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-rw-r--r--ChangeLog29
-rw-r--r--DESCRIPTION2
-rw-r--r--NAMESPACE2
-rw-r--r--R/FOCUS_PELMO_data.R14
-rw-r--r--R/PELMO_runs.R163
-rw-r--r--_pkgdown.yml3
-rw-r--r--docs/reference/FOCUS_GW_scenarios_2012.html10
-rw-r--r--docs/reference/FOCUS_PELMO_crop_sze_names.html121
-rw-r--r--docs/reference/FOCUS_PELMO_crops.html132
-rw-r--r--docs/reference/FOCUS_PELMO_location_codes.html113
-rw-r--r--docs/reference/PELMO_path.html112
-rw-r--r--docs/reference/PELMO_runs.html144
-rw-r--r--docs/reference/create_run_list.html116
-rw-r--r--docs/reference/evaluate_PELMO.html116
-rw-r--r--docs/reference/focus_80th.html113
-rw-r--r--docs/reference/get_flux.html101
-rw-r--r--docs/reference/get_interval.html101
-rw-r--r--docs/reference/index.html11
-rw-r--r--docs/reference/run_PELMO.html119
-rw-r--r--docs/reference/sum_periods.html101
-rw-r--r--man/FOCUS_PELMO_crops.Rd4
-rw-r--r--man/PELMO_runs.Rd17
-rw-r--r--man/focus_80th.Rd19
-rw-r--r--man/get_flux.Rd11
-rw-r--r--man/get_interval.Rd11
-rw-r--r--man/run_PELMO.Rd27
-rw-r--r--man/sum_periods.Rd11
-rw-r--r--tests/testthat/test_PELMO.R74
28 files changed, 1717 insertions, 80 deletions
diff --git a/ChangeLog b/ChangeLog
index 762acf3..38beb77 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,32 @@
+commit 15c1b8c5ddadf938ce13d3dd9da2a09d8749f740
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date: 2017-01-29 16:58:53 +0100
+
+ Setting up PELMO runs, execution and evaluation
+
+ It all works!
+
+commit bc97a35a32c4f47e29364488a3601f94c6e68d45
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date: 2017-01-27 18:33:45 +0100
+
+ Really use all scenarios in test data
+
+ Maize, that was used in the last commit, is not parameterised for
+ Jokioinen
+
+commit a4081ddfea726283874968c0b62a7f46e4fd1232
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date: 2017-01-27 18:23:35 +0100
+
+ Use all scenarios in the test data
+
+commit 3c82d26206e2f2e74600acd71a49c70eaed555c4
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date: 2017-01-27 08:17:08 +0100
+
+ Also test run with metabolites
+
commit 8fd050e57b7babfbdb1ccfabb468a0398396d466
Author: Johannes Ranke <jranke@uni-bremen.de>
Date: 2017-01-27 07:54:53 +0100
diff --git a/DESCRIPTION b/DESCRIPTION
index 81f8df2..97b5962 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: pfm
Type: Package
Title: Utilities for Pesticide Fate Modelling
Version: 0.4-2
-Date: 2017-01-27
+Date: 2017-01-29
Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de",
role = c("aut", "cre", "cph"))
Description: Utilities for simple calculations of predicted environmental
diff --git a/NAMESPACE b/NAMESPACE
index c795c89..feb5ca7 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -26,6 +26,8 @@ export(SFO_actual_twa)
export(SSLRC_mobility_classification)
export(TOXSWA_cwa)
export(endpoint)
+export(evaluate_PELMO)
+export(focus_80th)
export(geomean)
export(max_twa)
export(one_box)
diff --git a/R/FOCUS_PELMO_data.R b/R/FOCUS_PELMO_data.R
index 28888e7..89fe5f6 100644
--- a/R/FOCUS_PELMO_data.R
+++ b/R/FOCUS_PELMO_data.R
@@ -2,10 +2,10 @@
#'
#' 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
+#' 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}.
-#'
+#'
#' @docType data
#' @export
#' @examples
@@ -37,13 +37,13 @@ FOCUS_PELMO_crops = c(
tom = "Tomatoes",
vin = "Vines")
-#' FOCUS PELMO crop acronyms used for naming sceneario files
+#' FOCUS PELMO crop acronyms used for naming sceneario files
#'
#' 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.
-#'
+#'
#' @docType data
#' @export
#' @examples
@@ -85,6 +85,6 @@ FOCUS_PELMO_crop_sze_names = c(
#' @examples
#' print(FOCUS_PELMO_location_codes)
FOCUS_PELMO_location_codes = c(
- Cha = "C", Ham = "H", Jok = "J",
- Kre = "K", Oke = "N", Pia = "P",
+ Cha = "C", Ham = "H", Jok = "J",
+ Kre = "K", Oke = "N", Pia = "P",
Por = "O", Sev = "S", Thi = "T")
diff --git a/R/PELMO_runs.R b/R/PELMO_runs.R
index f599110..5d401ea 100644
--- a/R/PELMO_runs.R
+++ b/R/PELMO_runs.R
@@ -1,7 +1,10 @@
#' Set up runs for FOCUS PELMO
#'
#' Per default, the runs are also executed with FOCUS PELMO, and the results are processed
-#' and returned.
+#' and returned. Currently, only FOCUS PELMO as installed on Linux (or other Unix systems)
+#' using the \code{\link{install_PELMO}} from the \code{PELMO.installeR} package
+#' maintained on github is supported. In such installations, FOCUS PELMO is installed into
+#' package installation directory of \code{PELMO.installeR} and run with \code{wine}.
#'
#' @param runs 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,
@@ -15,6 +18,9 @@
#' @param cores The number of cores to execute PELMO runs in parallel
#' @param evaluate Should the results be returned?
#' @param overwrite Should an existing run directories be overwritten
+#' @references PELMO.installeR \url{https://jranke.github.io/PELMO.installeR}
+#'
+#' Wine \url{https://winehq.org}
#' @export
PELMO_runs <- function(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "auto",
execute = TRUE, cores = getOption("mc.cores", 2L),
@@ -80,26 +86,9 @@ PELMO_runs <- function(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "aut
add <- function(x) cat(paste0(x, "\r\n"), file = input_file, append = TRUE)
- # How many years do we calculate (26, 46 or 66)?
- psm <- readLines(psm_file, encoding = "latin1")
- number_of_apps_lines <- grep("number of application location", psm)
- absolute_apps_line <- grep(location_code,
- psm[number_of_apps_lines])
- period <- 1 # application every year
- if (length(absolute_apps_line) == 1) {
- apps_root <- number_of_apps_lines[absolute_apps_line]
- } else {
- apps_root <- number_of_apps_lines[1]
- }
-
- number_of_apps <- as.integer(substr(psm[apps_root], 1, 3))
- last_app_line <- psm[apps_root + number_of_apps]
- last_app_year <- as.integer(gsub("^.{2,3} .. (..) .*", "\\1",
- last_app_line))
- if (last_app_year > 26) period <- 2
- if (last_app_year > 46) period <- 3
+ interval <- get_interval(psm_file, location_code)
- n_years <- switch(as.character(period),
+ n_years <- switch(as.character(interval),
"1" = 26,
"2" = 46,
"3" = 66)
@@ -145,18 +134,23 @@ PELMO_runs <- function(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "aut
# the exe file from this directory
file.copy(file.path(PELMO_base, "lf90.eer"), run_dir)
}
+ run_list[[7]]
+ setup_run(run_list[[7]])
lapply(run_list, setup_run)
if (execute) {
run_PELMO(runs, version = version, PELMO_base = PELMO_base)
}
+
+ if (evaluate) {
+ evaluate_PELMO(runs, version = version, PELMO_base = PELMO_base)
+ }
}
-#' Run PELMO
-#'
#' @inheritParams PELMO_runs
#' @importFrom parallel mclapply
+#' @rdname PELMO_runs
#' @export
run_PELMO <- function(runs, version = "5.5.3", PELMO_base = "auto",
cores = getOption("mc.cores", 2L))
@@ -295,3 +289,128 @@ create_run_list <- function(runs, psm_dir = ".", check_psm_files = FALSE) {
}
return(run_list)
}
+
+#' @rdname PELMO_runs
+#' @inheritParams PELMO_runs
+#' @importFrom parallel mclapply
+#' @export
+evaluate_PELMO <- function(runs, version = "5.5.3", PELMO_base = "auto")
+{
+
+ if (PELMO_base[1] == "auto") {
+ PELMO_base = file.path(system.file(package = "PELMO.installeR"),
+ paste0("FOCUSPELMO.", gsub("\\.", "", version)))
+ }
+
+ for (run in runs) {
+ psm <- run$psm
+ crops <- setdiff(names(run), "psm")
+ for (crop in crops) {
+ for (scenario in run[[crop]]) {
+ run_dir <- file.path(PELMO_base, "FOCUS", PELMO_path(psm, crop, scenario))
+ echo_file <- readLines(file.path(run_dir, "ECHO.PLM"), encoding = "latin1")
+ parm_lines <- grep("\\*\\*\\* PARAMETERS OF", echo_file, value = TRUE)
+ acronyms <- gsub(".*\\((.*)\\).*", "\\1", parm_lines)
+ met_codes <- gsub(".*METABOLITE (..).*", "\\1", parm_lines)
+ met_codes[1] <- NA
+ names(met_codes) <- acronyms
+
+ psm_file <- file.path(run_dir, paste0(psm, ".psm"))
+ location_code <- FOCUS_PELMO_location_codes[scenario]
+ interval <- get_interval(psm_file, location_code)
+
+ # Get percolate for each period
+ wasser <- readLines(file.path(run_dir, "WASSER.PLM"))
+ percolate_lines <- grep("RECHARGE BELOW ROOT ZONE", wasser, value = TRUE)
+ percolate <- as.numeric(substr(percolate_lines, 40, 46))
+ percolate_period <- sum_periods(percolate, interval)
+
+ # Set up results that should match period.plm generated by the PELMO GUI
+ results_pfm <- list()
+ for (acronym in acronyms) {
+ results_pfm[[acronym]] <- list()
+ periods <- data.frame(
+ period = 1:20,
+ flux = NA,
+ percolate = 10 * percolate_period,
+ conc = NA)
+
+ if (is.na(met_codes[acronym])) {
+ chem_file <- file.path(run_dir, "CHEM.PLM")
+ } else {
+ chem_file <- file.path(run_dir, paste0("CHEM_", met_codes[acronym], ".PLM"))
+ }
+
+ annual_flux <- get_flux(chem_file)
+ periods$flux <- sum_periods(annual_flux, interval) * 1000
+
+ periods$conc <- 100 * periods$flux / periods$percolate
+
+ results_pfm[[acronym]]$periods <- periods
+ results_pfm[[acronym]]$focus <- focus_80th(periods$conc)
+ }
+ save(results_pfm, file = file.path(run_dir, "period_pfm.rda"))
+ }
+ }
+ }
+}
+
+#' Get the application interval in years from a psm file
+get_interval <- function(psm_file, location_code) {
+ # How many years do we calculate (26, 46 or 66)?
+ psm <- readLines(psm_file, encoding = "latin1")
+ number_of_apps_lines <- grep("number of application location", psm)
+ absolute_apps_line <- grep(location_code,
+ psm[number_of_apps_lines])
+ interval <- 1 # application every year
+ if (length(absolute_apps_line) == 1) {
+ apps_root <- number_of_apps_lines[absolute_apps_line]
+ } else {
+ apps_root <- number_of_apps_lines[1]
+ }
+
+ number_of_apps <- as.integer(substr(psm[apps_root], 1, 3))
+ last_app_line <- psm[apps_root + number_of_apps]
+ last_app_year <- as.integer(gsub("^.{2,3} .. (..) .*", "\\1",
+ last_app_line))
+ if (last_app_year > 26) interval <- 2
+ if (last_app_year > 46) interval <- 3
+ return(interval)
+}
+
+#' Sum up values according to FOCUS periods
+sum_periods <- function(annual, interval) {
+ n_years <- switch(as.character(interval),
+ "1" = 26,
+ "2" = 46,
+ "3" = 66)
+ period_start_years <- seq(from = 7, to = n_years, by = interval)
+ sapply(1:20, function(x) {
+ years_i <- period_start_years[x] + (0 : (interval - 1))
+ sum(annual[years_i])
+ })
+}
+
+#' Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file
+get_flux <- function(chem_file) {
+ chem <- readLines(chem_file)
+ lowest_focus_comp_lines <- grep("^ . 21 ", chem, value = TRUE)
+ lowest_focus_comp <- read.table(text = lowest_focus_comp_lines)
+ return(lowest_focus_comp$V9)
+}
+
+#' Calculate the 80th percentile according to FOCUS guidance
+#'
+#' 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.
+#' @param c_period A numeric vector of values to calculate the percentile from
+#' @param old Should the old calculation method be used (the 17th highest value)?
+#' @export
+focus_80th <- function(c_period, old = FALSE) {
+ c_period <- ifelse(is.na(c_period), 0, c_period)
+ c_period_sorted <- sort(c_period)
+ if (old) return(c_period_sorted[17])
+ else return(mean(c_period_sorted[c(16, 17)]))
+}
diff --git a/_pkgdown.yml b/_pkgdown.yml
index ff5f43d..829ba48 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -17,6 +17,9 @@ reference:
contents:
- PEC_soil
- soil_scenario_data_EFSA_2015
+ - title: Predicted environmental concentrations in groundwater
+ contents:
+ - PELMO_runs
- title: Predicted environmental concentrations in surface water
contents:
- PEC_sw_drift
diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html
index 64b42e9..fbc1649 100644
--- a/docs/reference/FOCUS_GW_scenarios_2012.html
+++ b/docs/reference/FOCUS_GW_scenarios_2012.html
@@ -70,10 +70,16 @@
</div>
- <p>Currently, only a small subset of the soil definitions are provided.</p>
+ <p>Currently, only scenario names with acronyms and a small subset of the soil definitions are provided. The
+soil definitions are from page 46ff. from FOCUS (2012).</p>
+ <pre><span class='no'>FOCUS_GW_scenarios_2012</span></pre>
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>An object of class <code>list</code> of length 2.</p>
+
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1.
@@ -147,6 +153,8 @@
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
+ <li><a href="#format">Format</a></li>
+
<li><a href="#references">References</a></li>
<li><a href="#examples">Examples</a></li>
diff --git a/docs/reference/FOCUS_PELMO_crop_sze_names.html b/docs/reference/FOCUS_PELMO_crop_sze_names.html
new file mode 100644
index 0000000..5777868
--- /dev/null
+++ b/docs/reference/FOCUS_PELMO_crop_sze_names.html
@@ -0,0 +1,121 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>FOCUS PELMO crop acronyms used for naming sceneario files — FOCUS_PELMO_crop_sze_names • pfm</title>
+
+<!-- jquery -->
+<script 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://cdn.mathjax.org/mathjax/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>FOCUS PELMO crop acronyms used for naming sceneario files</h1>
+ </div>
+
+
+ <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>
+
+
+ <pre><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; &quot;apples&quot; &quot;grass&quot; &quot;potato&quot; &quot;sbeets&quot; &quot;wcerea&quot; &quot;beans&quot; &quot;beans&quot; &quot;bushb&quot;
+#&gt; cab car cit cot lin mai soi woi
+#&gt; &quot;cabbag&quot; &quot;carrot&quot; &quot;citrus&quot; &quot;cotton&quot; &quot;linse&quot; &quot;maize&quot; &quot;rapesu&quot; &quot;rapewi&quot;
+#&gt; oni ape soy spr str sun tob tom
+#&gt; &quot;onions&quot; &quot;peas&quot; &quot;soyb&quot; &quot;scerea&quot; &quot;strawb&quot; &quot;sunflo&quot; &quot;tobacc&quot; &quot;tomato&quot;
+#&gt; vin
+#&gt; &quot;vines&quot; </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://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/FOCUS_PELMO_crops.html b/docs/reference/FOCUS_PELMO_crops.html
new file mode 100644
index 0000000..d9ad8d2
--- /dev/null
+++ b/docs/reference/FOCUS_PELMO_crops.html
@@ -0,0 +1,132 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>FOCUS PELMO crop names — FOCUS_PELMO_crops • pfm</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/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>FOCUS PELMO crop names</h1>
+ </div>
+
+
+ <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. &#39;Peas (animals)&#39; has the code <code>ape</code>.</p>
+
+
+ <pre><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; &quot;Apples&quot; &quot;Grass and alfalfa&quot; &quot;Potatoes&quot;
+#&gt; sug win fbe
+#&gt; &quot;Sugar beets&quot; &quot;Winter cereals&quot; &quot;Beans (field)&quot;
+#&gt; vbe bus cab
+#&gt; &quot;Beans (vegetables)&quot; &quot;Bushberries&quot; &quot;Cabbage&quot;
+#&gt; car cit cot
+#&gt; &quot;Carrots&quot; &quot;Citrus&quot; &quot;Cotton&quot;
+#&gt; lin mai soi
+#&gt; &quot;Linseed&quot; &quot;Maize&quot; &quot;Oil seed rape (summer)&quot;
+#&gt; woi oni ape
+#&gt; &quot;Oil seed rape (winter)&quot; &quot;Onions&quot; &quot;Peas (animals)&quot;
+#&gt; soy spr str
+#&gt; &quot;Soybeans&quot; &quot;Spring cereals&quot; &quot;Strawberries&quot;
+#&gt; sun tob tom
+#&gt; &quot;Sunflower&quot; &quot;Tobacco&quot; &quot;Tomatoes&quot;
+#&gt; vin
+#&gt; &quot;Vines&quot; </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://hadley.github.io/pkgdown/">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
new file mode 100644
index 0000000..8051d42
--- /dev/null
+++ b/docs/reference/FOCUS_PELMO_location_codes.html
@@ -0,0 +1,113 @@
+<!-- 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">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/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>Location codes in FOCUS PELMO</h1>
+ </div>
+
+
+ <p>A named character vector of one letter location codes used in FOCUS PELMO,
+indexed by three letter acronyms.</p>
+
+
+ <pre><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; &quot;C&quot; &quot;H&quot; &quot;J&quot; &quot;K&quot; &quot;N&quot; &quot;P&quot; &quot;O&quot; &quot;S&quot; &quot;T&quot; </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://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/PELMO_path.html b/docs/reference/PELMO_path.html
new file mode 100644
index 0000000..79aa89d
--- /dev/null
+++ b/docs/reference/PELMO_path.html
@@ -0,0 +1,112 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Create a path of run directories as the PELMO GUI does — PELMO_path • pfm</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<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://cdn.mathjax.org/mathjax/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>Create a path of run directories as the PELMO GUI does</h1>
+ </div>
+
+
+ <p>Create a path of run directories as the PELMO GUI does</p>
+
+
+ <pre><span class='fu'>PELMO_path</span>(<span class='no'>psm</span>, <span class='no'>crop</span>, <span class='no'>scenario</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>psm</dt>
+ <dd>The psm identifier</dd>
+ <dt>crop</dt>
+ <dd>The PELMO crop acronym</dd>
+ <dt>scenario</dt>
+ <dd>The scenario</dd>
+ </dl>
+
+
+ </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://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html
new file mode 100644
index 0000000..e872196
--- /dev/null
+++ b/docs/reference/PELMO_runs.html
@@ -0,0 +1,144 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Set up runs for FOCUS PELMO — PELMO_runs • pfm</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/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>Set up runs for FOCUS PELMO</h1>
+ </div>
+
+
+ <p>Per default, the runs are also executed with FOCUS PELMO, and 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
+package installation directory of <code>PELMO.installeR</code> and run with <code>wine</code>.</p>
+
+
+ <pre><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>
+ <dl class="dl-horizontal">
+ <dt>runs</dt>
+ <dd>A list of lists. Each inner lists has an element named &#39;psm&#39;
+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>.</dd>
+ <dt>psm_dir</dt>
+ <dd>The directory where the psm files are located</dd>
+ <dt>version</dt>
+ <dd>The FOCUS PELMO version</dd>
+ <dt>PELMO_base</dt>
+ <dd>Where the FOCUS PELMO installation is located</dd>
+ <dt>execute</dt>
+ <dd>Should PELMO be executed directly?</dd>
+ <dt>cores</dt>
+ <dd>The number of cores to execute PELMO runs in parallel</dd>
+ <dt>evaluate</dt>
+ <dd>Should the results be returned?</dd>
+ <dt>overwrite</dt>
+ <dd>Should an existing run directories be overwritten</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>PELMO.installeR <a href = 'https://jranke.github.io/PELMO.installeR'>https://jranke.github.io/PELMO.installeR</a></p>
+ <p>Wine <a href = 'https://winehq.org'>https://winehq.org</a></p>
+
+
+ </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="#references">References</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/create_run_list.html b/docs/reference/create_run_list.html
new file mode 100644
index 0000000..b2c9798
--- /dev/null
+++ b/docs/reference/create_run_list.html
@@ -0,0 +1,116 @@
+<!-- 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">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/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>Create a list of runs that we can traverse</h1>
+ </div>
+
+
+ <p>Create a list of runs that we can traverse</p>
+
+
+ <pre><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>
+ <dl class="dl-horizontal">
+ <dt>runs</dt>
+ <dd>A list of lists. Each inner lists has an element named &#39;psm&#39;
+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>.</dd>
+ <dt>psm_dir</dt>
+ <dd>The directory where the psm files are located</dd>
+ <dt>check_psm_files</dt>
+ <dd>Should we check if the psm file exists</dd>
+ </dl>
+
+
+ </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://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/evaluate_PELMO.html b/docs/reference/evaluate_PELMO.html
new file mode 100644
index 0000000..58e7843
--- /dev/null
+++ b/docs/reference/evaluate_PELMO.html
@@ -0,0 +1,116 @@
+<!-- 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>Evaluate PELMO runs — evaluate_PELMO • 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://cdn.mathjax.org/mathjax/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>Evaluate PELMO runs</h1>
+ </div>
+
+
+ <p>Evaluate PELMO runs</p>
+
+
+ <pre><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>
+ <dl class="dl-horizontal">
+ <dt>runs</dt>
+ <dd>A list of lists. Each inner lists has an element named &#39;psm&#39;
+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>.</dd>
+ <dt>version</dt>
+ <dd>The FOCUS PELMO version</dd>
+ <dt>PELMO_base</dt>
+ <dd>Where the FOCUS PELMO installation is located</dd>
+ </dl>
+
+
+ </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://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/focus_80th.html b/docs/reference/focus_80th.html
new file mode 100644
index 0000000..8160746
--- /dev/null
+++ b/docs/reference/focus_80th.html
@@ -0,0 +1,113 @@
+<!-- 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">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/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>Calculate the 80th percentile according to FOCUS guidance</h1>
+ </div>
+
+
+ <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>
+
+
+ <pre><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>
+ <dl class="dl-horizontal">
+ <dt>c_period</dt>
+ <dd>A numeric vector of values to calculate the percentile from</dd>
+ <dt>old</dt>
+ <dd>Should the old calculation method be used (the 17th highest value)?</dd>
+ </dl>
+
+
+ </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://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/get_flux.html b/docs/reference/get_flux.html
new file mode 100644
index 0000000..64ea25e
--- /dev/null
+++ b/docs/reference/get_flux.html
@@ -0,0 +1,101 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file — get_flux • pfm</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link 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://cdn.mathjax.org/mathjax/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>Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file</h1>
+ </div>
+
+
+ <p>Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file</p>
+
+
+ <pre><span class='fu'>get_flux</span>(<span class='no'>chem_file</span>)</pre>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ </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/get_interval.html b/docs/reference/get_interval.html
new file mode 100644
index 0000000..13171c1
--- /dev/null
+++ b/docs/reference/get_interval.html
@@ -0,0 +1,101 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Get the application interval in years from a psm file — get_interval • pfm</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" 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://cdn.mathjax.org/mathjax/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>Get the application interval in years from a psm file</h1>
+ </div>
+
+
+ <p>Get the application interval in years from a psm file</p>
+
+
+ <pre><span class='fu'>get_interval</span>(<span class='no'>psm_file</span>, <span class='no'>location_code</span>)</pre>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ </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/index.html b/docs/reference/index.html
index 8f57cd2..33713b6 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -67,7 +67,7 @@
<div class="col-md-9">
<div class="page-header">
<h1>Function reference</h1>
- <h4>version&nbsp;0.4-1</h4>
+ <h4>version&nbsp;0.4-2</h4>
</div>
<div class="contents">
@@ -117,6 +117,14 @@
<ul>
<li><code><a href="soil_scenario_data_EFSA_2015.html">soil_scenario_data_EFSA_2015</a></code></li>
</ul>
+ <h2 id="section-predicted-environmental-concentrations-in-groundwater" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-groundwater" class="anchor"></a>Predicted environmental concentrations in groundwater</h2>
+ <p class="section-desc"></p>
+
+
+ <p><a href="PELMO_runs.html">Set up runs for FOCUS PELMO</a></p>
+ <ul>
+ <li><code><a href="PELMO_runs.html">PELMO_runs</a></code></li><li><code><a href="PELMO_runs.html">run_PELMO</a></code></li><li><code><a href="PELMO_runs.html">evaluate_PELMO</a></code></li>
+ </ul>
<h2 id="section-predicted-environmental-concentrations-in-surface-water" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-surface-water" class="anchor"></a>Predicted environmental concentrations in surface water</h2>
<p class="section-desc"></p>
@@ -173,6 +181,7 @@
<ul class="nav nav-pills nav-stacked">
<li><a href="#section-general-utility-functions">General utility functions</a></li>
<li><a href="#section-predicted-environmental-concentrations-in-soil">Predicted environmental concentrations in soil</a></li>
+ <li><a href="#section-predicted-environmental-concentrations-in-groundwater">Predicted environmental concentrations in groundwater</a></li>
<li><a href="#section-predicted-environmental-concentrations-in-surface-water">Predicted environmental concentrations in surface water</a></li>
<li><a href="#section-classifications-and-indicators">Classifications and indicators</a></li>
</ul>
diff --git a/docs/reference/run_PELMO.html b/docs/reference/run_PELMO.html
new file mode 100644
index 0000000..067d3c1
--- /dev/null
+++ b/docs/reference/run_PELMO.html
@@ -0,0 +1,119 @@
+<!-- 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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+<title>Run PELMO — run_PELMO • pfm</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
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+<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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+<!-- Font Awesome icons -->
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+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
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+<script src="../pkgdown.js"></script>
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+<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>Run PELMO</h1>
+ </div>
+
+
+ <p>Run PELMO</p>
+
+
+ <pre><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>))</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>runs</dt>
+ <dd>A list of lists. Each inner lists has an element named &#39;psm&#39;
+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>.</dd>
+ <dt>version</dt>
+ <dd>The FOCUS PELMO version</dd>
+ <dt>PELMO_base</dt>
+ <dd>Where the FOCUS PELMO installation is located</dd>
+ <dt>cores</dt>
+ <dd>The number of cores to execute PELMO runs in parallel</dd>
+ </dl>
+
+
+ </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://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/sum_periods.html b/docs/reference/sum_periods.html
new file mode 100644
index 0000000..66466ac
--- /dev/null
+++ b/docs/reference/sum_periods.html
@@ -0,0 +1,101 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Sum up values according to FOCUS periods — sum_periods • 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://cdn.mathjax.org/mathjax/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>Sum up values according to FOCUS periods</h1>
+ </div>
+
+
+ <p>Sum up values according to FOCUS periods</p>
+
+
+ <pre><span class='fu'>sum_periods</span>(<span class='no'>annual</span>, <span class='no'>interval</span>)</pre>
+
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ </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/man/FOCUS_PELMO_crops.Rd b/man/FOCUS_PELMO_crops.Rd
index f6a41b4..91a010a 100644
--- a/man/FOCUS_PELMO_crops.Rd
+++ b/man/FOCUS_PELMO_crops.Rd
@@ -11,8 +11,8 @@ FOCUS_PELMO_crops
\description{
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
+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}.
}
\examples{
diff --git a/man/PELMO_runs.Rd b/man/PELMO_runs.Rd
index 71fe6ef..1d81e6d 100644
--- a/man/PELMO_runs.Rd
+++ b/man/PELMO_runs.Rd
@@ -2,11 +2,18 @@
% Please edit documentation in R/PELMO_runs.R
\name{PELMO_runs}
\alias{PELMO_runs}
+\alias{run_PELMO}
+\alias{evaluate_PELMO}
\title{Set up runs for FOCUS PELMO}
\usage{
PELMO_runs(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "auto",
execute = TRUE, cores = getOption("mc.cores", 2L), evaluate = TRUE,
overwrite = FALSE)
+
+run_PELMO(runs, version = "5.5.3", PELMO_base = "auto",
+ cores = getOption("mc.cores", 2L))
+
+evaluate_PELMO(runs, version = "5.5.3", PELMO_base = "auto")
}
\arguments{
\item{runs}{A list of lists. Each inner lists has an element named 'psm'
@@ -31,5 +38,13 @@ as used in \code{\link{FOCUS_GW_scenarios_2012}}.}
}
\description{
Per default, the runs are also executed with FOCUS PELMO, and the results are processed
-and returned.
+and returned. Currently, only FOCUS PELMO as installed on Linux (or other Unix systems)
+using the \code{\link{install_PELMO}} from the \code{PELMO.installeR} package
+maintained on github is supported. In such installations, FOCUS PELMO is installed into
+package installation directory of \code{PELMO.installeR} and run with \code{wine}.
+}
+\references{
+PELMO.installeR \url{https://jranke.github.io/PELMO.installeR}
+
+Wine \url{https://winehq.org}
}
diff --git a/man/focus_80th.Rd b/man/focus_80th.Rd
new file mode 100644
index 0000000..8436791
--- /dev/null
+++ b/man/focus_80th.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/PELMO_runs.R
+\name{focus_80th}
+\alias{focus_80th}
+\title{Calculate the 80th percentile according to FOCUS guidance}
+\usage{
+focus_80th(c_period, old = FALSE)
+}
+\arguments{
+\item{c_period}{A numeric vector of values to calculate the percentile from}
+
+\item{old}{Should the old calculation method be used (the 17th highest value)?}
+}
+\description{
+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.
+}
diff --git a/man/get_flux.Rd b/man/get_flux.Rd
new file mode 100644
index 0000000..93778cb
--- /dev/null
+++ b/man/get_flux.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/PELMO_runs.R
+\name{get_flux}
+\alias{get_flux}
+\title{Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file}
+\usage{
+get_flux(chem_file)
+}
+\description{
+Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file
+}
diff --git a/man/get_interval.Rd b/man/get_interval.Rd
new file mode 100644
index 0000000..a751996
--- /dev/null
+++ b/man/get_interval.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/PELMO_runs.R
+\name{get_interval}
+\alias{get_interval}
+\title{Get the application interval in years from a psm file}
+\usage{
+get_interval(psm_file, location_code)
+}
+\description{
+Get the application interval in years from a psm file
+}
diff --git a/man/run_PELMO.Rd b/man/run_PELMO.Rd
deleted file mode 100644
index a286c5c..0000000
--- a/man/run_PELMO.Rd
+++ /dev/null
@@ -1,27 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/PELMO_runs.R
-\name{run_PELMO}
-\alias{run_PELMO}
-\title{Run PELMO}
-\usage{
-run_PELMO(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "auto",
- cores = getOption("mc.cores", 2L))
-}
-\arguments{
-\item{runs}{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{\link{FOCUS_PELMO_crops}},
-that hold character vectors of three letter scenario acronyms
-as used in \code{\link{FOCUS_GW_scenarios_2012}}.}
-
-\item{psm_dir}{The directory where the psm files are located}
-
-\item{version}{The FOCUS PELMO version}
-
-\item{PELMO_base}{Where the FOCUS PELMO installation is located}
-
-\item{cores}{The number of cores to execute PELMO runs in parallel}
-}
-\description{
-Run PELMO
-}
diff --git a/man/sum_periods.Rd b/man/sum_periods.Rd
new file mode 100644
index 0000000..5051af4
--- /dev/null
+++ b/man/sum_periods.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/PELMO_runs.R
+\name{sum_periods}
+\alias{sum_periods}
+\title{Sum up values according to FOCUS periods}
+\usage{
+sum_periods(annual, interval)
+}
+\description{
+Sum up values according to FOCUS periods
+}
diff --git a/tests/testthat/test_PELMO.R b/tests/testthat/test_PELMO.R
index 7b7e2b6..ab0e37a 100644
--- a/tests/testthat/test_PELMO.R
+++ b/tests/testthat/test_PELMO.R
@@ -17,40 +17,33 @@ runs <- list(
pot = c("Cha", "Ham")),
list(
psm = "Pesticide_D_1_May_every_other_year_mets",
- mai = c("Cha")))
-
+ win = names(FOCUS_GW_scenarios_2012$names)))
test_that("PELMO paths are correctly created", {
psm_paths = c(
PELMO_path(runs[[1]]$psm, "fbe", "Por"),
PELMO_path(runs[[2]]$psm, "pot", "Ham"),
- PELMO_path(runs[[3]]$psm, "mai", "Cha"))
+ PELMO_path(runs[[3]]$psm, "win", "Cha"))
- # Check for psm files and put them into PELMO_base
- psm_new_locations <- character(0)
for (i in seq_along(psm_paths)) {
psm_file <- file.path(test_dir, psm_paths[i], paste0(runs[[i]]$psm, ".psm"))
expect_true(file.exists(psm_file))
psm_new_location <- file.path(PELMO_base, basename(psm_file))
- psm_new_locations[i] <- psm_new_location
- file.copy(psm_file, psm_new_location)
+ file.copy(psm_file, psm_new_location, overwrite = TRUE)
}
})
test_that("PELMO runs are correctly set up", {
# Prepare runs in analogy to the test archive
- PELMO_runs(runs, psm_dir = PELMO_base, execute = FALSE, overwrite = TRUE)
+ PELMO_runs(runs, psm_dir = PELMO_base, execute = FALSE, evaluate = FALSE, overwrite = TRUE)
# Check that input files are correctly generated in the right location
for (run in runs) {
psm <- run$psm
- # message(psm)
crops <- setdiff(names(run), "psm")
for (crop in crops) {
- # message(crop)
for (scenario in run[[crop]]) {
- # message(scenario)
pp <- PELMO_path(psm, crop, scenario)
input_new <- readLines(file.path(PELMO_base, "FOCUS", pp, "pelmo.inp"))
@@ -64,7 +57,7 @@ test_that("PELMO runs are correctly set up", {
})
test_that("PELMO runs can be run and give the expected result files", {
- run_PELMO(runs, cores = 5)
+ run_PELMO(runs, cores = 7)
plm_files <- c("CHEM.PLM", "ECHO.PLM",
"KONZCHEM.PLM", "KONZC_A1", "KONZC_B1",
@@ -75,9 +68,7 @@ test_that("PELMO runs can be run and give the expected result files", {
psm <- run$psm
crops <- setdiff(names(run), "psm")
for (crop in crops) {
- # message(crop)
for (scenario in run[[crop]]) {
- # message(scenario)
pp <- PELMO_path(psm, crop, scenario)
for (plm in plm_files) {
@@ -95,10 +86,57 @@ test_that("PELMO runs can be run and give the expected result files", {
})
test_that("PELMO runs are correctly evaluated", {
- evaluate_PELMO(runs, psm_dir = PELMO_base)
+ results <- evaluate_PELMO(runs)
+ # Check that if output is the same as in the test archive
+ for (run in runs) {
+ psm <- run$psm
+ crops <- setdiff(names(run), "psm")
+ for (crop in crops) {
+ for (scenario in run[[crop]]) {
+ pp <- PELMO_path(psm, crop, scenario)
-})
+ period_file <- readLines(file.path(test_dir, pp, "period.plm"), encoding = "latin1")
+
+ result_lines <- grep("^\tResults for.*in the percolate at 1 m soil depth$", period_file)
+ acronyms <- gsub(".*\\((.*)\\).*", "\\1", period_file[result_lines])
+ names(result_lines) <- acronyms
+
+ results <- list()
+ for (acronym in acronyms) {
+ results[[acronym]] <- list()
+ conc_lines <- result_lines[acronym] + 5:24
+ tmp <- read.table(text = period_file[conc_lines], sep = "\t")
+ results[[acronym]]$periods <- data.frame(
+ period = as.integer(tmp$V2),
+ flux = tmp$V3,
+ percolate = tmp$V4,
+ conc = tmp$V5)
+ tmp80 <- read.table(text = period_file[result_lines[acronym] + 27], sep = "\t")
+ results[[acronym]]$focus <- tmp80[[1, "V5"]]
+ }
-# Clean up
-unlink(psm_new_locations)
+ period_pfm_file <- file.path(PELMO_base, "FOCUS", pp, "period_pfm.rda")
+ load(period_pfm_file)
+
+ # Test for equality of all the components separately,
+ # as we need to adapt the tolerance
+ for (acronym in acronyms) {
+ p_pelmo <- results[[acronym]]$periods
+ p_test <- results_pfm[[acronym]]$periods
+ expect_equal(p_test$flux, p_pelmo$flux, tol = 1e-6, scale = 1)
+ expect_equal(p_test$percolate, p_pelmo$percolate)
+ # PELMO sets the concentration to 0 when the percolate is zero.
+ # We get NaN, which is more reasonable, but we need to
+ # take this into account for testing
+ p_test$conc <- ifelse(is.na(p_test$conc), 0, p_test$conc)
+ expect_equal(p_test$conc, p_pelmo$conc, tol = 1e-3, scale = 1)
+
+ # FOCUS PEC
+ expect_equal(results_pfm[[acronym]]$focus, results[[acronym]]$focus,
+ tol = 1e-3, scale = 1)
+ }
+ }
+ }
+ }
+})

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