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-rw-r--r--ChangeLog41
-rw-r--r--DESCRIPTION4
-rw-r--r--GNUmakefile2
-rw-r--r--R/EFSA_GW_interception_2014.R41
-rw-r--r--R/EFSA_washoff_2017.R42
-rw-r--r--R/PEC_sw_drainage_UK.R8
-rw-r--r--R/SSLRC_mobility_classification.R17
-rw-r--r--_pkgdown.yml2
-rw-r--r--build.log4
-rw-r--r--data/EFSA_GW_interception_2014.RDatabin0 -> 352 bytes
-rw-r--r--data/EFSA_washoff_2017.RDatabin0 -> 356 bytes
-rw-r--r--docs/404.html2
-rw-r--r--docs/README.html144
-rw-r--r--docs/authors.html2
-rw-r--r--docs/index.html2
-rw-r--r--docs/jquery.sticky-kit.min.js9
-rw-r--r--docs/reference/EFSA_GW_interception_2014.html198
-rw-r--r--docs/reference/EFSA_washoff_2017.html198
-rw-r--r--docs/reference/FOCUS_GW_scenarios_2012.html2
-rw-r--r--docs/reference/FOCUS_PELMO_crop_sze_names.html162
-rw-r--r--docs/reference/FOCUS_PELMO_crops.html174
-rw-r--r--docs/reference/FOCUS_PELMO_location_codes.html152
-rw-r--r--docs/reference/FOCUS_Step_12_scenarios.html2
-rw-r--r--docs/reference/FOMC_actual_twa.html2
-rw-r--r--docs/reference/GUS.html2
-rw-r--r--docs/reference/PEC_FOMC_accu_rel.html2
-rw-r--r--docs/reference/PEC_soil.html2
-rw-r--r--docs/reference/PEC_soil_mets.html2
-rw-r--r--docs/reference/PEC_sw_drainage_UK.html14
-rw-r--r--docs/reference/PEC_sw_drift.html2
-rw-r--r--docs/reference/PEC_sw_exposit_drainage.html2
-rw-r--r--docs/reference/PEC_sw_exposit_runoff.html2
-rw-r--r--docs/reference/PEC_sw_focus.html2
-rw-r--r--docs/reference/PEC_sw_sed.html2
-rw-r--r--docs/reference/PELMO_path.html157
-rw-r--r--docs/reference/PELMO_runs.html282
-rw-r--r--docs/reference/SFO_actual_twa.html2
-rw-r--r--docs/reference/SSLRC_mobility_classification.html23
-rw-r--r--docs/reference/TOXSWA_cwa.html2
-rw-r--r--docs/reference/buffers.html137
-rw-r--r--docs/reference/chent_focus_sw.html2
-rw-r--r--docs/reference/create_run_list.html161
-rw-r--r--docs/reference/drift_data_JKI.html2
-rw-r--r--docs/reference/endpoint.html2
-rw-r--r--docs/reference/focus_80th.html159
-rw-r--r--docs/reference/geomean.html2
-rw-r--r--docs/reference/get_flux.html149
-rw-r--r--docs/reference/get_interval.html153
-rw-r--r--docs/reference/get_vertex.html2
-rw-r--r--docs/reference/index.html14
-rw-r--r--docs/reference/max_twa.html2
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-rw-r--r--docs/reference/perc_runoff_exposit.html2
-rw-r--r--docs/reference/perc_runoff_reduction_exposit.html2
-rw-r--r--docs/reference/pfm_degradation.html2
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-rw-r--r--docs/reference/sawtooth.html2
-rw-r--r--docs/reference/soil_scenario_data_EFSA_2015.html2
-rw-r--r--docs/reference/soil_scenario_data_EFSA_2017.html2
-rw-r--r--docs/reference/sum_periods.html153
-rw-r--r--docs/reference/twa.html2
-rw-r--r--docs/sitemap.xml6
-rw-r--r--man/EFSA_GW_interception_2014.Rd48
-rw-r--r--man/EFSA_washoff_2017.Rd48
-rw-r--r--man/PEC_sw_drainage_UK.Rd10
-rw-r--r--man/SSLRC_mobility_classification.Rd13
-rw-r--r--tests/testthat/test_UK_drainage.R7
77 files changed, 758 insertions, 2042 deletions
diff --git a/ChangeLog b/ChangeLog
index 5e51af7..9e3ad5f 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -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
diff --git a/build.log b/build.log
index 6f7f78c..e001d03 100644
--- a/build.log
+++ b/build.log
@@ -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
new file mode 100644
index 0000000..14fded6
--- /dev/null
+++ b/data/EFSA_GW_interception_2014.RData
Binary files differ
diff --git a/data/EFSA_washoff_2017.RData b/data/EFSA_washoff_2017.RData
new file mode 100644
index 0000000..699c0c0
--- /dev/null
+++ b/data/EFSA_washoff_2017.RData
Binary files differ
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>
-
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-<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>
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- </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>
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-</li>
- </ul>
- </div><!--/.nav-collapse -->
- </div><!--/.container -->
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-
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- </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">&lt;</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">&gt;</span></code></pre></div>
-<div id="installation" class="section level2">
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-<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>
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-<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>
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diff --git a/docs/authors.html b/docs/authors.html
index 44d9236..ea71b72 100644
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<span class="navbar-brand">
<a class="navbar-link" href="index.html">pfm</a>
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diff --git a/docs/index.html b/docs/index.html
index 4bc5fc8..33b8434 100644
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<span class="navbar-brand">
<a class="navbar-link" href="index.html">pfm</a>
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deleted file mode 100644
index e2a3c6d..0000000
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diff --git a/docs/reference/EFSA_GW_interception_2014.html b/docs/reference/EFSA_GW_interception_2014.html
new file mode 100644
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+ <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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>#&gt; BBCH
+#&gt; Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x
+#&gt; Beans (field + vegetable) 0 0.25 0.40 0.40 0.70 0.70 0.70 0.70 0.70 0.80
+#&gt; Peas 0 0.35 0.55 0.55 0.85 0.85 0.85 0.85 0.85 0.85
+#&gt; Summer oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90
+#&gt; Winter oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90
+#&gt; Tomatoes 0 0.50 0.70 0.70 0.80 0.80 0.80 0.80 0.80 0.50
+#&gt; Spring cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80
+#&gt; 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 href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
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diff --git a/docs/reference/EFSA_washoff_2017.html b/docs/reference/EFSA_washoff_2017.html
new file mode 100644
index 0000000..1f7bce7
--- /dev/null
+++ b/docs/reference/EFSA_washoff_2017.html
@@ -0,0 +1,198 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html lang="en">
+ <head>
+ <meta charset="utf-8">
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+ <h1>Subset of EFSA crop washoff default values</h1>
+
+ <div class="hidden name"><code>EFSA_washoff_2017.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+
+ <p>Subset of EFSA crop washoff 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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>&lt;-</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'>#&gt; BBCH
+#&gt; Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x
+#&gt; Beans (field + vegetable) NA 0.60 0.75 0.75 0.80 0.80 0.80 0.80 0.80 0.35
+#&gt; Peas NA 0.40 0.60 0.60 0.65 0.65 0.65 0.65 0.65 0.35
+#&gt; Summer oilseed rape NA 0.40 0.50 0.50 0.60 0.60 0.60 0.60 0.60 0.50
+#&gt; Winter oilseed rape NA 0.10 0.40 0.40 0.55 0.55 0.55 0.55 0.55 0.30
+#&gt; Tomatoes NA 0.55 0.75 0.75 0.70 0.70 0.70 0.70 0.70 0.35
+#&gt; Spring cereals NA 0.40 0.50 0.50 0.65 0.65 0.65 0.65 0.65 0.55
+#&gt; 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>
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+
+
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 @@
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-<meta property="og:title" content="FOCUS PELMO crop acronyms used for naming sceneario files — FOCUS_PELMO_crop_sze_names" />
-
-<meta property="og:description" content="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." />
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-<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'>#&gt; app gra pot sug win fbe vbe bus
-#&gt; "apples" "grass" "potato" "sbeets" "wcerea" "beans" "beans" "bushb"
-#&gt; cab car cit cot lin mai soi woi
-#&gt; "cabbag" "carrot" "citrus" "cotton" "linse" "maize" "rapesu" "rapewi"
-#&gt; oni ape soy spr str sun tob tom
-#&gt; "onions" "peas" "soyb" "scerea" "strawb" "sunflo" "tobacc" "tomato"
-#&gt; vin
-#&gt; "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>
-
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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">
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-
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-<!-- Bootstrap -->
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
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-<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." />
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- </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>
-
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-</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'>#&gt; app gra pot
-#&gt; "Apples" "Grass and alfalfa" "Potatoes"
-#&gt; sug win fbe
-#&gt; "Sugar beets" "Winter cereals" "Beans (field)"
-#&gt; vbe bus cab
-#&gt; "Beans (vegetables)" "Bushberries" "Cabbage"
-#&gt; car cit cot
-#&gt; "Carrots" "Citrus" "Cotton"
-#&gt; lin mai soi
-#&gt; "Linseed" "Maize" "Oil seed rape (summer)"
-#&gt; woi oni ape
-#&gt; "Oil seed rape (winter)" "Onions" "Peas (animals)"
-#&gt; soy spr str
-#&gt; "Soybeans" "Spring cereals" "Strawberries"
-#&gt; sun tob tom
-#&gt; "Sunflower" "Tobacco" "Tomatoes"
-#&gt; vin
-#&gt; "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>
-
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-<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>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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- <div class="container template-reference-topic">
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- <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'>#&gt; Cha Ham Jok Kre Oke Pia Por Sev Thi
-#&gt; "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'>#&gt; [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 &quot;Konzept Runoff&quot;." />
</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">
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</span>
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diff --git a/docs/reference/PELMO_path.html b/docs/reference/PELMO_path.html
deleted file mode 100644
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- <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>
-
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-
- <p>Create a path of run directories as the PELMO GUI does</p>
-
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-
- <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>
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-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." />
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- <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>
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- <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'>&lt;-</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'>&lt;-</span> <span class='fu'>system.time</span>(
- <span class='no'>PECgw_1</span> <span class='kw'>&lt;-</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'>#&gt; $Pesticide_D
-#&gt; $Pesticide_D$win
-#&gt; FOCUS DUMMY D
-#&gt; Cha 0.025
-#&gt; Ham 1.621
-#&gt; Jok 0.388
-#&gt; Kre 0.467
-#&gt; Oke 1.608
-#&gt; Pia 0.848
-#&gt; Por 2.386
-#&gt; Sev 0.009
-#&gt; Thi 0.030
-#&gt;
-#&gt;
-#&gt; $Pesticide_D_1_day_pre_em_every_third_year
-#&gt; $Pesticide_D_1_day_pre_em_every_third_year$pot
-#&gt; FOCUS DUMMY D
-#&gt; Cha 0.010
-#&gt; Ham 0.014
-#&gt; Jok 0.009
-#&gt; Kre 0.027
-#&gt; Oke 0.085
-#&gt; Pia 0.051
-#&gt; Por 0.021
-#&gt; Sev 0.000
-#&gt; Thi 0.001
-#&gt;
-#&gt; </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'>#&gt; User System verstrichen
-#&gt; 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'>&lt;-</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'>#&gt; 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'>&lt;-</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'>&lt;-</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'>#&gt; $Pesticide_D_1_May_every_other_year_mets
-#&gt; $Pesticide_D_1_May_every_other_year_mets$win
-#&gt; FOCUS DUMMY D M1 M2
-#&gt; Cha 0.001 126.195 0.000
-#&gt; Ham 0.054 82.196 0.001
-#&gt; Kre 0.103 75.494 0.001
-#&gt;
-#&gt; </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'>#&gt; $`Mobility classification`
@@ -134,6 +144,11 @@ checked against the spreadsheet published on the CRC website</p>
#&gt;
#&gt; $`Percentage drained per mm of drain water`
#&gt; [1] 0.7
+#&gt; </div><div class='input'><span class='fu'>SSLRC_mobility_classification</span>(<span class='fl'>10000</span>)</div><div class='output co'>#&gt; $`Mobility classification`
+#&gt; [1] "Non mobile"
+#&gt;
+#&gt; $`Percentage drained per mm of drain water`
+#&gt; [1] 0.008
#&gt; </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>
-
-<!-- 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">
-
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
-<script src="../pkgdown.js"></script>
-
-<!-- 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>
- <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'>#&gt; $`3.01`
-#&gt; dissolved bound
-#&gt; No buffer 0 0
-#&gt; 5 m 40 40
-#&gt; 10 m 60 85
-#&gt; 20 m 80 95
-#&gt;
-#&gt; $`2.0`
-#&gt; dissolved bound
-#&gt; 1 0.0 0.0
-#&gt; 2 97.5 97.5
-#&gt; </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">
-
-<!-- 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="Create a list of runs that we can traverse — create_run_list" />
-
-<meta property="og:description" content="Create a list of runs that we can traverse" />
-<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>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>
-
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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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>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>
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-
-<!-- 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>
-
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
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-<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
-<![endif]-->
-
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- </head>
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- <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>
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-
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-
-<!-- clipboard.js -->
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-
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-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
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-<meta property="og:title" content="Get the application interval in years from a 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>
-
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-<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
deleted file mode 100644
index f7730a4..0000000
--- a/docs/reference/one_box-4.png
+++ /dev/null
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diff --git a/docs/reference/one_box-8.png b/docs/reference/one_box-8.png
deleted file mode 100644
index da3d439..0000000
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+++ /dev/null
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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
deleted file mode 100644
index 4e5eae3..0000000
--- a/docs/reference/plot.TOXSWA_cwa-10.png
+++ /dev/null
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diff --git a/docs/reference/plot.TOXSWA_cwa-6.png b/docs/reference/plot.TOXSWA_cwa-6.png
deleted file mode 100644
index c21eacc..0000000
--- a/docs/reference/plot.TOXSWA_cwa-6.png
+++ /dev/null
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diff --git a/docs/reference/plot.TOXSWA_cwa-8.png b/docs/reference/plot.TOXSWA_cwa-8.png
deleted file mode 100644
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--- a/docs/reference/plot.TOXSWA_cwa-8.png
+++ /dev/null
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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
deleted file mode 100644
index 06b2cde..0000000
--- a/docs/reference/plot.one_box-4.png
+++ /dev/null
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diff --git a/docs/reference/plot.one_box-8.png b/docs/reference/plot.one_box-8.png
deleted file mode 100644
index 3ff6e8a..0000000
--- a/docs/reference/plot.one_box-8.png
+++ /dev/null
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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
deleted file mode 100644
index 3ff6e8a..0000000
--- a/docs/reference/sawtooth-6.png
+++ /dev/null
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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 @@
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-<!-- Bootstrap -->
-
-<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.5.2</span>
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- <li>
- <a href="https://github.com/jranke/pfm">
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- <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>
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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", {

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