>, ] <span class='kw'><-</span> + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>0</span>, <span class='fl'>0.2</span>, <span class='fl'>0.8</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.9</span>, <span class='fl'>3</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>2</span>), <span class='fl'>0.8</span>) + <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>EFSA_GW_interception_2014</span>, + <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"../data/EFSA_GW_interception_2014.RData"</span>) +} +<span class='no'>EFSA_GW_interception_2014</span></div><div class='output co'>#> 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</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#source">Source</a></li> + + <li><a 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default values</p> + + </div> + + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + + <p>A matrix containing wash-off factors, currently only for some selected crops</p> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + + <p>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. <em>EFSA Journal</em> <b>15</b>(10) 4982 + doi:10.2903/j.efsa.2017.4982</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) { + <span class='co'># This is the code that was used to define the data</span> + <span class='no'>bbch</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='fl'>0</span>:<span class='fl'>9</span>, <span class='st'>"x"</span>) + <span class='no'>crops</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>( + <span class='st'>"Beans (field + vegetable)"</span>, + <span class='st'>"Peas"</span>, + <span class='st'>"Summer oilseed rape"</span>, <span class='st'>"Winter oilseed rape"</span>, + <span class='st'>"Tomatoes"</span>, + <span class='st'>"Spring cereals"</span>, <span class='st'>"Winter cereals"</span>) + <span class='no'>EFSA_washoff_2017</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></span>(<span class='fl'>NA</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>crops</span>), <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>bbch</span>), + <span class='kw'>dimnames</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>Crop</span> <span class='kw'>=</span> <span class='no'>crops</span>, <span class='kw'>BBCH</span> <span class='kw'>=</span> <span class='no'>bbch</span>)) + <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Beans (field + vegetable)"</span>, ] <span class='kw'><-</span> + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.6</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.75</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.8</span>, <span class='fl'>5</span>), <span class='fl'>0.35</span>) + <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Peas"</span>, ] <span class='kw'><-</span> + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.4</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.6</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.65</span>, <span class='fl'>5</span>), <span class='fl'>0.35</span>) + <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Summer oilseed rape"</span>, ] <span class='kw'><-</span> + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.4</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.5</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.6</span>, <span class='fl'>5</span>), <span class='fl'>0.5</span>) + <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Winter oilseed rape"</span>, ] <span class='kw'><-</span> + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.1</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.4</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.55</span>, <span class='fl'>5</span>), <span class='fl'>0.3</span>) + <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Tomatoes"</span>, ] <span class='kw'><-</span> + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.55</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.75</span>, <span class='fl'>2</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.7</span>, <span class='fl'>5</span>), <span class='fl'>0.35</span>) + <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Spring cereals"</span>, ] <span class='kw'><-</span> + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.4</span>, <span class='fl'>0.5</span>, <span class='fl'>0.5</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.65</span>, <span class='fl'>3</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.65</span>, <span class='fl'>2</span>), <span class='fl'>0.55</span>) + <span class='no'>EFSA_washoff_2017</span>[<span class='st'>"Winter cereals"</span>, ] <span class='kw'><-</span> + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>0.1</span>, <span class='fl'>0.4</span>, <span class='fl'>0.6</span>, <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.55</span>, <span class='fl'>3</span>), <span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span>(<span class='fl'>0.6</span>, <span class='fl'>2</span>), <span class='fl'>0.4</span>) + <span class='fu'><a href='https://rdrr.io/r/base/save.html'>save</a></span>(<span class='no'>EFSA_washoff_2017</span>, + <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"../data/EFSA_washoff_2017.RData"</span>) +} +<span class='no'>EFSA_washoff_2017</span></div><div class='output co'>#> 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</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#source">Source</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html index 90df1b8..6b2cbe1 100644 --- a/docs/reference/FOCUS_GW_scenarios_2012.html +++ b/docs/reference/FOCUS_GW_scenarios_2012.html @@ -67,7 +67,7 @@ soil definitions are from page 46ff. from FOCUS (2012)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/FOCUS_PELMO_crop_sze_names.html b/docs/reference/FOCUS_PELMO_crop_sze_names.html deleted file mode 100644 index 4612df6..0000000 --- a/docs/reference/FOCUS_PELMO_crop_sze_names.html +++ /dev/null @@ -1,162 +0,0 @@ -<!-- Generated by pkgdown: do not edit by hand --> -<!DOCTYPE html> -<html> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>FOCUS PELMO crop acronyms used for naming sceneario files — FOCUS_PELMO_crop_sze_names • pfm</title> - -<!-- jquery --> -<script 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The crop acronyms -in the file names are sometimes capitalized, sometimes not. The scenario -files used for Beans (field) and Beans (vegetable) are the same." /> -<meta name="twitter:card" content="summary" /> - - - -<!-- mathjax --> -<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> - -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/pfm"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>FOCUS PELMO crop acronyms used for naming sceneario files</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/FOCUS_PELMO_data.R'><code>R/FOCUS_PELMO_data.R</code></a></small> - <div class="hidden name"><code>FOCUS_PELMO_crop_sze_names.Rd</code></div> - </div> - - <div class="ref-description"> - - <p>A named character vector with the crop acronyms used in FOCUS PELMO 5.5.3 -for naming the .sze files located in the FOCUS directory. The crop acronyms -in the file names are sometimes capitalized, sometimes not. The scenario -files used for Beans (field) and Beans (vegetable) are the same.</p> - - </div> - - <pre class="usage"><span class='no'>FOCUS_PELMO_crop_sze_names</span></pre> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - - <p>An object of class <code>character</code> of length 25.</p> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>print</span>(<span class='no'>FOCUS_PELMO_crop_sze_names</span>)</div><div class='output co'>#> app gra pot sug win fbe vbe bus -#> "apples" "grass" "potato" "sbeets" "wcerea" "beans" "beans" "bushb" -#> cab car cit cot lin mai soi woi -#> "cabbag" "carrot" "citrus" "cotton" "linse" "maize" "rapesu" "rapewi" -#> oni ape soy spr str sun tob tom -#> "onions" "peas" "soyb" "scerea" "strawb" "sunflo" "tobacc" "tomato" -#> vin -#> "vines" </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - - <li><a href="#format">Format</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - - </div> -</div> - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> -</div> - - </footer> - </div> - - - - </body> -</html> - diff --git a/docs/reference/FOCUS_PELMO_crops.html b/docs/reference/FOCUS_PELMO_crops.html deleted file mode 100644 index 77b5c01..0000000 --- a/docs/reference/FOCUS_PELMO_crops.html +++ /dev/null @@ -1,174 +0,0 @@ -<!-- Generated by pkgdown: do not edit by hand --> -<!DOCTYPE html> -<html> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>FOCUS PELMO crop names — FOCUS_PELMO_crops • pfm</title> - -<!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> -<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> - -<!-- Font Awesome icons --> -<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> - -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> - -<!-- sticky kit --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> - -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> - - - -<meta property="og:title" content="FOCUS PELMO crop names — FOCUS_PELMO_crops" /> - -<meta property="og:description" content="A named character vector with the crop names used in the PELMO 5.5.3 GUI. -For the names, three letter codes were constructed by generally taking the -first three letters in lower case. Only when there is an expression in -parentheses, the first letter of this expression becomes the first letter -in the three letter code, i.e. 'Peas (animals)' has the code ape." /> -<meta name="twitter:card" content="summary" /> - - - -<!-- mathjax --> -<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> - -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/pfm"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>FOCUS PELMO crop names</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/FOCUS_PELMO_data.R'><code>R/FOCUS_PELMO_data.R</code></a></small> - <div class="hidden name"><code>FOCUS_PELMO_crops.Rd</code></div> - </div> - - <div class="ref-description"> - - <p>A named character vector with the crop names used in the PELMO 5.5.3 GUI. -For the names, three letter codes were constructed by generally taking the -first three letters in lower case. Only when there is an expression in -parentheses, the first letter of this expression becomes the first letter -in the three letter code, i.e. 'Peas (animals)' has the code <code>ape</code>.</p> - - </div> - - <pre class="usage"><span class='no'>FOCUS_PELMO_crops</span></pre> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - - <p>An object of class <code>character</code> of length 25.</p> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>print</span>(<span class='no'>FOCUS_PELMO_crops</span>)</div><div class='output co'>#> app gra pot -#> "Apples" "Grass and alfalfa" "Potatoes" -#> sug win fbe -#> "Sugar beets" "Winter cereals" "Beans (field)" -#> vbe bus cab -#> "Beans (vegetables)" "Bushberries" "Cabbage" -#> car cit cot -#> "Carrots" "Citrus" "Cotton" -#> lin mai soi -#> "Linseed" "Maize" "Oil seed rape (summer)" -#> woi oni ape -#> "Oil seed rape (winter)" "Onions" "Peas (animals)" -#> soy spr str -#> "Soybeans" "Spring cereals" "Strawberries" -#> sun tob tom -#> "Sunflower" "Tobacco" "Tomatoes" -#> vin -#> "Vines" </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - - <li><a href="#format">Format</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - - </div> -</div> - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> -</div> - - </footer> - </div> - - - - </body> -</html> - diff --git a/docs/reference/FOCUS_PELMO_location_codes.html b/docs/reference/FOCUS_PELMO_location_codes.html deleted file mode 100644 index c06c729..0000000 --- a/docs/reference/FOCUS_PELMO_location_codes.html +++ /dev/null @@ -1,152 +0,0 @@ -<!-- Generated by pkgdown: do not edit by hand --> -<!DOCTYPE html> -<html> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Location codes in FOCUS PELMO — FOCUS_PELMO_location_codes • pfm</title> - -<!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> -<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> - -<!-- Font Awesome icons --> -<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> - -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> - -<!-- sticky kit --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> - -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> - - - -<meta property="og:title" content="Location codes in FOCUS PELMO — FOCUS_PELMO_location_codes" /> - -<meta property="og:description" content="A named character vector of one letter location codes used in FOCUS PELMO, -indexed by three letter acronyms." /> -<meta name="twitter:card" content="summary" /> - - - -<!-- mathjax --> -<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> - -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/pfm"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Location codes in FOCUS PELMO</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/FOCUS_PELMO_data.R'><code>R/FOCUS_PELMO_data.R</code></a></small> - <div class="hidden name"><code>FOCUS_PELMO_location_codes.Rd</code></div> - </div> - - <div class="ref-description"> - - <p>A named character vector of one letter location codes used in FOCUS PELMO, -indexed by three letter acronyms.</p> - - </div> - - <pre class="usage"><span class='no'>FOCUS_PELMO_location_codes</span></pre> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - - <p>An object of class <code>character</code> of length 9.</p> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>print</span>(<span class='no'>FOCUS_PELMO_location_codes</span>)</div><div class='output co'>#> Cha Ham Jok Kre Oke Pia Por Sev Thi -#> "C" "H" "J" "K" "N" "P" "O" "S" "T" </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - - <li><a href="#format">Format</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - - </div> -</div> - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> -</div> - - </footer> - </div> - - - - </body> -</html> - diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html index 552723f..4eed02f 100644 --- a/docs/reference/FOCUS_Step_12_scenarios.html +++ b/docs/reference/FOCUS_Step_12_scenarios.html @@ -67,7 +67,7 @@ The text file is not included in the package as its licence is not clear." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/FOMC_actual_twa.html b/docs/reference/FOMC_actual_twa.html index 38b5f8c..ae6e38c 100644 --- a/docs/reference/FOMC_actual_twa.html +++ b/docs/reference/FOMC_actual_twa.html @@ -66,7 +66,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html index 88546fa..b44c120 100644 --- a/docs/reference/GUS.html +++ b/docs/reference/GUS.html @@ -68,7 +68,7 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/PEC_FOMC_accu_rel.html b/docs/reference/PEC_FOMC_accu_rel.html index 68436fb..e4d9bf4 100644 --- a/docs/reference/PEC_FOMC_accu_rel.html +++ b/docs/reference/PEC_FOMC_accu_rel.html @@ -66,7 +66,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index 96e2db6..81575f3 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -70,7 +70,7 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/PEC_soil_mets.html b/docs/reference/PEC_soil_mets.html index ce7c6b0..c3b09f4 100644 --- a/docs/reference/PEC_soil_mets.html +++ b/docs/reference/PEC_soil_mets.html @@ -66,7 +66,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html index 8c55eed..f641773 100644 --- a/docs/reference/PEC_sw_drainage_UK.html +++ b/docs/reference/PEC_sw_drainage_UK.html @@ -67,7 +67,7 @@ published on the CRC website" /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> @@ -153,6 +153,16 @@ published on the CRC website</p> <p>The predicted concentration in surface water in µg/L</p> + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> + + <p>HSE's Chemicals Regulation Division (CRD) Active substance + PECsw calculations (for UK specific authorisation requests) + <a href='https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm'>https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm</a> + accessed 2019-09-27</p> +<p>Drainage PECs Version 1.0 (2015) Spreadsheet published at + <a href='https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx'>https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx</a> + accessed 2019-09-27</p> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'>PEC_sw_drainage_UK</span>(<span class='fl'>150</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>100</span>)</div><div class='output co'>#> [1] 8.076923</div></pre> @@ -163,6 +173,8 @@ published on the CRC website</p> <li><a href="#arguments">Arguments</a></li> <li><a href="#value">Value</a></li> + + <li><a href="#references">References</a></li> <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html index c1551e2..14ccf79 100644 --- a/docs/reference/PEC_sw_drift.html +++ b/docs/reference/PEC_sw_drift.html @@ -68,7 +68,7 @@ with input via spray drift." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/PEC_sw_exposit_drainage.html b/docs/reference/PEC_sw_exposit_drainage.html index 641ee7d..1c2deac 100644 --- a/docs/reference/PEC_sw_exposit_drainage.html +++ b/docs/reference/PEC_sw_exposit_drainage.html @@ -72,7 +72,7 @@ details, see the discussion of the function arguments below." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/PEC_sw_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html index f659bff..30ef975 100644 --- a/docs/reference/PEC_sw_exposit_runoff.html +++ b/docs/reference/PEC_sw_exposit_runoff.html @@ -67,7 +67,7 @@ in the worksheet "Konzept Runoff"." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html index 599b020..1647b19 100644 --- a/docs/reference/PEC_sw_focus.html +++ b/docs/reference/PEC_sw_focus.html @@ -72,7 +72,7 @@ to be used with the FOCUS calculator." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html index 77e4269..fe65d96 100644 --- a/docs/reference/PEC_sw_sed.html +++ b/docs/reference/PEC_sw_sed.html @@ -69,7 +69,7 @@ PEC calculator" /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/PELMO_path.html b/docs/reference/PELMO_path.html deleted file mode 100644 index a67084c..0000000 --- a/docs/reference/PELMO_path.html +++ /dev/null @@ -1,157 +0,0 @@ -<!-- Generated by pkgdown: do not edit by hand --> -<!DOCTYPE html> -<html> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Create a path of run directories as the PELMO GUI does — PELMO_path • pfm</title> - -<!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> -<!-- Bootstrap --> - 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<span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/pfm"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Create a path of run directories as the PELMO GUI does</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PELMO_runs.R'><code>R/PELMO_runs.R</code></a></small> - <div class="hidden name"><code>PELMO_path.Rd</code></div> - </div> - - <div class="ref-description"> - - <p>Create a path of run directories as the PELMO GUI does</p> - - </div> - - <pre class="usage"><span class='fu'>PELMO_path</span>(<span class='no'>psm</span>, <span class='no'>crop</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>psm</th> - <td><p>The psm identifier</p></td> - </tr> - <tr> - <th>crop</th> - <td><p>The PELMO crop acronym</p></td> - </tr> - <tr> - <th>scenario</th> - <td><p>The scenario</p></td> - </tr> - </table> - - - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - </ul> - - </div> -</div> - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> -</div> - - </footer> - </div> - - - - </body> -</html> - diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html deleted file mode 100644 index 2a75191..0000000 --- a/docs/reference/PELMO_runs.html +++ /dev/null @@ -1,282 +0,0 @@ -<!-- Generated by pkgdown: do not edit by hand --> -<!DOCTYPE html> -<html> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Set up runs for FOCUS PELMO — PELMO_runs • pfm</title> - -<!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> -<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> - -<!-- Font Awesome icons --> -<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> - -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> - -<!-- sticky kit --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> - -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> - - - -<meta property="og:title" content="Set up runs for FOCUS PELMO — PELMO_runs" /> - -<meta property="og:description" content="Per default, the runs are not only set up but also executed with FOCUS -PELMO, the results are processed and returned. Currently, only FOCUS PELMO -as installed on Linux (or other Unix systems) -using the install_PELMO from the PELMO.installeR package -maintained on github is supported. In such installations, FOCUS PELMO is -installed into the package installation directory of PELMO.installeR -and run using wine." /> -<meta name="twitter:card" content="summary" /> - - - -<!-- mathjax --> -<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> - -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/pfm"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Set up runs for FOCUS PELMO</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PELMO_runs.R'><code>R/PELMO_runs.R</code></a></small> - <div class="hidden name"><code>PELMO_runs.Rd</code></div> - </div> - - <div class="ref-description"> - - <p>Per default, the runs are not only set up but also executed with FOCUS -PELMO, the results are processed and returned. Currently, only FOCUS PELMO -as installed on Linux (or other Unix systems) -using the <code>install_PELMO</code> from the <code>PELMO.installeR</code> package -maintained on github is supported. In such installations, FOCUS PELMO is -installed into the package installation directory of <code>PELMO.installeR</code> -and run using <code>wine</code>.</p> - - </div> - - <pre class="usage"><span class='fu'>PELMO_runs</span>(<span class='no'>runs</span>, <span class='kw'>psm_dir</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>version</span> <span class='kw'>=</span> <span class='st'>"5.5.3"</span>, <span class='kw'>PELMO_base</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>execute</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'>getOption</span>(<span class='st'>"mc.cores"</span>, <span class='fl'>2L</span>), <span class='kw'>evaluate</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) - -<span class='fu'>run_PELMO</span>(<span class='no'>runs</span>, <span class='kw'>version</span> <span class='kw'>=</span> <span class='st'>"5.5.3"</span>, <span class='kw'>PELMO_base</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, - <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'>getOption</span>(<span class='st'>"mc.cores"</span>, <span class='fl'>2L</span>)) - -<span class='fu'>evaluate_PELMO</span>(<span class='no'>runs</span>, <span class='kw'>version</span> <span class='kw'>=</span> <span class='st'>"5.5.3"</span>, <span class='kw'>PELMO_base</span> <span class='kw'>=</span> <span class='st'>"auto"</span>)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>runs</th> - <td><p>A list of lists. Each inner lists has an element named 'psm' -that holds the psm string, and elements named using three letter crop acronyms, -as used in <code><a href='FOCUS_PELMO_crops.html'>FOCUS_PELMO_crops</a></code>, -that hold character vectors of three letter scenario acronyms -as used in <code><a href='FOCUS_GW_scenarios_2012.html'>FOCUS_GW_scenarios_2012</a></code>.</p></td> - </tr> - <tr> - <th>psm_dir</th> - <td><p>The directory where the psm files are located</p></td> - </tr> - <tr> - <th>version</th> - <td><p>The FOCUS PELMO version</p></td> - </tr> - <tr> - <th>PELMO_base</th> - <td><p>Where the FOCUS PELMO installation is located</p></td> - </tr> - <tr> - <th>execute</th> - <td><p>Should PELMO be executed directly?</p></td> - </tr> - <tr> - <th>cores</th> - <td><p>The number of cores to execute PELMO runs in parallel</p></td> - </tr> - <tr> - <th>evaluate</th> - <td><p>Should the results be returned?</p></td> - </tr> - <tr> - <th>overwrite</th> - <td><p>Should existing run directories be overwritten?</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>If evaluate is TRUE, a list of lists of matrices holding the - PEC data.</p> - - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - - <p>As a side effect, an R data file (period_pfm.rda) is generated in each -run directory, holding the results for all FOCUS periods, equivalent to -the period.plm file generated by the FOCUS PELMO GUI.</p> - - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - - <p>PELMO.installeR <a href='https://pkgdown.jrwb.de/PELMO.installeR'>https://pkgdown.jrwb.de/PELMO.installeR</a></p> -<p>Wine <a href='https://winehq.org'>https://winehq.org</a></p> -<p>PELMO test results <a href='http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc'>http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc</a></p> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># Reproduce the official test results for annual application of Pesticide D</span> -<span class='co'># to winter cereals at the day before emergence</span> -<span class='no'>runs_1</span> <span class='kw'><-</span> <span class='fu'>list</span>( - <span class='fu'>list</span>(<span class='kw'>psm</span> <span class='kw'>=</span> <span class='st'>'Pesticide_D'</span>, - <span class='kw'>win</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Cha"</span>, <span class='st'>"Ham"</span>, <span class='st'>"Jok"</span>, <span class='st'>"Kre"</span>, <span class='st'>"Oke"</span>, <span class='st'>"Pia"</span>, <span class='st'>"Por"</span>, <span class='st'>"Sev"</span>, <span class='st'>"Thi"</span>)), - <span class='fu'>list</span>(<span class='kw'>psm</span> <span class='kw'>=</span> <span class='st'>'Pesticide_D_1_day_pre_em_every_third_year'</span>, - <span class='kw'>pot</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Cha"</span>, <span class='st'>"Ham"</span>, <span class='st'>"Jok"</span>, <span class='st'>"Kre"</span>, <span class='st'>"Oke"</span>, <span class='st'>"Pia"</span>, <span class='st'>"Por"</span>, <span class='st'>"Sev"</span>, <span class='st'>"Thi"</span>))) -<span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'>system.time</span>( - <span class='no'>PECgw_1</span> <span class='kw'><-</span> <span class='fu'>PELMO_runs</span>(<span class='no'>runs_1</span>, <span class='kw'>psm_dir</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>), - <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>15</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -) -<span class='fu'>print</span>(<span class='no'>PECgw_1</span>)</div><div class='output co'>#> $Pesticide_D -#> $Pesticide_D$win -#> FOCUS DUMMY D -#> Cha 0.025 -#> Ham 1.621 -#> Jok 0.388 -#> Kre 0.467 -#> Oke 1.608 -#> Pia 0.848 -#> Por 2.386 -#> Sev 0.009 -#> Thi 0.030 -#> -#> -#> $Pesticide_D_1_day_pre_em_every_third_year -#> $Pesticide_D_1_day_pre_em_every_third_year$pot -#> FOCUS DUMMY D -#> Cha 0.010 -#> Ham 0.014 -#> Jok 0.009 -#> Kre 0.027 -#> Oke 0.085 -#> Pia 0.051 -#> Por 0.021 -#> Sev 0.000 -#> Thi 0.001 -#> -#> </div><div class='input'><span class='co'># We get exactly the same PECgw values (on Linux, calling PELMO using Wine).</span> -<span class='fu'>print</span>(<span class='no'>time_1</span>)</div><div class='output co'>#> User System verstrichen -#> 0.395 0.093 30.590 </div><div class='input'><span class='kw'>if</span>(!<span class='fu'>inherits</span>(<span class='fu'>try</span>(<span class='no'>cpuinfo</span> <span class='kw'><-</span> <span class='fu'>readLines</span>(<span class='st'>"/proc/cpuinfo"</span>)), <span class='st'>"try-error"</span>)) { - <span class='fu'>cat</span>(<span class='fu'>gsub</span>(<span class='st'>"model name\t: "</span>, <span class='st'>"CPU model: "</span>, <span class='no'>cpuinfo</span>[<span class='fu'>grep</span>(<span class='st'>"model name"</span>, <span class='no'>cpuinfo</span>)[<span class='fl'>1</span>]])) -}</div><div class='output co'>#> CPU model: AMD Ryzen 7 1700 Eight-Core Processor</div><div class='input'> -<span class='co'># Demonstrate some results with metabolites.</span> -<span class='no'>runs_2</span> <span class='kw'><-</span> <span class='fu'>list</span>(<span class='fu'>list</span>(<span class='kw'>psm</span> <span class='kw'>=</span> <span class='st'>'Pesticide_D_1_May_every_other_year_mets'</span>, - <span class='kw'>win</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Cha"</span>, <span class='st'>"Ham"</span>, <span class='st'>"Kre"</span>))) -<span class='no'>PECgw_2</span> <span class='kw'><-</span> <span class='fu'>PELMO_runs</span>(<span class='no'>runs_2</span>, <span class='kw'>psm_dir</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>), - <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>print</span>(<span class='no'>PECgw_2</span>)</div><div class='output co'>#> $Pesticide_D_1_May_every_other_year_mets -#> $Pesticide_D_1_May_every_other_year_mets$win -#> FOCUS DUMMY D M1 M2 -#> Cha 0.001 126.195 0.000 -#> Ham 0.054 82.196 0.001 -#> Kre 0.103 75.494 0.001 -#> -#> </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - - <li><a href="#value">Value</a></li> - - <li><a href="#details">Details</a></li> - - <li><a href="#references">References</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - - </div> -</div> - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> -</div> - - </footer> - </div> - - - - </body> -</html> - diff --git a/docs/reference/SFO_actual_twa.html b/docs/reference/SFO_actual_twa.html index 1f3a140..1f172c6 100644 --- a/docs/reference/SFO_actual_twa.html +++ b/docs/reference/SFO_actual_twa.html @@ -66,7 +66,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/SSLRC_mobility_classification.html b/docs/reference/SSLRC_mobility_classification.html index ddb21de..b0ae939 100644 --- a/docs/reference/SSLRC_mobility_classification.html +++ b/docs/reference/SSLRC_mobility_classification.html @@ -34,7 +34,7 @@ <meta property="og:title" content="Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification" /> -<meta property="og:description" content="This implements the method specified in the UK data requirements handbook and was +<meta property="og:description" content="This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRC website" /> <meta name="twitter:card" content="summary" /> @@ -67,7 +67,7 @@ checked against the spreadsheet published on the CRC website" /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> @@ -106,7 +106,7 @@ checked against the spreadsheet published on the CRC website" /> <div class="ref-description"> - <p>This implements the method specified in the UK data requirements handbook and was + <p>This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRC website</p> </div> @@ -127,6 +127,16 @@ checked against the spreadsheet published on the CRC website</p> <p>A list containing the classification and the percentage of the compound transported per 10 mm drain water</p> + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> + + <p>HSE's Chemicals Regulation Division (CRD) Active substance + PECsw calculations (for UK specific authorisation requests) + <a href='https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm'>https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm</a> + accessed 2019-09-27</p> +<p>Drainage PECs Version 1.0 (2015) Spreadsheet published at + <a href='https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx'>https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx</a> + accessed 2019-09-27</p> + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'>SSLRC_mobility_classification</span>(<span class='fl'>100</span>)</div><div class='output co'>#> $`Mobility classification` @@ -134,6 +144,11 @@ checked against the spreadsheet published on the CRC website</p> #> #> $`Percentage drained per mm of drain water` #> [1] 0.7 +#> </div><div class='input'><span class='fu'>SSLRC_mobility_classification</span>(<span class='fl'>10000</span>)</div><div class='output co'>#> $`Mobility classification` +#> [1] "Non mobile" +#> +#> $`Percentage drained per mm of drain water` +#> [1] 0.008 #> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> @@ -142,6 +157,8 @@ checked against the spreadsheet published on the CRC website</p> <li><a href="#arguments">Arguments</a></li> <li><a href="#value">Value</a></li> + + <li><a href="#references">References</a></li> <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index ab741ae..8939850 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -67,7 +67,7 @@ Usually, an instance of this class will be generated by read.TOXSWA_cwa." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/buffers.html b/docs/reference/buffers.html deleted file mode 100644 index f04c3d0..0000000 --- a/docs/reference/buffers.html +++ /dev/null @@ -1,137 +0,0 @@ -<!-- Generated by pkgdown: do not edit by hand --> -<!DOCTYPE html> -<html> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Runoff reduction percentages as used in Exposit — buffers • pfm</title> - -<!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> -<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> - 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<span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <a class="navbar-brand" href="../index.html">pfm</a> - </div> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - - </ul> - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - </header> - - <div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Runoff reduction percentages as used in Exposit</h1> - </div> - - - <p>A table of the runoff reduction percentages used in Exposit 3 for different vegetated buffer widths</p> - - - <pre class="usage"><span class='no'>buffers</span></pre> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - - <p>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.</p><dl class='dl-horizontal'> - <dt>dissolved</dt><dd><p>The reduction percentage for the dissolved phase</p></dd> - <dt>bound</dt><dd><p>The reduction percentage for the particulate phase</p></dd> - </dl> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - - <p>Excel 3.01 spreadsheet available from - <a href = 'https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3'>https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3</a></p> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>print</span>(<span class='no'>perc_runoff_reduction_exposit</span>)</div><div class='output co'>#> $`3.01` -#> dissolved bound -#> No buffer 0 0 -#> 5 m 40 40 -#> 10 m 60 85 -#> 20 m 80 95 -#> -#> $`2.0` -#> dissolved bound -#> 1 0.0 0.0 -#> 2 97.5 97.5 -#> </div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - - <li><a href="#format">Format</a></li> - - <li><a href="#source">Source</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - - </div> -</div> - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> -</div> - - </footer> - </div> - - </body> -</html> diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html index 922c405..324f2fe 100644 --- a/docs/reference/chent_focus_sw.html +++ b/docs/reference/chent_focus_sw.html @@ -66,7 +66,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/create_run_list.html b/docs/reference/create_run_list.html deleted file mode 100644 index d3c5a97..0000000 --- a/docs/reference/create_run_list.html +++ /dev/null @@ -1,161 +0,0 @@ -<!-- Generated by pkgdown: do not edit by hand --> -<!DOCTYPE html> -<html> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Create a list of runs that we can traverse — create_run_list • pfm</title> - -<!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> -<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> - -<!-- Font Awesome icons --> -<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> - 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- - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/pfm"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Create a list of runs that we can traverse</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PELMO_runs.R'><code>R/PELMO_runs.R</code></a></small> - <div class="hidden name"><code>create_run_list.Rd</code></div> - </div> - - <div class="ref-description"> - - <p>Create a list of runs that we can traverse</p> - - </div> - - <pre class="usage"><span class='fu'>create_run_list</span>(<span class='no'>runs</span>, <span class='kw'>psm_dir</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>check_psm_files</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>runs</th> - <td><p>A list of lists. Each inner lists has an element named 'psm' -that holds the psm string, and elements named using three letter crop acronyms, -as used in <code><a href='FOCUS_PELMO_crops.html'>FOCUS_PELMO_crops</a></code>, -that hold character vectors of three letter scenario acronyms -as used in <code><a href='FOCUS_GW_scenarios_2012.html'>FOCUS_GW_scenarios_2012</a></code>.</p></td> - </tr> - <tr> - <th>psm_dir</th> - <td><p>The directory where the psm files are located</p></td> - </tr> - <tr> - <th>check_psm_files</th> - <td><p>Should we check if the psm file exists</p></td> - </tr> - </table> - - - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - </ul> - - </div> -</div> - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> -</div> - - </footer> - </div> - - - - </body> -</html> - diff --git a/docs/reference/drift_data_JKI.html b/docs/reference/drift_data_JKI.html index 665cb83..08d8399 100644 --- a/docs/reference/drift_data_JKI.html +++ b/docs/reference/drift_data_JKI.html @@ -69,7 +69,7 @@ published by the German Julius-Kühn Institute (JKI)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html index 2875b7a..99e407c 100644 --- a/docs/reference/endpoint.html +++ b/docs/reference/endpoint.html @@ -69,7 +69,7 @@ this function." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/focus_80th.html b/docs/reference/focus_80th.html deleted file mode 100644 index 60ecbdd..0000000 --- a/docs/reference/focus_80th.html +++ /dev/null @@ -1,159 +0,0 @@ -<!-- Generated by pkgdown: do not edit by hand --> -<!DOCTYPE html> -<html> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Calculate the 80th percentile according to FOCUS guidance — focus_80th • pfm</title> - -<!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> -<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> - -<!-- Font Awesome icons --> -<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> - -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> - -<!-- sticky kit --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> - -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> - - - -<meta property="og:title" content="Calculate the 80th percentile according to FOCUS guidance — focus_80th" /> - -<meta property="og:description" content="This is nowadays defined as the mean of the 16th and the 17th -highest value. Previously, the 17th highest values was used (FOCUS 2014, p. -18). NaN values need to be set to zero in order to reproduce the -values obtained by PELMO." /> -<meta name="twitter:card" content="summary" /> - - - -<!-- mathjax --> -<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> - -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/pfm"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Calculate the 80th percentile according to FOCUS guidance</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PELMO_runs.R'><code>R/PELMO_runs.R</code></a></small> - <div class="hidden name"><code>focus_80th.Rd</code></div> - </div> - - <div class="ref-description"> - - <p>This is nowadays defined as the mean of the 16th and the 17th -highest value. Previously, the 17th highest values was used (FOCUS 2014, p. -18). NaN values need to be set to zero in order to reproduce the -values obtained by PELMO.</p> - - </div> - - <pre class="usage"><span class='fu'>focus_80th</span>(<span class='no'>c_period</span>, <span class='kw'>old</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>c_period</th> - <td><p>A numeric vector of values to calculate the percentile from</p></td> - </tr> - <tr> - <th>old</th> - <td><p>Should the old calculation method be used (the 17th highest value)?</p></td> - </tr> - </table> - - - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - </ul> - - </div> -</div> - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> -</div> - - </footer> - </div> - - - - </body> -</html> - diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html index 5775b27..469e12f 100644 --- a/docs/reference/geomean.html +++ b/docs/reference/geomean.html @@ -69,7 +69,7 @@ returns 0 if at least one element of the vector is 0." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/get_flux.html b/docs/reference/get_flux.html deleted file mode 100644 index 2b138f8..0000000 --- a/docs/reference/get_flux.html +++ /dev/null @@ -1,149 +0,0 @@ -<!-- Generated by pkgdown: do not edit by hand --> -<!DOCTYPE html> -<html> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file — get_flux • pfm</title> - -<!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> -<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> - -<!-- Font Awesome icons --> -<link 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file" /> -<meta name="twitter:card" content="summary" /> - - - -<!-- mathjax --> -<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> - -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/pfm"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PELMO_runs.R'><code>R/PELMO_runs.R</code></a></small> - <div class="hidden name"><code>get_flux.Rd</code></div> - </div> - - <div class="ref-description"> - - <p>Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file</p> - - </div> - - <pre class="usage"><span class='fu'>get_flux</span>(<span class='no'>chem_file</span>)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>chem_file</th> - <td><p>The full path to a CHEM*.PLM file</p></td> - </tr> - </table> - - - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - </ul> - - </div> -</div> - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> -</div> - - </footer> - </div> - - - - </body> -</html> - diff --git a/docs/reference/get_interval.html b/docs/reference/get_interval.html deleted file mode 100644 index b6561fb..0000000 --- a/docs/reference/get_interval.html +++ /dev/null @@ -1,153 +0,0 @@ -<!-- Generated by pkgdown: do not edit by hand --> -<!DOCTYPE html> -<html> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Get the application interval in years from a psm file — get_interval • pfm</title> - -<!-- jquery --> -<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> -<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" 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psm file — get_interval" /> - -<meta property="og:description" content="Get the application interval in years from a psm file" /> -<meta name="twitter:card" content="summary" /> - - - -<!-- mathjax --> -<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> - -<!--[if lt IE 9]> -<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> -<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - </head> - - <body> - <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">pfm</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> - - </a> -</li> -<li> - <a href="../reference/index.html">Reference</a> -</li> - </ul> - - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/pfm"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Get the application interval in years from a psm file</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PELMO_runs.R'><code>R/PELMO_runs.R</code></a></small> - <div class="hidden name"><code>get_interval.Rd</code></div> - </div> - - <div class="ref-description"> - - <p>Get the application interval in years from a psm file</p> - - </div> - - <pre class="usage"><span class='fu'>get_interval</span>(<span class='no'>psm_file</span>, <span class='no'>location_code</span>)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>psm_file</th> - <td><p>The path to the .psm file</p></td> - </tr> - <tr> - <th>location_code</th> - <td><p>The location code</p></td> - </tr> - </table> - - - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - </ul> - - </div> -</div> - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> -</div> - - </footer> - </div> - - - - </body> -</html> - diff --git a/docs/reference/get_vertex.html b/docs/reference/get_vertex.html index 5c2205a..3d0bc2d 100644 --- a/docs/reference/get_vertex.html +++ b/docs/reference/get_vertex.html @@ -67,7 +67,7 @@ https://stackoverflow.com/a/717791" /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/index.html b/docs/reference/index.html index ca8cd18..e1acfc1 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -63,7 +63,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> @@ -205,6 +205,12 @@ <p><code><a href="PEC_FOMC_accu_rel.html">PEC_FOMC_accu_rel()</a></code> </p> </td> <td><p>Get the relative accumulation of an FOMC model over multiples of an interval</p></td> + </tr><tr> + + <td> + <p><code><a href="EFSA_washoff_2017.html">EFSA_washoff_2017</a></code> </p> + </td> + <td><p>Subset of EFSA crop washoff default values</p></td> </tr> </tbody><tbody> <tr> @@ -219,6 +225,12 @@ <p><code><a href="FOCUS_GW_scenarios_2012.html">FOCUS_GW_scenarios_2012</a></code> </p> </td> <td><p>A very small subset of the FOCUS Groundwater scenario definitions</p></td> + </tr><tr> + + <td> + <p><code><a href="EFSA_GW_interception_2014.html">EFSA_GW_interception_2014</a></code> </p> + </td> + <td><p>Subset of EFSA crop interception default values for groundwater modelling</p></td> </tr> </tbody><tbody> <tr> diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html index 1078f3e..1d24c2a 100644 --- a/docs/reference/max_twa.html +++ b/docs/reference/max_twa.html @@ -70,7 +70,7 @@ max_twa." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/one_box-4.png b/docs/reference/one_box-4.png Binary files differdeleted file mode 100644 index f7730a4..0000000 --- a/docs/reference/one_box-4.png +++ /dev/null diff --git a/docs/reference/one_box-8.png b/docs/reference/one_box-8.png Binary files differdeleted file mode 100644 index da3d439..0000000 --- a/docs/reference/one_box-8.png +++ /dev/null diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html index ebfb872..56d60c0 100644 --- a/docs/reference/one_box.html +++ b/docs/reference/one_box.html @@ -66,7 +66,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/perc_runoff_exposit.html b/docs/reference/perc_runoff_exposit.html index 745d1f1..a0f723f 100644 --- a/docs/reference/perc_runoff_exposit.html +++ b/docs/reference/perc_runoff_exposit.html @@ -66,7 +66,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/perc_runoff_reduction_exposit.html b/docs/reference/perc_runoff_reduction_exposit.html index 8b1da13..baded1c 100644 --- a/docs/reference/perc_runoff_reduction_exposit.html +++ b/docs/reference/perc_runoff_reduction_exposit.html @@ -66,7 +66,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html index 0154be0..7e4eab1 100644 --- a/docs/reference/pfm_degradation.html +++ b/docs/reference/pfm_degradation.html @@ -66,7 +66,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/plot.TOXSWA_cwa-10.png b/docs/reference/plot.TOXSWA_cwa-10.png Binary files differdeleted file mode 100644 index 4e5eae3..0000000 --- a/docs/reference/plot.TOXSWA_cwa-10.png +++ /dev/null diff --git a/docs/reference/plot.TOXSWA_cwa-6.png b/docs/reference/plot.TOXSWA_cwa-6.png Binary files differdeleted file mode 100644 index c21eacc..0000000 --- a/docs/reference/plot.TOXSWA_cwa-6.png +++ /dev/null diff --git a/docs/reference/plot.TOXSWA_cwa-8.png b/docs/reference/plot.TOXSWA_cwa-8.png Binary files differdeleted file mode 100644 index 04e09d6..0000000 --- a/docs/reference/plot.TOXSWA_cwa-8.png +++ /dev/null diff --git a/docs/reference/plot.TOXSWA_cwa.html b/docs/reference/plot.TOXSWA_cwa.html index 0a69f2e..8ca5b8e 100644 --- a/docs/reference/plot.TOXSWA_cwa.html +++ b/docs/reference/plot.TOXSWA_cwa.html @@ -67,7 +67,7 @@ segment of a TOXSWA surface water body." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/plot.one_box-4.png b/docs/reference/plot.one_box-4.png Binary files differdeleted file mode 100644 index 06b2cde..0000000 --- a/docs/reference/plot.one_box-4.png +++ /dev/null diff --git a/docs/reference/plot.one_box-8.png b/docs/reference/plot.one_box-8.png Binary files differdeleted file mode 100644 index 3ff6e8a..0000000 --- a/docs/reference/plot.one_box-8.png +++ /dev/null diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html index 89958c5..d048d22 100644 --- a/docs/reference/plot.one_box.html +++ b/docs/reference/plot.one_box.html @@ -66,7 +66,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html index f1d4a47..df84634 100644 --- a/docs/reference/read.TOXSWA_cwa.html +++ b/docs/reference/read.TOXSWA_cwa.html @@ -71,7 +71,7 @@ renamed to ConLiqWatLay in the out file." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/sawtooth-6.png b/docs/reference/sawtooth-6.png Binary files differdeleted file mode 100644 index 3ff6e8a..0000000 --- a/docs/reference/sawtooth-6.png +++ /dev/null diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html index 050e5eb..c6756a9 100644 --- a/docs/reference/sawtooth.html +++ b/docs/reference/sawtooth.html @@ -67,7 +67,7 @@ n and i are disregarded." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html index 5551d82..d5ef9e7 100644 --- a/docs/reference/soil_scenario_data_EFSA_2015.html +++ b/docs/reference/soil_scenario_data_EFSA_2015.html @@ -68,7 +68,7 @@ scenario and model adjustment factors from p. 15 and p. 17 are included." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/soil_scenario_data_EFSA_2017.html b/docs/reference/soil_scenario_data_EFSA_2017.html index bb898b8..f5044e7 100644 --- a/docs/reference/soil_scenario_data_EFSA_2017.html +++ b/docs/reference/soil_scenario_data_EFSA_2017.html @@ -68,7 +68,7 @@ scenario and model adjustment factors from p. 16 and p. 18 are included." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/reference/sum_periods.html b/docs/reference/sum_periods.html deleted file mode 100644 index 45d35c4..0000000 --- a/docs/reference/sum_periods.html +++ /dev/null @@ -1,153 +0,0 @@ -<!-- Generated by pkgdown: do not edit by hand --> -<!DOCTYPE html> -<html> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Sum up values according to FOCUS periods — 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navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/pfm"> - <span class="fa fa-github fa-lg"></span> - - </a> -</li> - </ul> - - </div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - </header> - -<div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Sum up values according to FOCUS periods</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/pfm/blob/master/R/PELMO_runs.R'><code>R/PELMO_runs.R</code></a></small> - <div class="hidden name"><code>sum_periods.Rd</code></div> - </div> - - <div class="ref-description"> - - <p>Sum up values according to FOCUS periods</p> - - </div> - - <pre class="usage"><span class='fu'>sum_periods</span>(<span class='no'>annual</span>, <span class='no'>interval</span>)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>annual</th> - <td><p>The annual flux as obtained by <code>get_flux</code></p></td> - </tr> - <tr> - <th>interval</th> - <td><p>The interval in years</p></td> - </tr> - </table> - - - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - </ul> - - </div> -</div> - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> -</div> - - </footer> - </div> - - - - </body> -</html> - diff --git a/docs/reference/twa.html b/docs/reference/twa.html index 016380a..2c21c67 100644 --- a/docs/reference/twa.html +++ b/docs/reference/twa.html @@ -68,7 +68,7 @@ is after one window has passed." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">pfm</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.7</span> </span> </div> diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 285ffb2..6eff936 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -4,6 +4,12 @@ <loc>https://pkgdown.jrwb.de/pfm/index.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html</loc> + </url> + <url> + <loc>https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html</loc> </url> <url> diff --git a/man/EFSA_GW_interception_2014.Rd b/man/EFSA_GW_interception_2014.Rd new file mode 100644 index 0000000..f2e8c1c --- /dev/null +++ b/man/EFSA_GW_interception_2014.Rd @@ -0,0 +1,48 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/EFSA_GW_interception_2014.R +\docType{data} +\name{EFSA_GW_interception_2014} +\alias{EFSA_GW_interception_2014} +\title{Subset of EFSA crop interception default values for groundwater modelling} +\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. \emph{EFSA Journal} +\bold{12}(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662 +} +\description{ +Subset of EFSA crop interception default values for groundwater modelling +} +\examples{ +\dontrun{ + # This is the code that was used to define the data + bbch <- paste0(0:9, "x") + crops <- c( + "Beans (field + vegetable)", + "Peas", + "Summer oilseed rape", "Winter oilseed rape", + "Tomatoes", + "Spring cereals", "Winter cereals") + EFSA_GW_interception_2014 <- matrix(NA, length(crops), length(bbch), + dimnames = list(Crop = crops, BBCH = bbch)) + EFSA_GW_interception_2014["Beans (field + vegetable)", ] <- + c(0, 0.25, rep(0.4, 2), rep(0.7, 5), 0.8) + EFSA_GW_interception_2014["Peas", ] <- + c(0, 0.35, rep(0.55, 2), rep(0.85, 5), 0.85) + EFSA_GW_interception_2014["Summer oilseed rape", ] <- + c(0, 0.4, rep(0.8, 2), rep(0.8, 5), 0.9) + EFSA_GW_interception_2014["Winter oilseed rape", ] <- + c(0, 0.4, rep(0.8, 2), rep(0.8, 5), 0.9) + EFSA_GW_interception_2014["Tomatoes", ] <- + c(0, 0.5, rep(0.7, 2), rep(0.8, 5), 0.5) + EFSA_GW_interception_2014["Spring cereals", ] <- + c(0, 0, 0.2, 0.8, rep(0.9, 3), rep(0.8, 2), 0.8) + EFSA_GW_interception_2014["Winter cereals", ] <- + c(0, 0, 0.2, 0.8, rep(0.9, 3), rep(0.8, 2), 0.8) + save(EFSA_GW_interception_2014, + file = "../data/EFSA_GW_interception_2014.RData") +} +EFSA_GW_interception_2014 +} diff --git a/man/EFSA_washoff_2017.Rd b/man/EFSA_washoff_2017.Rd new file mode 100644 index 0000000..b1ab30f --- /dev/null +++ b/man/EFSA_washoff_2017.Rd @@ -0,0 +1,48 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/EFSA_washoff_2017.R +\docType{data} +\name{EFSA_washoff_2017} +\alias{EFSA_washoff_2017} +\title{Subset of EFSA crop washoff default values} +\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. \emph{EFSA Journal} \bold{15}(10) 4982 + doi:10.2903/j.efsa.2017.4982 +} +\description{ +Subset of EFSA crop washoff default values +} +\examples{ +\dontrun{ + # This is the code that was used to define the data + bbch <- paste0(0:9, "x") + crops <- c( + "Beans (field + vegetable)", + "Peas", + "Summer oilseed rape", "Winter oilseed rape", + "Tomatoes", + "Spring cereals", "Winter cereals") + EFSA_washoff_2017 <- matrix(NA, length(crops), length(bbch), + dimnames = list(Crop = crops, BBCH = bbch)) + EFSA_washoff_2017["Beans (field + vegetable)", ] <- + c(NA, 0.6, rep(0.75, 2), rep(0.8, 5), 0.35) + EFSA_washoff_2017["Peas", ] <- + c(NA, 0.4, rep(0.6, 2), rep(0.65, 5), 0.35) + EFSA_washoff_2017["Summer oilseed rape", ] <- + c(NA, 0.4, rep(0.5, 2), rep(0.6, 5), 0.5) + EFSA_washoff_2017["Winter oilseed rape", ] <- + c(NA, 0.1, rep(0.4, 2), rep(0.55, 5), 0.3) + EFSA_washoff_2017["Tomatoes", ] <- + c(NA, 0.55, rep(0.75, 2), rep(0.7, 5), 0.35) + EFSA_washoff_2017["Spring cereals", ] <- + c(NA, 0.4, 0.5, 0.5, rep(0.65, 3), rep(0.65, 2), 0.55) + EFSA_washoff_2017["Winter cereals", ] <- + c(NA, 0.1, 0.4, 0.6, rep(0.55, 3), rep(0.6, 2), 0.4) + save(EFSA_washoff_2017, + file = "../data/EFSA_washoff_2017.RData") +} +EFSA_washoff_2017 +} diff --git a/man/PEC_sw_drainage_UK.Rd b/man/PEC_sw_drainage_UK.Rd index edb239e..c9f8ed4 100644 --- a/man/PEC_sw_drainage_UK.Rd +++ b/man/PEC_sw_drainage_UK.Rd @@ -34,6 +34,16 @@ published on the CRC website \examples{ PEC_sw_drainage_UK(150, Koc = 100) } +\references{ +HSE's Chemicals Regulation Division (CRD) Active substance + PECsw calculations (for UK specific authorisation requests) + \url{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 + \url{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 } diff --git a/man/SSLRC_mobility_classification.Rd b/man/SSLRC_mobility_classification.Rd index c7fd12d..797332b 100644 --- a/man/SSLRC_mobility_classification.Rd +++ b/man/SSLRC_mobility_classification.Rd @@ -14,11 +14,22 @@ A list containing the classification and the percentage of the compound transported per 10 mm drain water } \description{ -This implements the method specified in the UK data requirements handbook and was +This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet published on the CRC website } \examples{ SSLRC_mobility_classification(100) +SSLRC_mobility_classification(10000) +} +\references{ +HSE's Chemicals Regulation Division (CRD) Active substance + PECsw calculations (for UK specific authorisation requests) + \url{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 + \url{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 diff --git a/tests/testthat/test_UK_drainage.R b/tests/testthat/test_UK_drainage.R index 859f145..2789819 100644 --- a/tests/testthat/test_UK_drainage.R +++ b/tests/testthat/test_UK_drainage.R @@ -2,7 +2,10 @@ library(pfm) context("UK drainage PEC calculations") test_that("The mobility classification and the drained percentage are correct", { - # Expected results are from the CRD drainage calculator, retrieved 2015-06-11 + # Expected results are from the CRD drainage calculator, retrieved 2019-09-27 + # The last test result was 0.01 when this test was written 2015-06-11. + # I assume that the value of 0.008 was displayed as 0.01 by the spreadsheet + # available at that time expect_equivalent(SSLRC_mobility_classification(1), list("Very mobile", 1.9)) expect_equivalent(SSLRC_mobility_classification(15), list("Mobile", 1.9)) @@ -12,7 +15,7 @@ test_that("The mobility classification and the drained percentage are correct", expect_equivalent(SSLRC_mobility_classification(100), list("Moderately mobile", 0.7)) expect_equivalent(SSLRC_mobility_classification(800), list("Slightly mobile", 0.5)) expect_equivalent(SSLRC_mobility_classification(2000), list("Slightly mobile", 0.02)) - expect_equivalent(SSLRC_mobility_classification(5000), list("Non mobile", 0.01)) + expect_equivalent(SSLRC_mobility_classification(5000), list("Non mobile", 0.008)) }) test_that("UK drainflow PECs are correct", { |
