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-rw-r--r--GNUmakefile4
-rw-r--r--R/twa.R10
-rw-r--r--_pkgdown.yml32
-rw-r--r--docs/FOCUS_GW_scenarios_2012.html157
-rw-r--r--docs/GUS.html171
-rw-r--r--docs/PEC_soil.html231
-rw-r--r--docs/PEC_sw_drainage_UK.html127
-rw-r--r--docs/PEC_sw_drift.html134
-rw-r--r--docs/PEC_sw_sed.html131
-rw-r--r--docs/SFO_actual_twa.html126
-rw-r--r--docs/SSLRC_mobility_classification.html119
-rw-r--r--docs/TOXSWA_cwa.html179
-rw-r--r--docs/authors.html97
-rw-r--r--docs/css/bootstrap-responsive.css815
-rw-r--r--docs/css/bootstrap-responsive.min.css9
-rw-r--r--docs/css/bootstrap.css4983
-rw-r--r--docs/css/bootstrap.min.css9
-rw-r--r--docs/css/highlight.css28
-rw-r--r--docs/css/staticdocs.css25
-rw-r--r--docs/drift_data_JKI.html242
-rw-r--r--docs/endpoint.html158
-rw-r--r--docs/geomean.html121
-rw-r--r--docs/img/glyphicons-halflings-white.pngbin8777 -> 0 bytes
-rw-r--r--docs/img/glyphicons-halflings.pngbin13826 -> 0 bytes
-rw-r--r--docs/index.html257
-rw-r--r--docs/jquery.sticky-kit.min.js9
-rw-r--r--docs/js/bootstrap.js1825
-rw-r--r--docs/js/bootstrap.min.js6
-rw-r--r--docs/link.svg12
-rw-r--r--docs/pfm_degradation.html123
-rw-r--r--docs/pkgdown.css113
-rw-r--r--docs/pkgdown.js8
-rw-r--r--docs/plot.TOXSWA_cwa-2.pngbin7409 -> 0 bytes
-rw-r--r--docs/plot.TOXSWA_cwa.html124
-rw-r--r--docs/read.TOXSWA_cwa.html142
-rw-r--r--docs/reference.html164
-rw-r--r--docs/reference/FOCUS_GW_scenarios_2012.html171
-rw-r--r--docs/reference/GUS.html181
-rw-r--r--docs/reference/PEC_soil.html229
-rw-r--r--docs/reference/PEC_sw_drainage_UK.html137
-rw-r--r--docs/reference/PEC_sw_drift.html144
-rw-r--r--docs/reference/PEC_sw_sed.html142
-rw-r--r--docs/reference/SFO_actual_twa.html138
-rw-r--r--docs/reference/SSLRC_mobility_classification.html129
-rw-r--r--docs/reference/TOXSWA_cwa.html178
-rw-r--r--docs/reference/drift_data_JKI.html255
-rw-r--r--docs/reference/endpoint.html170
-rw-r--r--docs/reference/geomean.html127
-rw-r--r--docs/reference/index.html195
-rw-r--r--docs/reference/max_twa.html116
-rw-r--r--docs/reference/one_box-12.pngbin0 -> 9901 bytes
-rw-r--r--docs/reference/one_box-2.pngbin0 -> 5783 bytes
-rw-r--r--docs/reference/one_box-4.pngbin0 -> 5743 bytes
-rw-r--r--docs/reference/one_box-6.pngbin0 -> 5743 bytes
-rw-r--r--docs/reference/one_box-8.pngbin0 -> 9901 bytes
-rw-r--r--docs/reference/one_box.html137
-rw-r--r--docs/reference/pfm_degradation.html136
-rw-r--r--docs/reference/plot.TOXSWA_cwa-2.pngbin0 -> 7427 bytes
-rw-r--r--docs/reference/plot.TOXSWA_cwa.html138
-rw-r--r--docs/reference/plot.one_box-2.pngbin0 -> 10136 bytes
-rw-r--r--docs/reference/plot.one_box.html131
-rw-r--r--docs/reference/read.TOXSWA_cwa.html154
-rw-r--r--docs/reference/sawtooth-2.pngbin0 -> 6175 bytes
-rw-r--r--docs/reference/sawtooth-6.pngbin0 -> 13603 bytes
-rw-r--r--docs/reference/sawtooth-8.pngbin0 -> 13603 bytes
-rw-r--r--docs/reference/sawtooth.html142
-rw-r--r--docs/reference/soil_scenario_data_EFSA_2015.html157
-rw-r--r--docs/reference/twa.html138
-rw-r--r--docs/soil_scenario_data_EFSA_2015.html144
-rw-r--r--man/max_twa.Rd2
-rw-r--r--man/one_box.Rd4
-rw-r--r--man/sawtooth.Rd2
-rw-r--r--man/twa.Rd2
73 files changed, 3840 insertions, 10450 deletions
diff --git a/GNUmakefile b/GNUmakefile
index 5d396fc..f449880 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -26,10 +26,10 @@ roxygen:
"$(R_HOME)/bin/Rscript" -e 'library(devtools); document()'
@echo "DONE."
-sd: roxygen
+pd: roxygen
@echo "Building static documentation..."
# suppressWarnings to get rid of mbcsToSbcs warnings when plotting the 'µ' character
- "$(R_HOME)/bin/Rscript" -e 'suppressWarnings(staticdocs::build_site())'
+ "$(R_HOME)/bin/Rscript" -e 'suppressWarnings(pkgdown::build_site())'
@echo "DONE."
$(TGZ): $(pkgfiles)
diff --git a/R/twa.R b/R/twa.R
index 3865fd7..e14318f 100644
--- a/R/twa.R
+++ b/R/twa.R
@@ -35,13 +35,13 @@
#'
#' # Use a fitted mkinfit model
#' require(mkin)
-#' fit <- mkinfit("FOMC", FOCUS_2006_C)
+#' fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
#' pred_1 <- one_box(fit)
#' plot(pred_1)
#'
#' # Use a model with more than one observed variable
#' m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
-#' fit_2 <- mkinfit(m_2, FOCUS_2006_D)
+#' fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE)
#' pred_2 <- one_box(fit_2)
#' plot(pred_2)
one_box <- function(x,
@@ -138,7 +138,7 @@ plot.one_box <- function(x,
#' plot(sawtooth(pred, applications = applications))
#'
#' m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
-#' fit_2 <- mkinfit(m_2, FOCUS_2006_D)
+#' fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE)
#' pred_2 <- one_box(fit_2)
#' pred_2_saw <- sawtooth(pred_2, 2, 7)
#' plot(pred_2_saw, max_twa = 21, max_twa_var = "m1")
@@ -178,7 +178,7 @@ sawtooth <- function(x, n = 1, i = 365,
#'
#' @param x An object of type \code{\link{one_box}}
#' @param window The size of the moving window
-#' @seealso max_twa
+#' @seealso \code{\link{max_twa}}
#' @export
#' @examples
#' pred <- sawtooth(one_box(10),
@@ -200,7 +200,7 @@ twa.one_box <- function(x, window = 21)
#' The maximum time weighted average concentration for a moving window
#'
-#' @seealso twa
+#' @seealso \code{\link{twa}}
#' @inheritParams twa
#' @export
max_twa <- function(x, window = 21) UseMethod("max_twa")
diff --git a/_pkgdown.yml b/_pkgdown.yml
new file mode 100644
index 0000000..ff5f43d
--- /dev/null
+++ b/_pkgdown.yml
@@ -0,0 +1,32 @@
+title: pfm
+
+template:
+ bootswatch: spacelab
+
+reference:
+ - title: General utility functions
+ desc: Functions that are independent of specific fate modelling areas
+ contents:
+ - geomean
+ - one_box
+ - plot.one_box
+ - sawtooth
+ - twa
+ - max_twa
+ - title: Predicted environmental concentrations in soil
+ contents:
+ - PEC_soil
+ - soil_scenario_data_EFSA_2015
+ - title: Predicted environmental concentrations in surface water
+ contents:
+ - PEC_sw_drift
+ - drift_data_JKI
+ - PEC_sw_drainage_UK
+ - TOXSWA_cwa
+ - read.TOXSWA_cwa
+ - plot.TOXSWA_cwa
+ - title: Classifications and indicators
+ desc: Evaluating environmental fate properties
+ contents:
+ - SSLRC_mobility_classification
+ - GUS
diff --git a/docs/FOCUS_GW_scenarios_2012.html b/docs/FOCUS_GW_scenarios_2012.html
deleted file mode 100644
index 275e7e4..0000000
--- a/docs/FOCUS_GW_scenarios_2012.html
+++ /dev/null
@@ -1,157 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>FOCUS_GW_scenarios_2012. pfm 0.3-8</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="">
-
-<link href="css/bootstrap.css" rel="stylesheet">
-<link href="css/bootstrap-responsive.css" rel="stylesheet">
-<link href="css/highlight.css" rel="stylesheet">
-<link href="css/staticdocs.css" rel="stylesheet">
-
-<!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-<![endif]-->
-
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [ ['$','$'], ["\\(","\\)"] ],
- processEscapes: true
- }
- });
-</script>
-<script type="text/javascript"
- src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
- </head>
-
- <body>
- <div class="navbar">
- <div class="navbar-inner">
- <div class="container">
- <a class="brand" href="index.html">pfm 0.3-8</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html">Home</a></li>
- <li><a href="reference.html">Reference</a></li>
- </ul>
- </div>
- </div>
- </div>
-</div>
-
-
- <div class="container">
- <header>
-
- </header>
-
- <h1>A very small subset of the FOCUS Groundwater scenario defitions</h1>
-
-<div class="row">
- <div class="span8">
-
- <div class="Description">
- <h2>Description</h2>
-
- <p>Currently, only a small subset of the soil definitions are provided.</p>
-
- </div>
-
- <div class="References">
- <h2>References</h2>
-
- <p>FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1.
- FOrum for the Co-ordination of pesticde fate models and their USe.
- http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf</p>
-
- </div>
-
- <h2 id="examples">Examples</h2>
- <pre class="examples"><div class='input'><span class="symbol">FOCUS_GW_scenarios_2012</span></div>
-<div class='output'>$names
- Cha Ham Jok Kre Oke
- &quot;Châteaudun&quot; &quot;Hamburg&quot; &quot;Jokioinen&quot; &quot;Kremsmünster&quot; &quot;Okehampton&quot;
- Pia Por Sev Thi
- &quot;Piacenza&quot; &quot;Porto&quot; &quot;Sevilla&quot; &quot;Thiva&quot;
-
-$soils
- location horizon number pH_H2O perc_clay perc_oc rel_deg
-1 Cha Ap 1 8.0 30.0 1.39 1.0
-2 Cha B1 2 8.1 31.0 0.93 0.5
-3 Cha B2 3 8.2 25.0 0.70 0.5
-4 Cha II C1 4 8.5 26.0 0.30 0.3
-5 Cha II C1 5 8.5 26.0 0.30 0.0
-6 Cha II C2 6 8.5 24.0 0.27 0.0
-7 Cha M 7 8.3 31.0 0.21 0.0
-8 Ham Ap 1 6.4 7.2 1.50 1.0
-9 Ham BvI 2 5.6 6.7 1.00 0.5
-10 Ham BvII 3 5.6 0.9 0.20 0.3
-11 Ham Bv/Cv 4 5.7 0.0 0.00 0.3
-12 Ham Cv 5 5.5 0.0 0.00 0.3
-13 Ham Cv 6 5.5 0.0 0.00 0.0
-14 Jok Ap 1 6.2 3.6 4.06 1.0
-15 Jok Bs 2 5.6 1.8 0.84 0.5
-16 Jok BC1 3 5.4 1.2 0.36 0.3
-17 Jok BC2 4 5.4 1.7 0.29 0.3
-18 Jok BC2 5 5.4 1.7 0.29 0.0
-19 Jok Cg 6 5.3 1.9 0.21 0.0
-20 Kre &lt;NA&gt; 1 7.7 14.0 3.60 1.0
-21 Kre &lt;NA&gt; 2 7.0 25.0 1.00 0.5
-22 Kre &lt;NA&gt; 3 7.1 27.0 0.50 0.5
-23 Kre &lt;NA&gt; 4 7.1 27.0 0.50 0.3
-24 Kre &lt;NA&gt; 5 7.1 27.0 0.50 0.0
-25 Oke A 1 5.8 18.0 2.20 1.0
-26 Oke Bw1 2 6.3 17.0 0.70 0.5
-27 Oke BC 3 6.5 14.0 0.40 0.3
-28 Oke C 4 6.6 9.0 0.10 0.3
-29 Oke C 5 6.6 9.0 0.10 0.0
-30 Pia Ap 1 7.0 15.0 1.26 1.0
-31 Pia Ap 2 7.0 15.0 1.26 0.5
-32 Pia Bw 3 6.3 7.0 0.47 0.5
-33 Pia Bw 4 6.3 7.0 0.47 0.3
-34 Pia 2C 5 6.4 0.0 0.00 0.3
-35 Pia 2C 6 6.4 0.0 0.00 0.0
-36 Por &lt;NA&gt; 1 4.9 10.0 1.42 1.0
-37 Por &lt;NA&gt; 2 4.8 8.0 0.78 0.5
-38 Por &lt;NA&gt; 3 4.8 8.0 0.78 0.3
-39 Por &lt;NA&gt; 4 4.8 8.0 0.78 0.0
-40 Sev &lt;NA&gt; 1 7.3 14.0 0.93 1.0
-41 Sev &lt;NA&gt; 2 7.3 13.0 0.93 1.0
-42 Sev &lt;NA&gt; 3 7.8 15.0 0.70 0.5
-43 Sev &lt;NA&gt; 4 8.1 16.0 0.58 0.3
-44 Sev &lt;NA&gt; 5 8.1 16.0 0.58 0.0
-45 Sev &lt;NA&gt; 6 8.2 22.0 0.49 0.0
-46 Thi Ap1 1 7.7 25.3 0.74 1.0
-47 Thi Ap2 2 7.7 25.3 0.74 0.5
-48 Thi Bw 3 7.8 29.6 0.57 0.5
-49 Thi Bw 4 7.8 31.9 0.31 0.3
-50 Thi Ck1 5 7.8 32.9 0.18 0.3
-51 Thi Ck1 6 7.8 32.9 0.18 0.0
-
-</div></pre>
- </div>
- <div class="span4 sidebar">
- <!-- <ul>
- <li>FOCUS_GW_scenarios_2012</li>
- </ul>
- <ul>
-
- </ul> -->
-
-
-
-
- </div>
-</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
- </footer>
- </div>
- </body>
-</html> \ No newline at end of file
diff --git a/docs/GUS.html b/docs/GUS.html
deleted file mode 100644
index cb4e10e..0000000
--- a/docs/GUS.html
+++ /dev/null
@@ -1,171 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>GUS. pfm 0.3-8</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="
-Johannes Ranke
-">
-
-<link href="css/bootstrap.css" rel="stylesheet">
-<link href="css/bootstrap-responsive.css" rel="stylesheet">
-<link href="css/highlight.css" rel="stylesheet">
-<link href="css/staticdocs.css" rel="stylesheet">
-
-<!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-<![endif]-->
-
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [ ['$','$'], ["\\(","\\)"] ],
- processEscapes: true
- }
- });
-</script>
-<script type="text/javascript"
- src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
- </head>
-
- <body>
- <div class="navbar">
- <div class="navbar-inner">
- <div class="container">
- <a class="brand" href="index.html">pfm 0.3-8</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html">Home</a></li>
- <li><a href="reference.html">Reference</a></li>
- </ul>
- </div>
- </div>
- </div>
-</div>
-
-
- <div class="container">
- <header>
-
- </header>
-
- <h1>Groundwater ubiquity score based on Gustafson (1989)</h1>
-
-<div class="row">
- <div class="span8">
- <h2>Usage</h2>
- <pre><span class="functioncall"><a href='GUS.html'>GUS</a></span><span class="keyword">(</span><span class="symbol">...</span><span class="keyword">)</span>
-
-<span class="comment"># S3 method for numeric</span>
-<span class="functioncall"><a href='GUS.html'>GUS</a></span><span class="keyword">(</span><span class="symbol">DT50</span><span class="keyword">,</span> <span class="symbol">Koc</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span>
-
-<span class="comment"># S3 method for chent</span>
-<span class="functioncall"><a href='GUS.html'>GUS</a></span><span class="keyword">(</span><span class="symbol">chent</span><span class="keyword">,</span> <span class="argument">degradation_value</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"DT50ref"</span><span class="keyword">,</span>
- <span class="argument">lab_field</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"laboratory"</span><span class="keyword">,</span> <span class="argument">redox</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"aerobic"</span><span class="keyword">,</span> <span class="argument">sorption_value</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"Kfoc"</span><span class="keyword">,</span>
- <span class="argument">degradation_aggregator</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="symbol">geomean</span><span class="keyword">,</span> <span class="argument">sorption_aggregator</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="symbol">geomean</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span>
-
-<span class="comment"># S3 method for GUS_result</span>
-<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/print'>print</a></span><span class="keyword">(</span><span class="symbol">x</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">,</span> <span class="argument">digits</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">1</span><span class="keyword">)</span></pre>
-
- <h2>Arguments</h2>
- <dl>
- <dt>...</dt>
- <dd>Included in the generic to allow for further arguments later. Therefore
-this also had to be added to the specific methods.</dd>
- <dt>DT50</dt>
- <dd>Half-life of the chemical in soil. Should be a field
-half-life according to Gustafson (1989). However, leaching to the sub-soil
-can not completely be excluded in field dissipation experiments and Gustafson
-did not refer to any normalisation procedure, but says the field study should
-be conducted under use conditions.</dd>
- <dt>Koc</dt>
- <dd>The sorption constant normalised to organic carbon. Gustafson
-does not mention the nonlinearity of the sorption constant commonly
-found and usually described by Freundlich sorption, therefore it is
-unclear at which reference concentration the Koc should be observed
-(and if the reference concentration would be in soil or in porewater).</dd>
- <dt>chent</dt>
- <dd>If a chent is given with appropriate information present in its
-chyaml field, this information is used, with defaults specified below.</dd>
- <dt>degradation_value</dt>
- <dd>Which of the available degradation values should
-be used?</dd>
- <dt>lab_field</dt>
- <dd>Should laboratory or field half-lives be used? This
-defaults to lab in this implementation, in order to avoid
-double-accounting for mobility. If comparability with the original GUS
-values given by Gustafson (1989) is desired, non-normalised first-order
-field half-lives obtained under actual use conditions should be used.</dd>
- <dt>redox</dt>
- <dd>Aerobic or anaerobic degradation data</dd>
- <dt>sorption_value</dt>
- <dd>Which of the available sorption values should be used?
-Defaults to Kfoc as this is what is generally available from the European
-pesticide peer review process. These values generally use a reference
-concentration of 1 mg/L in porewater, that means they would be expected to
-be Koc values at a concentration of 1 mg/L in the water phase.</dd>
- <dt>degradation_aggregator</dt>
- <dd>Function for aggregating half-lives</dd>
- <dt>sorption_aggregator</dt>
- <dd>Function for aggregation Koc values</dd>
- <dt>x</dt>
- <dd>An object of class GUS_result to be printed</dd>
- <dt>digits</dt>
- <dd>The number of digits used in the print method</dd>
- </dl>
-
- <div class="Value">
- <h2>Value</h2>
-
- <p><dl>
-A list with the DT50 and Koc used as well as the resulting score
- of class GUS_result
-</dl></p>
-
- </div>
-
- <div class="Description">
- <h2>Description</h2>
-
- <p>The groundwater ubiquity score GUS is calculated according to
-the following equation
-$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$</p>
-
- </div>
-
- <div class="References">
- <h2>References</h2>
-
- <p>Gustafson, David I. (1989) Groundwater ubiquity score: a simple
-method for assessing pesticide leachability. <em>Environmental
-toxicology and chemistry</em> <b>8</b>(4) 339–57.</p>
-
- </div>
- </div>
- <div class="span4 sidebar">
- <!-- <ul>
- <li>GUS</li><li>GUS.chent</li><li>GUS.numeric</li><li>print.GUS_result</li>
- </ul>
- <ul>
-
- </ul> -->
-
-
-
- <h2>Author</h2>
-
-Johannes Ranke
-
-
- </div>
-</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
- </footer>
- </div>
- </body>
-</html> \ No newline at end of file
diff --git a/docs/PEC_soil.html b/docs/PEC_soil.html
deleted file mode 100644
index 9a10757..0000000
--- a/docs/PEC_soil.html
+++ /dev/null
@@ -1,231 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>PEC_soil. pfm 0.3-8</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="
-Johannes Ranke
-">
-
-<link href="css/bootstrap.css" rel="stylesheet">
-<link href="css/bootstrap-responsive.css" rel="stylesheet">
-<link href="css/highlight.css" rel="stylesheet">
-<link href="css/staticdocs.css" rel="stylesheet">
-
-<!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-<![endif]-->
-
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- <a class="brand" href="index.html">pfm 0.3-8</a>
- <div class="nav">
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- <li><a href="index.html">Home</a></li>
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- <header>
-
- </header>
-
- <h1>Calculate predicted environmental concentrations in soil</h1>
-
-<div class="row">
- <div class="span8">
- <h2>Usage</h2>
- <pre><span class="functioncall"><a href='PEC_soil.html'>PEC_soil</a></span><span class="keyword">(</span><span class="symbol">rate</span><span class="keyword">,</span> <span class="argument">rate_units</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"g/ha"</span><span class="keyword">,</span> <span class="argument">interception</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">0</span><span class="keyword">,</span> <span class="argument">mixing_depth</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">5</span><span class="keyword">,</span>
- <span class="argument">PEC_units</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"mg/kg"</span><span class="keyword">,</span> <span class="argument">PEC_pw_units</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"mg/L"</span><span class="keyword">,</span> <span class="argument">interval</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">NA</span><span class="keyword">,</span>
- <span class="argument">n_periods</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">Inf</span><span class="keyword">,</span> <span class="argument">tillage_depth</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">20</span><span class="keyword">,</span> <span class="argument">chent</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">NA</span><span class="keyword">,</span> <span class="argument">DT50</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">NA</span><span class="keyword">,</span>
- <span class="argument">Koc</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">NA</span><span class="keyword">,</span> <span class="argument">Kom</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="symbol">Koc</span><span class="keyword">/</span><span class="number">1.724</span><span class="keyword">,</span> <span class="argument">t_avg</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">0</span><span class="keyword">,</span> <span class="argument">scenarios</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"default"</span><span class="keyword">,</span>
- <span class="string">"EFSA_2015"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">porewater</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">)</span></pre>
-
- <h2>Arguments</h2>
- <dl>
- <dt>rate</dt>
- <dd>Application rate in units specified below</dd>
- <dt>rate_units</dt>
- <dd>Defaults to g/ha</dd>
- <dt>interception</dt>
- <dd>The fraction of the application rate that does not reach the soil</dd>
- <dt>mixing_depth</dt>
- <dd>Mixing depth in cm</dd>
- <dt>PEC_units</dt>
- <dd>Requested units for the calculated PEC. Only mg/kg currently supported</dd>
- <dt>PEC_pw_units</dt>
- <dd>Only mg/L currently supported</dd>
- <dt>interval</dt>
- <dd>Period of the deeper mixing, defaults to 365, which is a year if
-rate units are in days</dd>
- <dt>n_periods</dt>
- <dd>Number of periods to be considered for long term PEC calculations</dd>
- <dt>tillage_depth</dt>
- <dd>Periodic (see interval) deeper mixing in cm</dd>
- <dt>chent</dt>
- <dd>An optional chent object holding substance specific information. Can
-also be a name for the substance as a character string</dd>
- <dt>DT50</dt>
- <dd>If specified, overrides soil DT50 endpoints from a chent object
-If DT50 is not specified here and not available from the chent object, zero
-degradation is assumed</dd>
- <dt>Koc</dt>
- <dd>If specified, overrides Koc endpoints from a chent object</dd>
- <dt>Kom</dt>
- <dd>Calculated from Koc by default, but can explicitly be specified
-as Kom here</dd>
- <dt>t_avg</dt>
- <dd>Averaging times for time weighted average concentrations</dd>
- <dt>scenarios</dt>
- <dd>If this is &#39;default&#39;, the DT50 will be used without correction
-and soil properties as specified in the REACH guidance (R.16, Table
-R.16-9) are used for porewater PEC calculations. If this is &quot;EFSA_2015&quot;,
-the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when
-&#39;chents&#39; is specified, the DegT50 with destination &#39;PECgw&#39; will be used),
-and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also
-model and scenario adjustment factors from the EFSA guidance are used.</dd>
- <dt>porewater</dt>
- <dd>Should equilibrium porewater concentrations be estimated
-based on Kom and the organic carbon fraction of the soil instead of total
-soil concentrations? Based on equation (7) given in the PPR panel opinion
-(EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015,
-p. 13).</dd>
- </dl>
-
- <div class="Value">
- <h2>Value</h2>
-
- <p><dl>
-The predicted concentration in soil
-</dl></p>
-
- </div>
-
- <div class="Description">
- <h2>Description</h2>
-
- <p>This is a basic calculation of a contaminant concentration in bulk soil
-based on complete, instantaneous mixing. If an interval is given, an
-attempt is made at calculating a long term maximum concentration using
-the concepts layed out for example in the PPR panel opinion (EFSA 2012).</p>
-
- </div>
-
- <div class="Details">
- <h2>Details</h2>
-
- <p>This assumes that the complete load to soil during the time specified by
-&#39;interval&#39; (typically 365 days) is dosed at once. As in the PPR panel
-opinion cited below (PPR panel 2012), only temperature correction using the
-Arrhenius equation is performed.</p>
-
- <p>Total soil and porewater PEC values for the scenarios as defined in the EFSA
-guidance (2015, p. 13) can easily be calculated.</p>
-
- </div>
-
- <div class="Note">
- <h2>Note</h2>
-
- <p>If temperature information is available in the selected scenarios, as
- e.g. in the EFSA scenarios, the DT50 for groundwater modelling
- (destination &#39;PECgw&#39;) is taken from the chent object, otherwise the DT50
- with destination &#39;PECsoil&#39;.</p>
-
- </div>
-
- <div class="References">
- <h2>References</h2>
-
- <p>EFSA Panel on Plant Protection Products and their Residues (2012)
- Scientific Opinion on the science behind the guidance for scenario
- selection and scenario parameterisation for predicting environmental
- concentrations of plant protection products in soil. <em>EFSA Journal</em>
- <b>10</b>(2) 2562, doi:10.2903/j.efsa.2012.2562</p>
-
- <p>EFSA (European Food Safety Authority) (2015) EFSA guidance document for
- predicting environmental concentrations of active substances of plant
- protection products and transformation products of these active substances
- in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093
- doi:10.2903/j.efsa.2015.4093</p>
-
- </div>
-
- <h2 id="examples">Examples</h2>
- <pre class="examples"><div class='input'><span class="functioncall"><a href='PEC_soil.html'>PEC_soil</a></span><span class="keyword">(</span><span class="number">100</span><span class="keyword">,</span> <span class="argument">interception</span> <span class="argument">=</span> <span class="number">0.25</span><span class="keyword">)</span></div>
-<div class='output'> scenario
-t_avg default
- 0 0.1
-</div>
-<div class='input'>
-<span class="comment"># This is example 1 starting at p. 79 of the EFSA guidance (2015)</span>
-<span class="functioncall"><a href='PEC_soil.html'>PEC_soil</a></span><span class="keyword">(</span><span class="number">1000</span><span class="keyword">,</span> <span class="argument">interval</span> <span class="argument">=</span> <span class="number">365</span><span class="keyword">,</span> <span class="argument">DT50</span> <span class="argument">=</span> <span class="number">250</span><span class="keyword">,</span> <span class="argument">t_avg</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">21</span><span class="keyword">)</span><span class="keyword">,</span>
- <span class="argument">scenarios</span> <span class="argument">=</span> <span class="string">"EFSA_2015"</span><span class="keyword">)</span></div>
-<div class='output'> scenario
-t_avg CTN CTC CTS
- 0 21.96827 11.53750 9.145259
- 21 21.78517 11.40701 9.017370
-</div>
-<div class='input'><span class="functioncall"><a href='PEC_soil.html'>PEC_soil</a></span><span class="keyword">(</span><span class="number">1000</span><span class="keyword">,</span> <span class="argument">interval</span> <span class="argument">=</span> <span class="number">365</span><span class="keyword">,</span> <span class="argument">DT50</span> <span class="argument">=</span> <span class="number">250</span><span class="keyword">,</span> <span class="argument">t_av</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">21</span><span class="keyword">)</span><span class="keyword">,</span>
- <span class="argument">Kom</span> <span class="argument">=</span> <span class="number">1000</span><span class="keyword">,</span> <span class="argument">scenarios</span> <span class="argument">=</span> <span class="string">"EFSA_2015"</span><span class="keyword">,</span> <span class="argument">porewater</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span></div>
-<div class='output'> scenario
-t_avg CLN CLC CLS
- 0 0.7589401 0.6674322 0.9147861
- 21 0.7506036 0.6590345 0.8987279
-</div>
-<div class='input'>
-<span class="comment"># The following is from example 4 starting at p. 85 of the EFSA guidance (2015)</span>
-<span class="comment"># Metabolite M2</span>
-<span class="comment"># Calculate total and porewater soil concentrations for tier 1 scenarios</span>
-<span class="comment"># Relative molar mass is 100/300, formation fraction is 0.7 * 1</span>
-<span class="symbol">results_pfm</span> <span class="assignement">&lt;-</span> <span class="functioncall"><a href='PEC_soil.html'>PEC_soil</a></span><span class="keyword">(</span><span class="number">100</span><span class="keyword">/</span><span class="number">300</span> <span class="keyword">*</span> <span class="number">0.7</span> <span class="keyword">*</span> <span class="number">1</span> <span class="keyword">*</span> <span class="number">1000</span><span class="keyword">,</span> <span class="argument">interval</span> <span class="argument">=</span> <span class="number">365</span><span class="keyword">,</span> <span class="argument">DT50</span> <span class="argument">=</span> <span class="number">250</span><span class="keyword">,</span> <span class="argument">t_avg</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">21</span><span class="keyword">)</span><span class="keyword">,</span>
- <span class="argument">scenarios</span> <span class="argument">=</span> <span class="string">"EFSA_2015"</span><span class="keyword">)</span>
-<span class="symbol">results_pfm_pw</span> <span class="assignement">&lt;-</span> <span class="functioncall"><a href='PEC_soil.html'>PEC_soil</a></span><span class="keyword">(</span><span class="number">100</span><span class="keyword">/</span><span class="number">300</span> <span class="keyword">*</span> <span class="number">0.7</span> <span class="keyword">*</span> <span class="number">1000</span><span class="keyword">,</span> <span class="argument">interval</span> <span class="argument">=</span> <span class="number">365</span><span class="keyword">,</span> <span class="argument">DT50</span> <span class="argument">=</span> <span class="number">250</span><span class="keyword">,</span> <span class="argument">t_av</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">21</span><span class="keyword">)</span><span class="keyword">,</span>
- <span class="argument">Kom</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">,</span> <span class="argument">scenarios</span> <span class="argument">=</span> <span class="string">"EFSA_2015"</span><span class="keyword">,</span> <span class="argument">porewater</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span></div></pre>
- </div>
- <div class="span4 sidebar">
- <!-- <ul>
- <li>PEC_soil</li>
- </ul>
- <ul>
-
- </ul> -->
-
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-
- <h2>Author</h2>
-
-Johannes Ranke
-
-
- </div>
-</div>
-
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-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
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diff --git a/docs/PEC_sw_drainage_UK.html b/docs/PEC_sw_drainage_UK.html
deleted file mode 100644
index 9c28968..0000000
--- a/docs/PEC_sw_drainage_UK.html
+++ /dev/null
@@ -1,127 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>PEC_sw_drainage_UK. pfm 0.3-8</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-Johannes Ranke
-">
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- <header>
-
- </header>
-
- <h1>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</h1>
-
-<div class="row">
- <div class="span8">
- <h2>Usage</h2>
- <pre><span class="functioncall"><a href='PEC_sw_drainage_UK.html'>PEC_sw_drainage_UK</a></span><span class="keyword">(</span><span class="symbol">rate</span><span class="keyword">,</span> <span class="argument">interception</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">0</span><span class="keyword">,</span> <span class="symbol">Koc</span><span class="keyword">,</span> <span class="argument">latest_application</span>&nbsp;<span class="argument">=</span>&nbsp;NULL<span class="keyword">,</span>
- <span class="argument">soil_DT50</span>&nbsp;<span class="argument">=</span>&nbsp;NULL<span class="keyword">,</span> <span class="argument">model</span>&nbsp;<span class="argument">=</span>&nbsp;NULL<span class="keyword">,</span> <span class="argument">model_parms</span>&nbsp;<span class="argument">=</span>&nbsp;NULL<span class="keyword">)</span></pre>
-
- <h2>Arguments</h2>
- <dl>
- <dt>rate</dt>
- <dd>Application rate in g/ha</dd>
- <dt>interception</dt>
- <dd>The fraction of the application rate that does not reach the soil</dd>
- <dt>Koc</dt>
- <dd>The sorption coefficient normalised to organic carbon in L/kg</dd>
- <dt>latest_application</dt>
- <dd>Latest application date, formatted as e.g. &quot;01 July&quot;</dd>
- <dt>soil_DT50</dt>
- <dd>Soil degradation half-life, if SFO kinetics are to be used</dd>
- <dt>model</dt>
- <dd>The soil degradation model to be used. Either one of &quot;FOMC&quot;,
-&quot;DFOP&quot;, &quot;HS&quot;, or &quot;IORE&quot;, or an mkinmod object</dd>
- <dt>model_parms</dt>
- <dd>A named numeric vector containing the model parameters</dd>
- </dl>
-
- <div class="Value">
- <h2>Value</h2>
-
- <p><dl>
-The predicted concentration in surface water in µg/L
-</dl></p>
-
- </div>
-
- <div class="Description">
- <h2>Description</h2>
-
- <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>
-
- <h2 id="examples">Examples</h2>
- <pre class="examples"><div class='input'><span class="functioncall"><a href='PEC_sw_drainage_UK.html'>PEC_sw_drainage_UK</a></span><span class="keyword">(</span><span class="number">150</span><span class="keyword">,</span> <span class="argument">Koc</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">)</span></div>
-<div class='output'>[1] 8.076923
-</div></pre>
- </div>
- <div class="span4 sidebar">
- <!-- <ul>
- <li>PEC_sw_drainage_UK</li>
- </ul>
- <ul>
-
- </ul> -->
-
-
-
- <h2>Author</h2>
-
-Johannes Ranke
-
-
- </div>
-</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
- </footer>
- </div>
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-</html> \ No newline at end of file
diff --git a/docs/PEC_sw_drift.html b/docs/PEC_sw_drift.html
deleted file mode 100644
index 3654d2f..0000000
--- a/docs/PEC_sw_drift.html
+++ /dev/null
@@ -1,134 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>PEC_sw_drift. pfm 0.3-8</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="
-Johannes Ranke
-">
-
-<link href="css/bootstrap.css" rel="stylesheet">
-<link href="css/bootstrap-responsive.css" rel="stylesheet">
-<link href="css/highlight.css" rel="stylesheet">
-<link href="css/staticdocs.css" rel="stylesheet">
-
-<!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-<![endif]-->
-
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [ ['$','$'], ["\\(","\\)"] ],
- processEscapes: true
- }
- });
-</script>
-<script type="text/javascript"
- src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
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- <div class="navbar">
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- <a class="brand" href="index.html">pfm 0.3-8</a>
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- <li><a href="index.html">Home</a></li>
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- </div>
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- </div>
-</div>
-
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- <div class="container">
- <header>
-
- </header>
-
- <h1>Calculate predicted environmental concentrations in surface water due to drift</h1>
-
-<div class="row">
- <div class="span8">
- <h2>Usage</h2>
- <pre><span class="functioncall"><a href='PEC_sw_drift.html'>PEC_sw_drift</a></span><span class="keyword">(</span><span class="symbol">rate</span><span class="keyword">,</span> <span class="argument">applications</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">1</span><span class="keyword">,</span> <span class="argument">water_depth</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">30</span><span class="keyword">,</span>
- <span class="argument">drift_percentages</span>&nbsp;<span class="argument">=</span>&nbsp;NULL<span class="keyword">,</span> <span class="argument">drift_data</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"JKI"</span><span class="keyword">,</span> <span class="argument">crop</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"Ackerbau"</span><span class="keyword">,</span>
- <span class="argument">distances</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">1</span><span class="keyword">,</span> <span class="number">5</span><span class="keyword">,</span> <span class="number">10</span><span class="keyword">,</span> <span class="number">20</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">rate_units</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"g/ha"</span><span class="keyword">,</span> <span class="argument">PEC_units</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"µg/L"</span><span class="keyword">)</span></pre>
-
- <h2>Arguments</h2>
- <dl>
- <dt>rate</dt>
- <dd>Application rate in units specified below</dd>
- <dt>applications</dt>
- <dd>Number of applications for selection of drift percentile</dd>
- <dt>water_depth</dt>
- <dd>Depth of the water body in cm</dd>
- <dt>drift_percentages</dt>
- <dd>Percentage drift values for which to calculate PECsw.
-&#39;drift_data&#39; and &#39;distances&#39; if not NULL.</dd>
- <dt>drift_data</dt>
- <dd>Source of drift percentage data</dd>
- <dt>crop</dt>
- <dd>Crop name (use German names for JKI data), defaults to &quot;Ackerbau&quot;</dd>
- <dt>distances</dt>
- <dd>The distances in m for which to get PEC values</dd>
- <dt>rate_units</dt>
- <dd>Defaults to g/ha</dd>
- <dt>PEC_units</dt>
- <dd>Requested units for the calculated PEC. Only µg/L currently supported</dd>
- </dl>
-
- <div class="Value">
- <h2>Value</h2>
-
- <p><dl>
-The predicted concentration in surface water
-</dl></p>
-
- </div>
-
- <div class="Description">
- <h2>Description</h2>
-
- <p>This is a basic, vectorised form of a simple calculation of a contaminant
-concentration in surface water based on complete, instantaneous mixing
-with input via spray drift.</p>
-
- </div>
-
- <h2 id="examples">Examples</h2>
- <pre class="examples"><div class='input'><span class="functioncall"><a href='PEC_sw_drift.html'>PEC_sw_drift</a></span><span class="keyword">(</span><span class="number">100</span><span class="keyword">)</span></div>
-<div class='output'> 1 m 5 m 10 m 20 m
-0.92333333 0.19000000 0.09666667 0.05000000
-</div></pre>
- </div>
- <div class="span4 sidebar">
- <!-- <ul>
- <li>PEC_sw_drift</li>
- </ul>
- <ul>
-
- </ul> -->
-
-
-
- <h2>Author</h2>
-
-Johannes Ranke
-
-
- </div>
-</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
- </footer>
- </div>
- </body>
-</html> \ No newline at end of file
diff --git a/docs/PEC_sw_sed.html b/docs/PEC_sw_sed.html
deleted file mode 100644
index 8161eda..0000000
--- a/docs/PEC_sw_sed.html
+++ /dev/null
@@ -1,131 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>PEC_sw_sed. pfm 0.3-8</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="
-Johannes Ranke
-">
-
-<link href="css/bootstrap.css" rel="stylesheet">
-<link href="css/bootstrap-responsive.css" rel="stylesheet">
-<link href="css/highlight.css" rel="stylesheet">
-<link href="css/staticdocs.css" rel="stylesheet">
-
-<!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-<![endif]-->
-
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [ ['$','$'], ["\\(","\\)"] ],
- processEscapes: true
- }
- });
-</script>
-<script type="text/javascript"
- src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
- </head>
-
- <body>
- <div class="navbar">
- <div class="navbar-inner">
- <div class="container">
- <a class="brand" href="index.html">pfm 0.3-8</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html">Home</a></li>
- <li><a href="reference.html">Reference</a></li>
- </ul>
- </div>
- </div>
- </div>
-</div>
-
-
- <div class="container">
- <header>
-
- </header>
-
- <h1>Calculate predicted environmental concentrations in sediment from surface
-water concentrations</h1>
-
-<div class="row">
- <div class="span8">
- <h2>Usage</h2>
- <pre><span class="functioncall"><a href='PEC_sw_sed.html'>PEC_sw_sed</a></span><span class="keyword">(</span><span class="symbol">PEC_sw</span><span class="keyword">,</span> <span class="argument">percentage</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">100</span><span class="keyword">,</span> <span class="argument">method</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"percentage"</span><span class="keyword">,</span>
- <span class="argument">sediment_depth</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">5</span><span class="keyword">,</span> <span class="argument">water_depth</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">30</span><span class="keyword">,</span> <span class="argument">sediment_density</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">1.3</span><span class="keyword">,</span>
- <span class="argument">PEC_sed_units</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"µg/kg"</span><span class="keyword">,</span> <span class="string">"mg/kg"</span><span class="keyword">)</span><span class="keyword">)</span></pre>
-
- <h2>Arguments</h2>
- <dl>
- <dt>PEC_sw</dt>
- <dd>Numeric vector or matrix of surface water concentrations in µg/L for
-which the corresponding sediment concentration is to be estimated</dd>
- <dt>percentage</dt>
- <dd>The percentage in sediment, used for the percentage method</dd>
- <dt>method</dt>
- <dd>The method used for the calculation</dd>
- <dt>sediment_depth</dt>
- <dd>Depth of the sediment layer</dd>
- <dt>water_depth</dt>
- <dd>Depth of the water body in cm</dd>
- <dt>sediment_density</dt>
- <dd>The density of the sediment in L/kg (equivalent to
-g/cm3)</dd>
- <dt>PEC_sed_units</dt>
- <dd>The units of the estimated sediment PEC value</dd>
- </dl>
-
- <div class="Value">
- <h2>Value</h2>
-
- <p><dl>
-The predicted concentration in sediment
-</dl></p>
-
- </div>
-
- <div class="Description">
- <h2>Description</h2>
-
- <p>The method &#39;percentage&#39; is equivalent to what is used in the CRD spreadsheet
-PEC calculator</p>
-
- </div>
-
- <h2 id="examples">Examples</h2>
- <pre class="examples"><div class='input'><span class="functioncall"><a href='PEC_sw_sed.html'>PEC_sw_sed</a></span><span class="keyword">(</span><span class="functioncall"><a href='PEC_sw_drift.html'>PEC_sw_drift</a></span><span class="keyword">(</span><span class="number">100</span><span class="keyword">,</span> <span class="argument">distances</span> <span class="argument">=</span> <span class="number">1</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">percentage</span> <span class="argument">=</span> <span class="number">50</span><span class="keyword">)</span></div>
-<div class='output'> 1 m
-2.130769
-</div></pre>
- </div>
- <div class="span4 sidebar">
- <!-- <ul>
- <li>PEC_sw_sed</li>
- </ul>
- <ul>
-
- </ul> -->
-
-
-
- <h2>Author</h2>
-
-Johannes Ranke
-
-
- </div>
-</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
- </footer>
- </div>
- </body>
-</html> \ No newline at end of file
diff --git a/docs/SFO_actual_twa.html b/docs/SFO_actual_twa.html
deleted file mode 100644
index 053457d..0000000
--- a/docs/SFO_actual_twa.html
+++ /dev/null
@@ -1,126 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>SFO_actual_twa. pfm 0.3-8</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="
-Johannes Ranke
-">
-
-<link href="css/bootstrap.css" rel="stylesheet">
-<link href="css/bootstrap-responsive.css" rel="stylesheet">
-<link href="css/highlight.css" rel="stylesheet">
-<link href="css/staticdocs.css" rel="stylesheet">
-
-<!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-<![endif]-->
-
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [ ['$','$'], ["\\(","\\)"] ],
- processEscapes: true
- }
- });
-</script>
-<script type="text/javascript"
- src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
- </head>
-
- <body>
- <div class="navbar">
- <div class="navbar-inner">
- <div class="container">
- <a class="brand" href="index.html">pfm 0.3-8</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html">Home</a></li>
- <li><a href="reference.html">Reference</a></li>
- </ul>
- </div>
- </div>
- </div>
-</div>
-
-
- <div class="container">
- <header>
-
- </header>
-
- <h1>Actual and maximum moving window time average concentrations for SFO kinetics</h1>
-
-<div class="row">
- <div class="span8">
- <h2>Usage</h2>
- <pre><span class="functioncall"><a href='SFO_actual_twa.html'>SFO_actual_twa</a></span><span class="keyword">(</span><span class="argument">DT50</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">1000</span><span class="keyword">,</span> <span class="argument">times</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">1</span><span class="keyword">,</span> <span class="number">2</span><span class="keyword">,</span> <span class="number">4</span><span class="keyword">,</span> <span class="number">7</span><span class="keyword">,</span> <span class="number">14</span><span class="keyword">,</span> <span class="number">21</span><span class="keyword">,</span> <span class="number">28</span><span class="keyword">,</span> <span class="number">42</span><span class="keyword">,</span> <span class="number">50</span><span class="keyword">,</span>
- <span class="number">100</span><span class="keyword">)</span><span class="keyword">)</span></pre>
-
- <h2>Arguments</h2>
- <dl>
- <dt>DT50</dt>
- <dd>The half-life.</dd>
- <dt>times</dt>
- <dd>The output times, and window sizes for time weighted average concentrations</dd>
- </dl>
-
- <div class="Source">
- <h2>Source</h2>
-
- <p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
- Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1,
- 18 December 2014, p. 251</p>
-
- </div>
-
- <div class="Description">
- <h2>Description</h2>
-
- <p>Actual and maximum moving window time average concentrations for SFO kinetics</p>
-
- </div>
-
- <h2 id="examples">Examples</h2>
- <pre class="examples"><div class='input'><span class="functioncall"><a href='SFO_actual_twa.html'>SFO_actual_twa</a></span><span class="keyword">(</span><span class="number">10</span><span class="keyword">)</span></div>
-<div class='output'> actual twa
-0 1.0000000000 NaN
-1 0.9330329915 0.9661297
-2 0.8705505633 0.9337803
-4 0.7578582833 0.8733416
-7 0.6155722067 0.7923030
-14 0.3789291416 0.6400113
-21 0.2332582479 0.5267498
-28 0.1435872944 0.4412651
-42 0.0544094102 0.3248093
-50 0.0312500000 0.2795222
-100 0.0009765625 0.1441286
-</div></pre>
- </div>
- <div class="span4 sidebar">
- <!-- <ul>
- <li>SFO_actual_twa</li>
- </ul>
- <ul>
-
- </ul> -->
-
-
-
- <h2>Author</h2>
-
-Johannes Ranke
-
-
- </div>
-</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
- </footer>
- </div>
- </body>
-</html> \ No newline at end of file
diff --git a/docs/SSLRC_mobility_classification.html b/docs/SSLRC_mobility_classification.html
deleted file mode 100644
index 7a57c50..0000000
--- a/docs/SSLRC_mobility_classification.html
+++ /dev/null
@@ -1,119 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>SSLRC_mobility_classification. pfm 0.3-8</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="
-Johannes Ranke
-">
-
-<link href="css/bootstrap.css" rel="stylesheet">
-<link href="css/bootstrap-responsive.css" rel="stylesheet">
-<link href="css/highlight.css" rel="stylesheet">
-<link href="css/staticdocs.css" rel="stylesheet">
-
-<!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-<![endif]-->
-
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [ ['$','$'], ["\\(","\\)"] ],
- processEscapes: true
- }
- });
-</script>
-<script type="text/javascript"
- src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
- </head>
-
- <body>
- <div class="navbar">
- <div class="navbar-inner">
- <div class="container">
- <a class="brand" href="index.html">pfm 0.3-8</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html">Home</a></li>
- <li><a href="reference.html">Reference</a></li>
- </ul>
- </div>
- </div>
- </div>
-</div>
-
-
- <div class="container">
- <header>
-
- </header>
-
- <h1>Determine the SSLRC mobility classification for a chemical substance from its Koc</h1>
-
-<div class="row">
- <div class="span8">
- <h2>Usage</h2>
- <pre><span class="functioncall"><a href='SSLRC_mobility_classification.html'>SSLRC_mobility_classification</a></span><span class="keyword">(</span><span class="symbol">Koc</span><span class="keyword">)</span></pre>
-
- <h2>Arguments</h2>
- <dl>
- <dt>Koc</dt>
- <dd>The sorption coefficient normalised to organic carbon in L/kg</dd>
- </dl>
-
- <div class="Value">
- <h2>Value</h2>
-
- <p><dl>
-A list containing the classification and the percentage of the
- compound transported per 10 mm drain water
-</dl></p>
-
- </div>
-
- <div class="Description">
- <h2>Description</h2>
-
- <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>
-
- <h2 id="examples">Examples</h2>
- <pre class="examples"><div class='input'><span class="functioncall"><a href='SSLRC_mobility_classification.html'>SSLRC_mobility_classification</a></span><span class="keyword">(</span><span class="number">100</span><span class="keyword">)</span></div>
-<div class='output'>$`Mobility classification`
-[1] &quot;Moderately mobile&quot;
-
-$`Percentage drained per mm of drain water`
-[1] 0.7
-
-</div></pre>
- </div>
- <div class="span4 sidebar">
- <!-- <ul>
- <li>SSLRC_mobility_classification</li>
- </ul>
- <ul>
-
- </ul> -->
-
-
-
- <h2>Author</h2>
-
-Johannes Ranke
-
-
- </div>
-</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
- </footer>
- </div>
- </body>
-</html> \ No newline at end of file
diff --git a/docs/TOXSWA_cwa.html b/docs/TOXSWA_cwa.html
deleted file mode 100644
index 561af84..0000000
--- a/docs/TOXSWA_cwa.html
+++ /dev/null
@@ -1,179 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>TOXSWA_cwa. pfm 0.3-8</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="">
-
-<link href="css/bootstrap.css" rel="stylesheet">
-<link href="css/bootstrap-responsive.css" rel="stylesheet">
-<link href="css/highlight.css" rel="stylesheet">
-<link href="css/staticdocs.css" rel="stylesheet">
-
-<!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-<![endif]-->
-
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [ ['$','$'], ["\\(","\\)"] ],
- processEscapes: true
- }
- });
-</script>
-<script type="text/javascript"
- src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
- </head>
-
- <body>
- <div class="navbar">
- <div class="navbar-inner">
- <div class="container">
- <a class="brand" href="index.html">pfm 0.3-8</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html">Home</a></li>
- <li><a href="reference.html">Reference</a></li>
- </ul>
- </div>
- </div>
- </div>
-</div>
-
-
- <div class="container">
- <header>
-
- </header>
-
- <h1>R6 class for holding TOXSWA cwa concentration data and associated statistics</h1>
-
-<div class="row">
- <div class="span8">
- <h2>Usage</h2>
- <pre><span class="symbol">TOXSWA_cwa</span></pre>
-
- <div class="Format">
- <h2>Format</h2>
-
- <p>An <code><a href='http://www.rdocumentation.org/packages/R6/topics/R6Class'>R6Class</a></code> generator object.</p>
-
- </div>
-
- <div class="Description">
- <h2>Description</h2>
-
- <p>An R6 class for holding TOXSWA cwa concentration data and some associated statistics.
-Usually, an instance of this class will be generated by <code><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></code>.</p>
-
- </div>
-
- <div class="Fields">
- <h2>Fields</h2>
-
- <p></p>
-
- <p><dl>
-<dt><code>filename</code></dt><dd>Length one character vector.</dd></p>
-
- <p><dt><code>basedir</code></dt><dd>Length one character vector.</dd></p>
-
- <p><dt><code>segment</code></dt><dd>Length one integer, specifying for which segment the cwa data were read.</dd></p>
-
- <p><dt><code>cwas</code></dt><dd>Dataframe holding the concentrations.</dd></p>
-
- <p><dt><code>events</code></dt><dd>List of dataframes holding the event statistics for each threshold.</dd></p>
-
- <p><dt><code>windows</code></dt><dd>Matrix of maximum time weighted average concentrations (TWAC_max)
-and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d)
-for the requested moving window sizes in days.</dd></p>
-
- <p></dl></p>
-
- </div>
-
- <div class="Methods">
- <h2>Methods</h2>
-
- <p></p>
-
- <p><dl>
- <dt><code>get_events(threshold, total = FALSE)</code></dt><dd>
- Populate a datataframe with event information for the specified threshold value
- in µg/L. If <code>total = TRUE</code>, the total concentration including the amount
- adsorbed to suspended matter will be used. The resulting dataframe is stored in the
- <code>events</code> field of the object.
- </dd></p>
-
- <p><dt><code>moving_windows(windows, total = FALSE)</code></dt><dd>
- Add to the <code>windows</code> field described above.
- Again, if <code>total = TRUE</code>, the total concentration including the amount
- adsorbed to suspended matter will be used.
- </dd></p>
-
- <p></dl></p>
-
- <p></p>
-
- </div>
-
- <h2 id="examples">Examples</h2>
- <pre class="examples"><div class='input'><span class="symbol">H_sw_R1_stream</span> <span class="assignement">&lt;-</span> <span class="functioncall"><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span><span class="keyword">(</span><span class="string">"00003s_pa.cwa"</span><span class="keyword">,</span>
- <span class="argument">basedir</span> <span class="argument">=</span> <span class="string">"SwashProjects/project_H_sw/TOXSWA"</span><span class="keyword">,</span>
- <span class="argument">zipfile</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/devtools/topics/system.file'>system.file</a></span><span class="keyword">(</span><span class="string">"testdata/SwashProjects.zip"</span><span class="keyword">,</span>
- <span class="argument">package</span> <span class="argument">=</span> <span class="string">"pfm"</span><span class="keyword">)</span><span class="keyword">)</span>
-<span class="symbol">H_sw_R1_stream</span><span class="keyword">$</span><span class="functioncall">get_events</span><span class="keyword">(</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">2</span><span class="keyword">,</span> <span class="number">10</span><span class="keyword">)</span><span class="keyword">)</span>
-<span class="symbol">H_sw_R1_stream</span><span class="keyword">$</span><span class="functioncall">moving_windows</span><span class="keyword">(</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">7</span><span class="keyword">,</span> <span class="number">21</span><span class="keyword">)</span><span class="keyword">)</span>
-<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/print'>print</a></span><span class="keyword">(</span><span class="symbol">H_sw_R1_stream</span><span class="keyword">)</span></div>
-<div class='output'>&lt;TOXSWA_cwa&gt; data from file 00003s_pa.cwa segment 20
- datetime t t_firstjan t_rel_to_max cwa_mug_per_L
-20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0
-40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0
-60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0
-80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0
-100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0
-120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0
- cwa_tot_mug_per_L
-20 0
-40 0
-60 0
-80 0
-100 0
-120 0
-Moving window analysis
- window max_TWAC max_AUC_h max_AUC_d
-1 7 days 2.3926551 401.9660 16.74859
-2 21 days 0.8369248 421.8101 17.57542
-Event statistics for threshold 2
- t_start cwa_max duration pre_interval AUC_h AUC_d
-1 44.375 4.167238 0.208 44.375 17.77202 0.740501
-2 55.042 40.584010 0.583 10.459 398.21189 16.592162
-Event statistics for threshold 10
- t_start cwa_max duration pre_interval AUC_h AUC_d
-1 55.083 40.58401 0.459 55.083 379.433 15.80971
-</div></pre>
- </div>
- <div class="span4 sidebar">
- <!-- <ul>
- <li>TOXSWA_cwa</li>
- </ul>
- <ul>
- <li>data</li>
- </ul> -->
-
-
-
-
- </div>
-</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
- </footer>
- </div>
- </body>
-</html> \ No newline at end of file
diff --git a/docs/authors.html b/docs/authors.html
new file mode 100644
index 0000000..0830cef
--- /dev/null
+++ b/docs/authors.html
@@ -0,0 +1,97 @@
+<!-- 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>Authors • 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-authors">
+ <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="contents col-md-12">
+ <div class="page-header">
+ <h1>Authors</h1>
+ </div>
+
+ <ul class="list-unstyled">
+ <li>
+ <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright&nbsp;holder.
+ </p>
+ </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/css/bootstrap-responsive.css b/docs/css/bootstrap-responsive.css
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diff --git a/docs/css/bootstrap-responsive.min.css b/docs/css/bootstrap-responsive.min.css
deleted file mode 100644
index 1f55036..0000000
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-
- <h1>Deposition from spray drift expressed as percent of the applied dose as
-published by the JKI</h1>
-
-<div class="row">
- <div class="span8">
-
- <div class="Format">
- <h2>Format</h2>
-
- <p>A list currently containing matrices with spray drift percentage
-data for field crops (Ackerbau), and Pome/stone fruit, early and late
-(Obstbau frueh, spaet).</p>
-
- </div>
-
- <div class="Source">
- <h2>Source</h2>
-
- <p>JKI (2010) Spreadsheet &#39;Tabelle der Abdrifteckwerte.xls&#39;, retrieved
-from
-http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html
-on 2015-06-11</p>
-
- </div>
-
- <div class="Description">
- <h2>Description</h2>
-
- <p>Deposition from spray drift expressed as percent of the applied dose as
-published by the German Julius-Kühn Institute (JKI).</p>
-
- </div>
-
- <div class="Details">
- <h2>Details</h2>
-
- <p>The data were extracted from the spreadsheet cited below using the R code
-given in the example section. The spreadsheet is not included in the package
-as its licence is not clear.</p>
-
- </div>
-
- <h2 id="examples">Examples</h2>
- <pre class="examples"><div class='input'>
-<span class="comment">## Not run: ------------------------------------</span>
-<span class="comment"># # This is the code that was used to extract the data</span>
-<span class="comment"># library(readxl)</span>
-<span class="comment"># abdrift_path &lt;- "inst/extdata/Tabelle der Abdrifteckwerte.xls"</span>
-<span class="comment"># JKI_crops &lt;- c("Ackerbau", "Obstbau frueh", "Obstbau spaet")</span>
-<span class="comment"># names(JKI_crops) &lt;- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late")</span>
-<span class="comment"># drift_data_JKI &lt;- list()</span>
-<span class="comment"># </span>
-<span class="comment"># for (n in 1:8) {</span>
-<span class="comment"># drift_data_raw &lt;- read_excel(abdrift_path, sheet = n + 1, skip = 2)</span>
-<span class="comment"># drift_data &lt;- as.matrix(drift_data_raw[1:9, 2:4]) </span>
-<span class="comment"># dimnames(drift_data) &lt;- list(distance = as.integer(drift_data_raw[1:9, 1]),</span>
-<span class="comment"># crop = JKI_crops)</span>
-<span class="comment"># drift_data_JKI[[n]] &lt;- drift_data</span>
-<span class="comment"># }</span>
-<span class="comment"># save(drift_data_JKI, file = "data/drift_data_JKI.RData")</span>
-<span class="comment">## ---------------------------------------------</span>
-
-<span class="comment"># And this is the resulting data</span>
-<span class="symbol">drift_data_JKI</span></div>
-<div class='output'>[[1]]
- crop
-distance Ackerbau Obstbau frueh Obstbau spaet
- 1 2.77 NA NA
- 3 NA 29.20 15.73
- 5 0.57 19.89 8.41
- 10 0.29 11.81 3.60
- 15 0.20 5.55 1.81
- 20 0.15 2.77 1.09
- 30 0.10 1.04 0.54
- 40 0.07 0.52 0.32
- 50 0.06 0.30 0.22
-
-[[2]]
- crop
-distance Ackerbau Obstbau frueh Obstbau spaet
- 1 2.38 NA NA
- 3 NA 25.53 12.13
- 5 0.47 16.87 6.81
- 10 0.24 9.61 3.11
- 15 0.16 5.61 1.58
- 20 0.12 2.59 0.90
- 30 0.08 0.87 0.40
- 40 0.06 0.40 0.23
- 50 0.05 0.22 0.15
-
-[[3]]
- crop
-distance Ackerbau Obstbau frueh Obstbau spaet
- 1 2.01 NA NA
- 3 NA 23.96 11.01
- 5 0.41 15.79 6.04
- 10 0.20 8.96 2.67
- 15 0.14 4.24 1.39
- 20 0.10 2.01 0.80
- 30 0.07 0.70 0.36
- 40 0.05 0.33 0.21
- 50 0.04 0.19 0.13
-
-[[4]]
- crop
-distance Ackerbau Obstbau frueh Obstbau spaet
- 1 1.85 NA NA
- 3 NA 23.61 10.12
- 5 0.38 15.42 5.60
- 10 0.19 8.66 2.50
- 15 0.13 4.01 1.28
- 20 0.10 1.89 0.75
- 30 0.06 0.66 0.35
- 40 0.05 0.31 0.20
- 50 0.04 0.17 0.13
-
-[[5]]
- crop
-distance Ackerbau Obstbau frueh Obstbau spaet
- 1 1.75 NA NA
- 3 NA 23.12 9.74
- 5 0.36 15.06 5.41
- 10 0.18 8.42 2.43
- 15 0.12 3.83 1.24
- 20 0.09 1.81 0.72
- 30 0.06 0.63 0.34
- 40 0.05 0.30 0.20
- 50 0.04 0.17 0.13
-
-[[6]]
- crop
-distance Ackerbau Obstbau frueh Obstbau spaet
- 1 1.64 NA NA
- 3 NA 22.76 9.21
- 5 0.34 14.64 5.18
- 10 0.17 8.04 2.38
- 15 0.11 3.71 1.20
- 20 0.09 1.75 0.68
- 30 0.06 0.61 0.31
- 40 0.04 0.29 0.17
- 50 0.03 0.16 0.11
-
-[[7]]
- crop
-distance Ackerbau Obstbau frueh Obstbau spaet
- 1 1.61 NA NA
- 3 NA 22.69 9.10
- 5 0.33 14.45 5.11
- 10 0.17 7.83 2.33
- 15 0.11 3.62 1.20
- 20 0.08 1.71 0.67
- 30 0.06 0.60 0.30
- 40 0.04 0.28 0.17
- 50 0.03 0.16 0.11
-
-[[8]]
- crop
-distance Ackerbau Obstbau frueh Obstbau spaet
- 1 1.52 NA NA
- 3 NA 22.24 8.66
- 5 0.31 14.09 4.92
- 10 0.16 7.58 2.29
- 15 0.11 3.48 1.14
- 20 0.08 1.65 0.65
- 30 0.05 0.57 0.29
- 40 0.04 0.27 0.16
- 50 0.03 0.15 0.11
-
-</div></pre>
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- <!-- <ul>
- <li>drift_data_JKI</li>
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-
- <body>
- <div class="navbar">
- <div class="navbar-inner">
- <div class="container">
- <a class="brand" href="index.html">pfm 0.3-8</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html">Home</a></li>
- <li><a href="reference.html">Reference</a></li>
- </ul>
- </div>
- </div>
- </div>
-</div>
-
-
- <div class="container">
- <header>
-
- </header>
-
- <h1>Retrieve endpoint information from the chyaml field of a chent object</h1>
-
-<div class="row">
- <div class="span8">
- <h2>Usage</h2>
- <pre><span class="functioncall"><a href='endpoint.html'>endpoint</a></span><span class="keyword">(</span><span class="symbol">chent</span><span class="keyword">,</span> <span class="argument">medium</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"soil"</span><span class="keyword">,</span> <span class="argument">type</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"degradation"</span><span class="keyword">,</span> <span class="string">"sorption"</span><span class="keyword">)</span><span class="keyword">,</span>
- <span class="argument">lab_field</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">NA</span><span class="keyword">,</span> <span class="string">"laboratory"</span><span class="keyword">,</span> <span class="string">"field"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">redox</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">NA</span><span class="keyword">,</span> <span class="string">"aerobic"</span><span class="keyword">,</span>
- <span class="string">"anaerobic"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">value</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"DT50ref"</span><span class="keyword">,</span> <span class="string">"Kfoc"</span><span class="keyword">,</span> <span class="string">"N"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">aggregator</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="symbol">geomean</span><span class="keyword">,</span>
- <span class="argument">raw</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">signif</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">3</span><span class="keyword">)</span>
-
-<span class="functioncall"><a href='endpoint.html'>soil_DT50</a></span><span class="keyword">(</span><span class="symbol">chent</span><span class="keyword">,</span> <span class="argument">aggregator</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="symbol">geomean</span><span class="keyword">,</span> <span class="argument">signif</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">3</span><span class="keyword">,</span>
- <span class="argument">lab_field</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"laboratory"</span><span class="keyword">,</span> <span class="argument">value</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"DT50ref"</span><span class="keyword">,</span> <span class="argument">redox</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"aerobic"</span><span class="keyword">,</span>
- <span class="argument">raw</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">)</span>
-
-<span class="functioncall"><a href='endpoint.html'>soil_Kfoc</a></span><span class="keyword">(</span><span class="symbol">chent</span><span class="keyword">,</span> <span class="argument">aggregator</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="symbol">geomean</span><span class="keyword">,</span> <span class="argument">signif</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">3</span><span class="keyword">,</span> <span class="argument">value</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"Kfoc"</span><span class="keyword">,</span>
- <span class="argument">raw</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">)</span>
-
-<span class="functioncall"><a href='endpoint.html'>soil_N</a></span><span class="keyword">(</span><span class="symbol">chent</span><span class="keyword">,</span> <span class="argument">aggregator</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="symbol">mean</span><span class="keyword">,</span> <span class="argument">signif</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">3</span><span class="keyword">,</span> <span class="argument">raw</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">)</span>
-
-<span class="functioncall"><a href='endpoint.html'>soil_sorption</a></span><span class="keyword">(</span><span class="symbol">chent</span><span class="keyword">,</span> <span class="argument">values</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"Kfoc"</span><span class="keyword">,</span> <span class="string">"N"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">aggregators</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">Kfoc</span> <span class="argument">=</span>
- <span class="symbol">geomean</span><span class="keyword">,</span> <span class="argument">Koc</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="symbol">geomean</span><span class="keyword">,</span> <span class="argument">N</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="symbol">mean</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">signif</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">Kfoc</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">3</span><span class="keyword">,</span> <span class="argument">N</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">3</span><span class="keyword">)</span><span class="keyword">,</span>
- <span class="argument">raw</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">)</span></pre>
-
- <h2>Arguments</h2>
- <dl>
- <dt>chent</dt>
- <dd>The chent object to get the information from</dd>
- <dt>medium</dt>
- <dd>The medium for which information is sought</dd>
- <dt>type</dt>
- <dd>The information type</dd>
- <dt>lab_field</dt>
- <dd>If not NA, do we want laboratory or field endpoints</dd>
- <dt>redox</dt>
- <dd>If not NA, are we looking for aerobic or anaerobic data</dd>
- <dt>value</dt>
- <dd>The name of the value we want. The list given in the
-usage section is not exclusive</dd>
- <dt>aggregator</dt>
- <dd>The aggregator function. Can be mean,
-<code><a href='geomean.html'>geomean</a></code>, or identity, for example.</dd>
- <dt>raw</dt>
- <dd>Should the number(s) be returned as stored in the chent
-object (could be a character value) to retain original information
-about precision?</dd>
- <dt>signif</dt>
- <dd>How many significant digits do we want</dd>
- <dt>values</dt>
- <dd>The values to be returned</dd>
- <dt>aggregators</dt>
- <dd>A named vector of aggregator functions to be used</dd>
- </dl>
-
- <div class="Value">
- <h2>Value</h2>
-
- <p><dl>
-The result from applying the aggregator function to
- the values converted to a numeric vector, rounded to the
- given number of significant digits, or, if raw = TRUE,
- the values as a character value, retaining any implicit
- information on precision that may be present.
-</dl></p>
-
- </div>
-
- <div class="Description">
- <h2>Description</h2>
-
- <p>R6 class objects of class chent represent chemical entities
-and can hold a list of information loaded from a chemical yaml file in their
-chyaml field. Such information is extracted and optionally aggregated by
-this function.</p>
-
- </div>
-
- <div class="Details">
- <h2>Details</h2>
-
- <p>The functions <code>soil_*</code> are functions to extract soil specific endpoints.
-For the Freundlich exponent, the capital letter <code>N</code> is used in order to
-facilitate dealing with such data in R. In pesticide fate modelling, this
-exponent is often called 1/n.</p>
-
- </div>
- </div>
- <div class="span4 sidebar">
- <!-- <ul>
- <li>endpoint</li><li>soil_DT50</li><li>soil_Kfoc</li><li>soil_N</li><li>soil_sorption</li>
- </ul>
- <ul>
-
- </ul> -->
-
-
-
-
- </div>
-</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
- </footer>
- </div>
- </body>
-</html> \ No newline at end of file
diff --git a/docs/geomean.html b/docs/geomean.html
deleted file mode 100644
index 3530c32..0000000
--- a/docs/geomean.html
+++ /dev/null
@@ -1,121 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>geomean. pfm 0.3-8</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="
-Johannes Ranke
-">
-
-<link href="css/bootstrap.css" rel="stylesheet">
-<link href="css/bootstrap-responsive.css" rel="stylesheet">
-<link href="css/highlight.css" rel="stylesheet">
-<link href="css/staticdocs.css" rel="stylesheet">
-
-<!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-<![endif]-->
-
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [ ['$','$'], ["\\(","\\)"] ],
- processEscapes: true
- }
- });
-</script>
-<script type="text/javascript"
- src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
- </head>
-
- <body>
- <div class="navbar">
- <div class="navbar-inner">
- <div class="container">
- <a class="brand" href="index.html">pfm 0.3-8</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html">Home</a></li>
- <li><a href="reference.html">Reference</a></li>
- </ul>
- </div>
- </div>
- </div>
-</div>
-
-
- <div class="container">
- <header>
-
- </header>
-
- <h1>Calculate the geometric mean</h1>
-
-<div class="row">
- <div class="span8">
- <h2>Usage</h2>
- <pre><span class="functioncall"><a href='geomean.html'>geomean</a></span><span class="keyword">(</span><span class="symbol">x</span><span class="keyword">,</span> <span class="argument">na.rm</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">TRUE</span><span class="keyword">)</span></pre>
-
- <h2>Arguments</h2>
- <dl>
- <dt>x</dt>
- <dd>Vector of numbers</dd>
- <dt>na.rm</dt>
- <dd>Should NA values be omitted?</dd>
- </dl>
-
- <div class="Value">
- <h2>Value</h2>
-
- <p><dl>
-The geometric mean
-</dl></p>
-
- </div>
-
- <div class="Description">
- <h2>Description</h2>
-
- <p>Based on some posts in a thread on Stackoverflow
-<a href = 'http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in'>http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in</a>
-This function checks for negative values, removes NA values per default and
-returns 0 if at least one element of the vector is 0.</p>
-
- </div>
-
- <h2 id="examples">Examples</h2>
- <pre class="examples"><div class='input'><span class="functioncall"><a href='geomean.html'>geomean</a></span><span class="keyword">(</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">1</span><span class="keyword">,</span> <span class="number">3</span><span class="keyword">,</span> <span class="number">9</span><span class="keyword">)</span><span class="keyword">)</span></div>
-<div class='output'>[1] 3
-</div>
-<div class='input'><span class="functioncall"><a href='geomean.html'>geomean</a></span><span class="keyword">(</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">1</span><span class="keyword">,</span> <span class="number">3</span><span class="keyword">,</span> <span class="number">NA</span><span class="keyword">,</span> <span class="number">9</span><span class="keyword">)</span><span class="keyword">)</span></div>
-<div class='output'>[1] 3
-</div>
-<div class='input'><span class="comment">## Not run: geomean(c(1, -3, 9)) # returns an error</span></div></pre>
- </div>
- <div class="span4 sidebar">
- <!-- <ul>
- <li>geomean</li>
- </ul>
- <ul>
-
- </ul> -->
-
-
-
- <h2>Author</h2>
-
-Johannes Ranke
-
-
- </div>
-</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
- </footer>
- </div>
- </body>
-</html> \ No newline at end of file
diff --git a/docs/img/glyphicons-halflings-white.png b/docs/img/glyphicons-halflings-white.png
deleted file mode 100644
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--- a/docs/img/glyphicons-halflings-white.png
+++ /dev/null
Binary files differ
diff --git a/docs/img/glyphicons-halflings.png b/docs/img/glyphicons-halflings.png
deleted file mode 100644
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--- a/docs/img/glyphicons-halflings.png
+++ /dev/null
Binary files differ
diff --git a/docs/index.html b/docs/index.html
index a82dcae..4aa129c 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -1,65 +1,55 @@
<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>Home. pfm 0.3-8</title>
+<!-- Generated by pkgdown: do not edit by hand --><html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="">
-
-<link href="css/bootstrap.css" rel="stylesheet">
-<link href="css/bootstrap-responsive.css" rel="stylesheet">
-<link href="css/highlight.css" rel="stylesheet">
-<link href="css/staticdocs.css" rel="stylesheet">
-
-<!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
+<title>Utilities for Pesticide Fate Modelling • 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]-->
-
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [ ['$','$'], ["\\(","\\)"] ],
- processEscapes: true
- }
- });
-</script>
-<script type="text/javascript"
- src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
- </head>
-
- <body>
- <div class="navbar">
- <div class="navbar-inner">
- <div class="container">
- <a class="brand" href="index.html">pfm 0.3-8</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html">Home</a></li>
- <li><a href="reference.html">Reference</a></li>
- </ul>
- </div>
+</head>
+<body>
+ <div class="container template-home">
+ <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 -->
-
- <div class="container">
- <header>
-
- </header>
- <div class="row">
- <div class="span8">
- <h1>pfm</h1>
-
-<p>The R package <strong>pfm</strong> provides some utilities for dealing with FOCUS pesticide fate modelling tools,
-(currently only TOXSWA cwa and out files), made available under the GNU public license.
-This means:</p>
-
-<pre><code>This program is free software: you can redistribute it and/or modify it under
+ </header><div class="row">
+ <div class="contents col-md-9">
+ <div id="pfm" class="section level1">
+<div class="page-header"><h1 class="hasAnchor">
+<a href="#pfm" class="anchor"> </a>pfm</h1></div>
+<p>The R package <strong>pfm</strong> provides some utilities for 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="st"> </span>you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
-Foundation, either version 3 of the License, or (at your option) any later
+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 in the hope that it will be useful, but WITHOUT
@@ -68,49 +58,32 @@ FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
details.
You should have received a copy of the GNU General Public License along with
-this program. If not, see &lt;http://www.gnu.org/licenses/&gt;
-</code></pre>
-
-<h2>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>
-
-<pre><code class="r">library(devtools)
-install_github(&quot;jranke/pfm&quot;, subdir = &quot;pkg&quot;, quick = TRUE)
-</code></pre>
-
-<h2>Use</h2>
-
-<h3>Analyse TOXSWA output</h3>
-
+this program. If not, see &lt;http:<span class="er">//</span>www.gnu.org/licenses/<span class="er">&gt;</span></code></pre></div>
+<div id="installation" class="section level2">
+<h2 class="hasAnchor">
+<a href="#installation" class="anchor"> </a>Installation</h2>
+<p>You can install the package from <a href="http://github.com/jranke/pfm">github</a>, e.g. using the <code>devtools</code> package. Using <code>quick = TRUE</code> skips docs, multiple-architecture builds, demos, and vignettes, to make installation as fast and painless as possible.</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(devtools)
+<span class="kw">install_github</span>(<span class="st">"jranke/pfm"</span>, <span class="dt">subdir =</span> <span class="st">"pkg"</span>, <span class="dt">quick =</span> <span class="ot">TRUE</span>)</code></pre></div>
+</div>
+<div id="use" class="section level2">
+<h2 class="hasAnchor">
+<a href="#use" class="anchor"> </a>Use</h2>
+<div id="analyse-toxswa-output" class="section level3">
+<h3 class="hasAnchor">
+<a href="#analyse-toxswa-output" class="anchor"> </a>Analyse TOXSWA output</h3>
<p>Read in and analyse a cwa file:</p>
-
-<pre><code class="r">library(pfm, quietly = TRUE)
-</code></pre>
-
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(pfm, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</code></pre></div>
<pre><code>##
## Initialize Python Version 2.7.9 (default, Jun 29 2016, 13:11:10)
-## [GCC 4.9.2]
-</code></pre>
-
-<pre><code class="r">example_cwa &lt;- read.TOXSWA_cwa(&quot;00003s_pa.cwa&quot;)
-plot(example_cwa)
-</code></pre>
-
-<p><img src="README_files/figure-html/unnamed-chunk-3-1.png" width="672" /></p>
-
-<p>Get events above thresholds of 20 and 100 µg/L,
-and do a moving window analysis for windows of 7 days
-and 21 days, print the results:</p>
-
-<pre><code class="r">example_cwa$get_events(c(20, 100))
-example_cwa$moving_windows(c(7, 21))
-print(example_cwa)
-</code></pre>
-
+## [GCC 4.9.2]</code></pre>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">example_cwa &lt;-<span class="st"> </span><span class="kw"><a href="reference/read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></span>(<span class="st">"00003s_pa.cwa"</span>)
+<span class="kw">plot</span>(example_cwa)</code></pre></div>
+<p><img src="README_files/figure-html/unnamed-chunk-3-1.png" width="672"></p>
+<p>Get events above thresholds of 20 and 100 µg/L, and do a moving window analysis for windows of 7 days and 21 days, print the results:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">example_cwa$<span class="kw">get_events</span>(<span class="kw">c</span>(<span class="dv">20</span>, <span class="dv">100</span>))
+example_cwa$<span class="kw">moving_windows</span>(<span class="kw">c</span>(<span class="dv">7</span>, <span class="dv">21</span>))
+<span class="kw">print</span>(example_cwa)</code></pre></div>
<pre><code>## &lt;TOXSWA_cwa&gt; data from file 00003s_pa.cwa segment 20
## datetime t t_firstjan t_rel_to_max cwa_mug_per_L
## 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0
@@ -134,35 +107,23 @@ print(example_cwa)
## t_start cwa_max duration pre_interval AUC_h AUC_d
## 1 55.083 40.58401 0.417 55.083 365.7912 15.2413
## Event statistics for threshold 100
-## No events found
-</code></pre>
-
-<p>This can also be done with out files, the function reads
-out files from current TOXSWA versions as well as cwa files
-from old TOXSWA versions.</p>
-
-<h3>Calculate PEC soil</h3>
-
-<p>Simple PEC soil calculation for an application rate of 100 g/ha and
-25% interception, assuming complete mixing into 5 cm and a soil bulk
-density of 1.5 kg/L, output in mg/kg:</p>
-
-<pre><code class="r">PEC_soil(100, interception = 0.25)
-</code></pre>
-
+## No events found</code></pre>
+<p>This can also be done with out files, the function reads out files from current TOXSWA versions as well as cwa files from old TOXSWA versions.</p>
+</div>
+<div id="calculate-pec-soil" class="section level3">
+<h3 class="hasAnchor">
+<a href="#calculate-pec-soil" class="anchor"> </a>Calculate PEC soil</h3>
+<p>Simple PEC soil calculation for an application rate of 100 g/ha and 25% interception, assuming complete mixing into 5 cm and a soil bulk density of 1.5 kg/L, output in mg/kg:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="reference/PEC_soil.html">PEC_soil</a></span>(<span class="dv">100</span>, <span class="dt">interception =</span> <span class="fl">0.25</span>)</code></pre></div>
<pre><code>## scenario
## t_avg default
-## 0 0.1
-</code></pre>
-
-<h3>Rautmann drift data</h3>
-
-<p>Some of the drift percentage data published by the JKI are included. To
-see the data for one application:</p>
-
-<pre><code class="r">drift_data_JKI[1]
-</code></pre>
-
+## 0 0.1</code></pre>
+</div>
+<div id="rautmann-drift-data" class="section level3">
+<h3 class="hasAnchor">
+<a href="#rautmann-drift-data" class="anchor"> </a>Rautmann drift data</h3>
+<p>Some of the drift percentage data published by the JKI are included. To see the data for one application:</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">drift_data_JKI[<span class="dv">1</span>]</code></pre></div>
<pre><code>## [[1]]
## crop
## distance Ackerbau Obstbau frueh Obstbau spaet
@@ -174,35 +135,41 @@ see the data for one application:</p>
## 20 0.15 2.77 1.09
## 30 0.10 1.04 0.54
## 40 0.07 0.52 0.32
-## 50 0.06 0.30 0.22
-</code></pre>
-
-<h3>PEC surface water due to drift</h3>
-
-<p>Initial PEC values for an application of 100 g/ha in the vicinity of a 30 cm
-deep water body are obtained using</p>
+## 50 0.06 0.30 0.22</code></pre>
+</div>
+<div id="pec-surface-water-due-to-drift" class="section level3">
+<h3 class="hasAnchor">
+<a href="#pec-surface-water-due-to-drift" class="anchor"> </a>PEC surface water due to drift</h3>
+<p>Initial PEC values for an application of 100 g/ha in the vicinity of a 30 cm deep water body are obtained using</p>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="reference/PEC_sw_drift.html">PEC_sw_drift</a></span>(<span class="dv">100</span>, <span class="dt">applications =</span> <span class="dv">1</span>)</code></pre></div>
+<pre><code>## 1 m 5 m 10 m 20 m
+## 0.92333333 0.19000000 0.09666667 0.05000000</code></pre>
+</div>
+</div>
+</div>
+ </div>
-<pre><code class="r">PEC_sw_drift(100, applications = 1)
-</code></pre>
+ <div class="col-md-3" id="sidebar">
+ <h2>License</h2>
+<p>GPL</p>
+<h2>Developers</h2>
+<ul class="list-unstyled">
+<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li>
+</ul>
+</div>
+</div>
-<pre><code>## 1 m 5 m 10 m 20 m
-## 0.92333333 0.19000000 0.09666667 0.05000000
-</code></pre>
- </div>
+ <footer><div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
- <div class="span3 offset1 sidebar">
- <h2>Authors</h2>
- <ul>
- <li><a href='mailto:jranke@uni-bremen.de'>Johannes Ranke</a> [aut, cre, cph]</li>
- </ul>
- </div>
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
+
</footer>
- </div>
+</div>
+
</body>
-</html> \ No newline at end of file
+</html>
diff --git a/docs/jquery.sticky-kit.min.js b/docs/jquery.sticky-kit.min.js
new file mode 100644
index 0000000..e2a3c6d
--- /dev/null
+++ b/docs/jquery.sticky-kit.min.js
@@ -0,0 +1,9 @@
+/*
+ Sticky-kit v1.1.2 | WTFPL | Leaf Corcoran 2015 | http://leafo.net
+*/
+(function(){var b,f;b=this.jQuery||window.jQuery;f=b(window);b.fn.stick_in_parent=function(d){var A,w,J,n,B,K,p,q,k,E,t;null==d&&(d={});t=d.sticky_class;B=d.inner_scrolling;E=d.recalc_every;k=d.parent;q=d.offset_top;p=d.spacer;w=d.bottoming;null==q&&(q=0);null==k&&(k=void 0);null==B&&(B=!0);null==t&&(t="is_stuck");A=b(document);null==w&&(w=!0);J=function(a,d,n,C,F,u,r,G){var v,H,m,D,I,c,g,x,y,z,h,l;if(!a.data("sticky_kit")){a.data("sticky_kit",!0);I=A.height();g=a.parent();null!=k&&(g=g.closest(k));
+if(!g.length)throw"failed to find stick parent";v=m=!1;(h=null!=p?p&&a.closest(p):b("<div />"))&&h.css("position",a.css("position"));x=function(){var c,f,e;if(!G&&(I=A.height(),c=parseInt(g.css("border-top-width"),10),f=parseInt(g.css("padding-top"),10),d=parseInt(g.css("padding-bottom"),10),n=g.offset().top+c+f,C=g.height(),m&&(v=m=!1,null==p&&(a.insertAfter(h),h.detach()),a.css({position:"",top:"",width:"",bottom:""}).removeClass(t),e=!0),F=a.offset().top-(parseInt(a.css("margin-top"),10)||0)-q,
+u=a.outerHeight(!0),r=a.css("float"),h&&h.css({width:a.outerWidth(!0),height:u,display:a.css("display"),"vertical-align":a.css("vertical-align"),"float":r}),e))return l()};x();if(u!==C)return D=void 0,c=q,z=E,l=function(){var b,l,e,k;if(!G&&(e=!1,null!=z&&(--z,0>=z&&(z=E,x(),e=!0)),e||A.height()===I||x(),e=f.scrollTop(),null!=D&&(l=e-D),D=e,m?(w&&(k=e+u+c>C+n,v&&!k&&(v=!1,a.css({position:"fixed",bottom:"",top:c}).trigger("sticky_kit:unbottom"))),e<F&&(m=!1,c=q,null==p&&("left"!==r&&"right"!==r||a.insertAfter(h),
+h.detach()),b={position:"",width:"",top:""},a.css(b).removeClass(t).trigger("sticky_kit:unstick")),B&&(b=f.height(),u+q>b&&!v&&(c-=l,c=Math.max(b-u,c),c=Math.min(q,c),m&&a.css({top:c+"px"})))):e>F&&(m=!0,b={position:"fixed",top:c},b.width="border-box"===a.css("box-sizing")?a.outerWidth()+"px":a.width()+"px",a.css(b).addClass(t),null==p&&(a.after(h),"left"!==r&&"right"!==r||h.append(a)),a.trigger("sticky_kit:stick")),m&&w&&(null==k&&(k=e+u+c>C+n),!v&&k)))return v=!0,"static"===g.css("position")&&g.css({position:"relative"}),
+a.css({position:"absolute",bottom:d,top:"auto"}).trigger("sticky_kit:bottom")},y=function(){x();return l()},H=function(){G=!0;f.off("touchmove",l);f.off("scroll",l);f.off("resize",y);b(document.body).off("sticky_kit:recalc",y);a.off("sticky_kit:detach",H);a.removeData("sticky_kit");a.css({position:"",bottom:"",top:"",width:""});g.position("position","");if(m)return null==p&&("left"!==r&&"right"!==r||a.insertAfter(h),h.remove()),a.removeClass(t)},f.on("touchmove",l),f.on("scroll",l),f.on("resize",
+y),b(document.body).on("sticky_kit:recalc",y),a.on("sticky_kit:detach",H),setTimeout(l,0)}};n=0;for(K=this.length;n<K;n++)d=this[n],J(b(d));return this}}).call(this);
diff --git a/docs/js/bootstrap.js b/docs/js/bootstrap.js
deleted file mode 100644
index 5d6e65b..0000000
--- a/docs/js/bootstrap.js
+++ /dev/null
@@ -1,1825 +0,0 @@
-/* ===================================================
- * bootstrap-transition.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#transitions
- * ===================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ========================================================== */
-
-
-!function ($) {
-
- $(function () {
-
- "use strict"; // jshint ;_;
-
-
- /* CSS TRANSITION SUPPORT (http://www.modernizr.com/)
- * ======================================================= */
-
- $.support.transition = (function () {
-
- var transitionEnd = (function () {
-
- var el = document.createElement('bootstrap')
- , transEndEventNames = {
- 'WebkitTransition' : 'webkitTransitionEnd'
- , 'MozTransition' : 'transitionend'
- , 'OTransition' : 'oTransitionEnd'
- , 'msTransition' : 'MSTransitionEnd'
- , 'transition' : 'transitionend'
- }
- , name
-
- for (name in transEndEventNames){
- if (el.style[name] !== undefined) {
- return transEndEventNames[name]
- }
- }
-
- }())
-
- return transitionEnd && {
- end: transitionEnd
- }
-
- })()
-
- })
-
-}(window.jQuery);/* ==========================================================
- * bootstrap-alert.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#alerts
- * ==========================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ========================================================== */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* ALERT CLASS DEFINITION
- * ====================== */
-
- var dismiss = '[data-dismiss="alert"]'
- , Alert = function (el) {
- $(el).on('click', dismiss, this.close)
- }
-
- Alert.prototype.close = function (e) {
- var $this = $(this)
- , selector = $this.attr('data-target')
- , $parent
-
- if (!selector) {
- selector = $this.attr('href')
- selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7
- }
-
- $parent = $(selector)
-
- e && e.preventDefault()
-
- $parent.length || ($parent = $this.hasClass('alert') ? $this : $this.parent())
-
- $parent.trigger(e = $.Event('close'))
-
- if (e.isDefaultPrevented()) return
-
- $parent.removeClass('in')
-
- function removeElement() {
- $parent
- .trigger('closed')
- .remove()
- }
-
- $.support.transition && $parent.hasClass('fade') ?
- $parent.on($.support.transition.end, removeElement) :
- removeElement()
- }
-
-
- /* ALERT PLUGIN DEFINITION
- * ======================= */
-
- $.fn.alert = function (option) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('alert')
- if (!data) $this.data('alert', (data = new Alert(this)))
- if (typeof option == 'string') data[option].call($this)
- })
- }
-
- $.fn.alert.Constructor = Alert
-
-
- /* ALERT DATA-API
- * ============== */
-
- $(function () {
- $('body').on('click.alert.data-api', dismiss, Alert.prototype.close)
- })
-
-}(window.jQuery);/* ============================================================
- * bootstrap-button.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#buttons
- * ============================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ============================================================ */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* BUTTON PUBLIC CLASS DEFINITION
- * ============================== */
-
- var Button = function (element, options) {
- this.$element = $(element)
- this.options = $.extend({}, $.fn.button.defaults, options)
- }
-
- Button.prototype.setState = function (state) {
- var d = 'disabled'
- , $el = this.$element
- , data = $el.data()
- , val = $el.is('input') ? 'val' : 'html'
-
- state = state + 'Text'
- data.resetText || $el.data('resetText', $el[val]())
-
- $el[val](data[state] || this.options[state])
-
- // push to event loop to allow forms to submit
- setTimeout(function () {
- state == 'loadingText' ?
- $el.addClass(d).attr(d, d) :
- $el.removeClass(d).removeAttr(d)
- }, 0)
- }
-
- Button.prototype.toggle = function () {
- var $parent = this.$element.parent('[data-toggle="buttons-radio"]')
-
- $parent && $parent
- .find('.active')
- .removeClass('active')
-
- this.$element.toggleClass('active')
- }
-
-
- /* BUTTON PLUGIN DEFINITION
- * ======================== */
-
- $.fn.button = function (option) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('button')
- , options = typeof option == 'object' && option
- if (!data) $this.data('button', (data = new Button(this, options)))
- if (option == 'toggle') data.toggle()
- else if (option) data.setState(option)
- })
- }
-
- $.fn.button.defaults = {
- loadingText: 'loading...'
- }
-
- $.fn.button.Constructor = Button
-
-
- /* BUTTON DATA-API
- * =============== */
-
- $(function () {
- $('body').on('click.button.data-api', '[data-toggle^=button]', function ( e ) {
- var $btn = $(e.target)
- if (!$btn.hasClass('btn')) $btn = $btn.closest('.btn')
- $btn.button('toggle')
- })
- })
-
-}(window.jQuery);/* ==========================================================
- * bootstrap-carousel.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#carousel
- * ==========================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ========================================================== */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* CAROUSEL CLASS DEFINITION
- * ========================= */
-
- var Carousel = function (element, options) {
- this.$element = $(element)
- this.options = options
- this.options.slide && this.slide(this.options.slide)
- this.options.pause == 'hover' && this.$element
- .on('mouseenter', $.proxy(this.pause, this))
- .on('mouseleave', $.proxy(this.cycle, this))
- }
-
- Carousel.prototype = {
-
- cycle: function (e) {
- if (!e) this.paused = false
- this.options.interval
- && !this.paused
- && (this.interval = setInterval($.proxy(this.next, this), this.options.interval))
- return this
- }
-
- , to: function (pos) {
- var $active = this.$element.find('.active')
- , children = $active.parent().children()
- , activePos = children.index($active)
- , that = this
-
- if (pos > (children.length - 1) || pos < 0) return
-
- if (this.sliding) {
- return this.$element.one('slid', function () {
- that.to(pos)
- })
- }
-
- if (activePos == pos) {
- return this.pause().cycle()
- }
-
- return this.slide(pos > activePos ? 'next' : 'prev', $(children[pos]))
- }
-
- , pause: function (e) {
- if (!e) this.paused = true
- clearInterval(this.interval)
- this.interval = null
- return this
- }
-
- , next: function () {
- if (this.sliding) return
- return this.slide('next')
- }
-
- , prev: function () {
- if (this.sliding) return
- return this.slide('prev')
- }
-
- , slide: function (type, next) {
- var $active = this.$element.find('.active')
- , $next = next || $active[type]()
- , isCycling = this.interval
- , direction = type == 'next' ? 'left' : 'right'
- , fallback = type == 'next' ? 'first' : 'last'
- , that = this
- , e = $.Event('slide')
-
- this.sliding = true
-
- isCycling && this.pause()
-
- $next = $next.length ? $next : this.$element.find('.item')[fallback]()
-
- if ($next.hasClass('active')) return
-
- if ($.support.transition && this.$element.hasClass('slide')) {
- this.$element.trigger(e)
- if (e.isDefaultPrevented()) return
- $next.addClass(type)
- $next[0].offsetWidth // force reflow
- $active.addClass(direction)
- $next.addClass(direction)
- this.$element.one($.support.transition.end, function () {
- $next.removeClass([type, direction].join(' ')).addClass('active')
- $active.removeClass(['active', direction].join(' '))
- that.sliding = false
- setTimeout(function () { that.$element.trigger('slid') }, 0)
- })
- } else {
- this.$element.trigger(e)
- if (e.isDefaultPrevented()) return
- $active.removeClass('active')
- $next.addClass('active')
- this.sliding = false
- this.$element.trigger('slid')
- }
-
- isCycling && this.cycle()
-
- return this
- }
-
- }
-
-
- /* CAROUSEL PLUGIN DEFINITION
- * ========================== */
-
- $.fn.carousel = function (option) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('carousel')
- , options = $.extend({}, $.fn.carousel.defaults, typeof option == 'object' && option)
- if (!data) $this.data('carousel', (data = new Carousel(this, options)))
- if (typeof option == 'number') data.to(option)
- else if (typeof option == 'string' || (option = options.slide)) data[option]()
- else if (options.interval) data.cycle()
- })
- }
-
- $.fn.carousel.defaults = {
- interval: 5000
- , pause: 'hover'
- }
-
- $.fn.carousel.Constructor = Carousel
-
-
- /* CAROUSEL DATA-API
- * ================= */
-
- $(function () {
- $('body').on('click.carousel.data-api', '[data-slide]', function ( e ) {
- var $this = $(this), href
- , $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7
- , options = !$target.data('modal') && $.extend({}, $target.data(), $this.data())
- $target.carousel(options)
- e.preventDefault()
- })
- })
-
-}(window.jQuery);/* =============================================================
- * bootstrap-collapse.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#collapse
- * =============================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ============================================================ */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* COLLAPSE PUBLIC CLASS DEFINITION
- * ================================ */
-
- var Collapse = function (element, options) {
- this.$element = $(element)
- this.options = $.extend({}, $.fn.collapse.defaults, options)
-
- if (this.options.parent) {
- this.$parent = $(this.options.parent)
- }
-
- this.options.toggle && this.toggle()
- }
-
- Collapse.prototype = {
-
- constructor: Collapse
-
- , dimension: function () {
- var hasWidth = this.$element.hasClass('width')
- return hasWidth ? 'width' : 'height'
- }
-
- , show: function () {
- var dimension
- , scroll
- , actives
- , hasData
-
- if (this.transitioning) return
-
- dimension = this.dimension()
- scroll = $.camelCase(['scroll', dimension].join('-'))
- actives = this.$parent && this.$parent.find('> .accordion-group > .in')
-
- if (actives && actives.length) {
- hasData = actives.data('collapse')
- if (hasData && hasData.transitioning) return
- actives.collapse('hide')
- hasData || actives.data('collapse', null)
- }
-
- this.$element[dimension](0)
- this.transition('addClass', $.Event('show'), 'shown')
- this.$element[dimension](this.$element[0][scroll])
- }
-
- , hide: function () {
- var dimension
- if (this.transitioning) return
- dimension = this.dimension()
- this.reset(this.$element[dimension]())
- this.transition('removeClass', $.Event('hide'), 'hidden')
- this.$element[dimension](0)
- }
-
- , reset: function (size) {
- var dimension = this.dimension()
-
- this.$element
- .removeClass('collapse')
- [dimension](size || 'auto')
- [0].offsetWidth
-
- this.$element[size !== null ? 'addClass' : 'removeClass']('collapse')
-
- return this
- }
-
- , transition: function (method, startEvent, completeEvent) {
- var that = this
- , complete = function () {
- if (startEvent.type == 'show') that.reset()
- that.transitioning = 0
- that.$element.trigger(completeEvent)
- }
-
- this.$element.trigger(startEvent)
-
- if (startEvent.isDefaultPrevented()) return
-
- this.transitioning = 1
-
- this.$element[method]('in')
-
- $.support.transition && this.$element.hasClass('collapse') ?
- this.$element.one($.support.transition.end, complete) :
- complete()
- }
-
- , toggle: function () {
- this[this.$element.hasClass('in') ? 'hide' : 'show']()
- }
-
- }
-
-
- /* COLLAPSIBLE PLUGIN DEFINITION
- * ============================== */
-
- $.fn.collapse = function (option) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('collapse')
- , options = typeof option == 'object' && option
- if (!data) $this.data('collapse', (data = new Collapse(this, options)))
- if (typeof option == 'string') data[option]()
- })
- }
-
- $.fn.collapse.defaults = {
- toggle: true
- }
-
- $.fn.collapse.Constructor = Collapse
-
-
- /* COLLAPSIBLE DATA-API
- * ==================== */
-
- $(function () {
- $('body').on('click.collapse.data-api', '[data-toggle=collapse]', function ( e ) {
- var $this = $(this), href
- , target = $this.attr('data-target')
- || e.preventDefault()
- || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '') //strip for ie7
- , option = $(target).data('collapse') ? 'toggle' : $this.data()
- $(target).collapse(option)
- })
- })
-
-}(window.jQuery);/* ============================================================
- * bootstrap-dropdown.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#dropdowns
- * ============================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ============================================================ */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* DROPDOWN CLASS DEFINITION
- * ========================= */
-
- var toggle = '[data-toggle="dropdown"]'
- , Dropdown = function (element) {
- var $el = $(element).on('click.dropdown.data-api', this.toggle)
- $('html').on('click.dropdown.data-api', function () {
- $el.parent().removeClass('open')
- })
- }
-
- Dropdown.prototype = {
-
- constructor: Dropdown
-
- , toggle: function (e) {
- var $this = $(this)
- , $parent
- , selector
- , isActive
-
- if ($this.is('.disabled, :disabled')) return
-
- selector = $this.attr('data-target')
-
- if (!selector) {
- selector = $this.attr('href')
- selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7
- }
-
- $parent = $(selector)
- $parent.length || ($parent = $this.parent())
-
- isActive = $parent.hasClass('open')
-
- clearMenus()
-
- if (!isActive) $parent.toggleClass('open')
-
- return false
- }
-
- }
-
- function clearMenus() {
- $(toggle).parent().removeClass('open')
- }
-
-
- /* DROPDOWN PLUGIN DEFINITION
- * ========================== */
-
- $.fn.dropdown = function (option) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('dropdown')
- if (!data) $this.data('dropdown', (data = new Dropdown(this)))
- if (typeof option == 'string') data[option].call($this)
- })
- }
-
- $.fn.dropdown.Constructor = Dropdown
-
-
- /* APPLY TO STANDARD DROPDOWN ELEMENTS
- * =================================== */
-
- $(function () {
- $('html').on('click.dropdown.data-api', clearMenus)
- $('body')
- .on('click.dropdown', '.dropdown form', function (e) { e.stopPropagation() })
- .on('click.dropdown.data-api', toggle, Dropdown.prototype.toggle)
- })
-
-}(window.jQuery);/* =========================================================
- * bootstrap-modal.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#modals
- * =========================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ========================================================= */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* MODAL CLASS DEFINITION
- * ====================== */
-
- var Modal = function (content, options) {
- this.options = options
- this.$element = $(content)
- .delegate('[data-dismiss="modal"]', 'click.dismiss.modal', $.proxy(this.hide, this))
- }
-
- Modal.prototype = {
-
- constructor: Modal
-
- , toggle: function () {
- return this[!this.isShown ? 'show' : 'hide']()
- }
-
- , show: function () {
- var that = this
- , e = $.Event('show')
-
- this.$element.trigger(e)
-
- if (this.isShown || e.isDefaultPrevented()) return
-
- $('body').addClass('modal-open')
-
- this.isShown = true
-
- escape.call(this)
- backdrop.call(this, function () {
- var transition = $.support.transition && that.$element.hasClass('fade')
-
- if (!that.$element.parent().length) {
- that.$element.appendTo(document.body) //don't move modals dom position
- }
-
- that.$element
- .show()
-
- if (transition) {
- that.$element[0].offsetWidth // force reflow
- }
-
- that.$element.addClass('in')
-
- transition ?
- that.$element.one($.support.transition.end, function () { that.$element.trigger('shown') }) :
- that.$element.trigger('shown')
-
- })
- }
-
- , hide: function (e) {
- e && e.preventDefault()
-
- var that = this
-
- e = $.Event('hide')
-
- this.$element.trigger(e)
-
- if (!this.isShown || e.isDefaultPrevented()) return
-
- this.isShown = false
-
- $('body').removeClass('modal-open')
-
- escape.call(this)
-
- this.$element.removeClass('in')
-
- $.support.transition && this.$element.hasClass('fade') ?
- hideWithTransition.call(this) :
- hideModal.call(this)
- }
-
- }
-
-
- /* MODAL PRIVATE METHODS
- * ===================== */
-
- function hideWithTransition() {
- var that = this
- , timeout = setTimeout(function () {
- that.$element.off($.support.transition.end)
- hideModal.call(that)
- }, 500)
-
- this.$element.one($.support.transition.end, function () {
- clearTimeout(timeout)
- hideModal.call(that)
- })
- }
-
- function hideModal(that) {
- this.$element
- .hide()
- .trigger('hidden')
-
- backdrop.call(this)
- }
-
- function backdrop(callback) {
- var that = this
- , animate = this.$element.hasClass('fade') ? 'fade' : ''
-
- if (this.isShown && this.options.backdrop) {
- var doAnimate = $.support.transition && animate
-
- this.$backdrop = $('<div class="modal-backdrop ' + animate + '" />')
- .appendTo(document.body)
-
- if (this.options.backdrop != 'static') {
- this.$backdrop.click($.proxy(this.hide, this))
- }
-
- if (doAnimate) this.$backdrop[0].offsetWidth // force reflow
-
- this.$backdrop.addClass('in')
-
- doAnimate ?
- this.$backdrop.one($.support.transition.end, callback) :
- callback()
-
- } else if (!this.isShown && this.$backdrop) {
- this.$backdrop.removeClass('in')
-
- $.support.transition && this.$element.hasClass('fade')?
- this.$backdrop.one($.support.transition.end, $.proxy(removeBackdrop, this)) :
- removeBackdrop.call(this)
-
- } else if (callback) {
- callback()
- }
- }
-
- function removeBackdrop() {
- this.$backdrop.remove()
- this.$backdrop = null
- }
-
- function escape() {
- var that = this
- if (this.isShown && this.options.keyboard) {
- $(document).on('keyup.dismiss.modal', function ( e ) {
- e.which == 27 && that.hide()
- })
- } else if (!this.isShown) {
- $(document).off('keyup.dismiss.modal')
- }
- }
-
-
- /* MODAL PLUGIN DEFINITION
- * ======================= */
-
- $.fn.modal = function (option) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('modal')
- , options = $.extend({}, $.fn.modal.defaults, $this.data(), typeof option == 'object' && option)
- if (!data) $this.data('modal', (data = new Modal(this, options)))
- if (typeof option == 'string') data[option]()
- else if (options.show) data.show()
- })
- }
-
- $.fn.modal.defaults = {
- backdrop: true
- , keyboard: true
- , show: true
- }
-
- $.fn.modal.Constructor = Modal
-
-
- /* MODAL DATA-API
- * ============== */
-
- $(function () {
- $('body').on('click.modal.data-api', '[data-toggle="modal"]', function ( e ) {
- var $this = $(this), href
- , $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7
- , option = $target.data('modal') ? 'toggle' : $.extend({}, $target.data(), $this.data())
-
- e.preventDefault()
- $target.modal(option)
- })
- })
-
-}(window.jQuery);/* ===========================================================
- * bootstrap-tooltip.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#tooltips
- * Inspired by the original jQuery.tipsy by Jason Frame
- * ===========================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ========================================================== */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* TOOLTIP PUBLIC CLASS DEFINITION
- * =============================== */
-
- var Tooltip = function (element, options) {
- this.init('tooltip', element, options)
- }
-
- Tooltip.prototype = {
-
- constructor: Tooltip
-
- , init: function (type, element, options) {
- var eventIn
- , eventOut
-
- this.type = type
- this.$element = $(element)
- this.options = this.getOptions(options)
- this.enabled = true
-
- if (this.options.trigger != 'manual') {
- eventIn = this.options.trigger == 'hover' ? 'mouseenter' : 'focus'
- eventOut = this.options.trigger == 'hover' ? 'mouseleave' : 'blur'
- this.$element.on(eventIn, this.options.selector, $.proxy(this.enter, this))
- this.$element.on(eventOut, this.options.selector, $.proxy(this.leave, this))
- }
-
- this.options.selector ?
- (this._options = $.extend({}, this.options, { trigger: 'manual', selector: '' })) :
- this.fixTitle()
- }
-
- , getOptions: function (options) {
- options = $.extend({}, $.fn[this.type].defaults, options, this.$element.data())
-
- if (options.delay && typeof options.delay == 'number') {
- options.delay = {
- show: options.delay
- , hide: options.delay
- }
- }
-
- return options
- }
-
- , enter: function (e) {
- var self = $(e.currentTarget)[this.type](this._options).data(this.type)
-
- if (!self.options.delay || !self.options.delay.show) return self.show()
-
- clearTimeout(this.timeout)
- self.hoverState = 'in'
- this.timeout = setTimeout(function() {
- if (self.hoverState == 'in') self.show()
- }, self.options.delay.show)
- }
-
- , leave: function (e) {
- var self = $(e.currentTarget)[this.type](this._options).data(this.type)
-
- if (this.timeout) clearTimeout(this.timeout)
- if (!self.options.delay || !self.options.delay.hide) return self.hide()
-
- self.hoverState = 'out'
- this.timeout = setTimeout(function() {
- if (self.hoverState == 'out') self.hide()
- }, self.options.delay.hide)
- }
-
- , show: function () {
- var $tip
- , inside
- , pos
- , actualWidth
- , actualHeight
- , placement
- , tp
-
- if (this.hasContent() && this.enabled) {
- $tip = this.tip()
- this.setContent()
-
- if (this.options.animation) {
- $tip.addClass('fade')
- }
-
- placement = typeof this.options.placement == 'function' ?
- this.options.placement.call(this, $tip[0], this.$element[0]) :
- this.options.placement
-
- inside = /in/.test(placement)
-
- $tip
- .remove()
- .css({ top: 0, left: 0, display: 'block' })
- .appendTo(inside ? this.$element : document.body)
-
- pos = this.getPosition(inside)
-
- actualWidth = $tip[0].offsetWidth
- actualHeight = $tip[0].offsetHeight
-
- switch (inside ? placement.split(' ')[1] : placement) {
- case 'bottom':
- tp = {top: pos.top + pos.height, left: pos.left + pos.width / 2 - actualWidth / 2}
- break
- case 'top':
- tp = {top: pos.top - actualHeight, left: pos.left + pos.width / 2 - actualWidth / 2}
- break
- case 'left':
- tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth}
- break
- case 'right':
- tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width}
- break
- }
-
- $tip
- .css(tp)
- .addClass(placement)
- .addClass('in')
- }
- }
-
- , isHTML: function(text) {
- // html string detection logic adapted from jQuery
- return typeof text != 'string'
- || ( text.charAt(0) === "<"
- && text.charAt( text.length - 1 ) === ">"
- && text.length >= 3
- ) || /^(?:[^<]*<[\w\W]+>[^>]*$)/.exec(text)
- }
-
- , setContent: function () {
- var $tip = this.tip()
- , title = this.getTitle()
-
- $tip.find('.tooltip-inner')[this.isHTML(title) ? 'html' : 'text'](title)
- $tip.removeClass('fade in top bottom left right')
- }
-
- , hide: function () {
- var that = this
- , $tip = this.tip()
-
- $tip.removeClass('in')
-
- function removeWithAnimation() {
- var timeout = setTimeout(function () {
- $tip.off($.support.transition.end).remove()
- }, 500)
-
- $tip.one($.support.transition.end, function () {
- clearTimeout(timeout)
- $tip.remove()
- })
- }
-
- $.support.transition && this.$tip.hasClass('fade') ?
- removeWithAnimation() :
- $tip.remove()
- }
-
- , fixTitle: function () {
- var $e = this.$element
- if ($e.attr('title') || typeof($e.attr('data-original-title')) != 'string') {
- $e.attr('data-original-title', $e.attr('title') || '').removeAttr('title')
- }
- }
-
- , hasContent: function () {
- return this.getTitle()
- }
-
- , getPosition: function (inside) {
- return $.extend({}, (inside ? {top: 0, left: 0} : this.$element.offset()), {
- width: this.$element[0].offsetWidth
- , height: this.$element[0].offsetHeight
- })
- }
-
- , getTitle: function () {
- var title
- , $e = this.$element
- , o = this.options
-
- title = $e.attr('data-original-title')
- || (typeof o.title == 'function' ? o.title.call($e[0]) : o.title)
-
- return title
- }
-
- , tip: function () {
- return this.$tip = this.$tip || $(this.options.template)
- }
-
- , validate: function () {
- if (!this.$element[0].parentNode) {
- this.hide()
- this.$element = null
- this.options = null
- }
- }
-
- , enable: function () {
- this.enabled = true
- }
-
- , disable: function () {
- this.enabled = false
- }
-
- , toggleEnabled: function () {
- this.enabled = !this.enabled
- }
-
- , toggle: function () {
- this[this.tip().hasClass('in') ? 'hide' : 'show']()
- }
-
- }
-
-
- /* TOOLTIP PLUGIN DEFINITION
- * ========================= */
-
- $.fn.tooltip = function ( option ) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('tooltip')
- , options = typeof option == 'object' && option
- if (!data) $this.data('tooltip', (data = new Tooltip(this, options)))
- if (typeof option == 'string') data[option]()
- })
- }
-
- $.fn.tooltip.Constructor = Tooltip
-
- $.fn.tooltip.defaults = {
- animation: true
- , placement: 'top'
- , selector: false
- , template: '<div class="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>'
- , trigger: 'hover'
- , title: ''
- , delay: 0
- }
-
-}(window.jQuery);
-/* ===========================================================
- * bootstrap-popover.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#popovers
- * ===========================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * =========================================================== */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* POPOVER PUBLIC CLASS DEFINITION
- * =============================== */
-
- var Popover = function ( element, options ) {
- this.init('popover', element, options)
- }
-
-
- /* NOTE: POPOVER EXTENDS BOOTSTRAP-TOOLTIP.js
- ========================================== */
-
- Popover.prototype = $.extend({}, $.fn.tooltip.Constructor.prototype, {
-
- constructor: Popover
-
- , setContent: function () {
- var $tip = this.tip()
- , title = this.getTitle()
- , content = this.getContent()
-
- $tip.find('.popover-title')[this.isHTML(title) ? 'html' : 'text'](title)
- $tip.find('.popover-content > *')[this.isHTML(content) ? 'html' : 'text'](content)
-
- $tip.removeClass('fade top bottom left right in')
- }
-
- , hasContent: function () {
- return this.getTitle() || this.getContent()
- }
-
- , getContent: function () {
- var content
- , $e = this.$element
- , o = this.options
-
- content = $e.attr('data-content')
- || (typeof o.content == 'function' ? o.content.call($e[0]) : o.content)
-
- return content
- }
-
- , tip: function () {
- if (!this.$tip) {
- this.$tip = $(this.options.template)
- }
- return this.$tip
- }
-
- })
-
-
- /* POPOVER PLUGIN DEFINITION
- * ======================= */
-
- $.fn.popover = function (option) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('popover')
- , options = typeof option == 'object' && option
- if (!data) $this.data('popover', (data = new Popover(this, options)))
- if (typeof option == 'string') data[option]()
- })
- }
-
- $.fn.popover.Constructor = Popover
-
- $.fn.popover.defaults = $.extend({} , $.fn.tooltip.defaults, {
- placement: 'right'
- , content: ''
- , template: '<div class="popover"><div class="arrow"></div><div class="popover-inner"><h3 class="popover-title"></h3><div class="popover-content"><p></p></div></div></div>'
- })
-
-}(window.jQuery);/* =============================================================
- * bootstrap-scrollspy.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#scrollspy
- * =============================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ============================================================== */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* SCROLLSPY CLASS DEFINITION
- * ========================== */
-
- function ScrollSpy( element, options) {
- var process = $.proxy(this.process, this)
- , $element = $(element).is('body') ? $(window) : $(element)
- , href
- this.options = $.extend({}, $.fn.scrollspy.defaults, options)
- this.$scrollElement = $element.on('scroll.scroll.data-api', process)
- this.selector = (this.options.target
- || ((href = $(element).attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7
- || '') + ' .nav li > a'
- this.$body = $('body')
- this.refresh()
- this.process()
- }
-
- ScrollSpy.prototype = {
-
- constructor: ScrollSpy
-
- , refresh: function () {
- var self = this
- , $targets
-
- this.offsets = $([])
- this.targets = $([])
-
- $targets = this.$body
- .find(this.selector)
- .map(function () {
- var $el = $(this)
- , href = $el.data('target') || $el.attr('href')
- , $href = /^#\w/.test(href) && $(href)
- return ( $href
- && href.length
- && [[ $href.position().top, href ]] ) || null
- })
- .sort(function (a, b) { return a[0] - b[0] })
- .each(function () {
- self.offsets.push(this[0])
- self.targets.push(this[1])
- })
- }
-
- , process: function () {
- var scrollTop = this.$scrollElement.scrollTop() + this.options.offset
- , scrollHeight = this.$scrollElement[0].scrollHeight || this.$body[0].scrollHeight
- , maxScroll = scrollHeight - this.$scrollElement.height()
- , offsets = this.offsets
- , targets = this.targets
- , activeTarget = this.activeTarget
- , i
-
- if (scrollTop >= maxScroll) {
- return activeTarget != (i = targets.last()[0])
- && this.activate ( i )
- }
-
- for (i = offsets.length; i--;) {
- activeTarget != targets[i]
- && scrollTop >= offsets[i]
- && (!offsets[i + 1] || scrollTop <= offsets[i + 1])
- && this.activate( targets[i] )
- }
- }
-
- , activate: function (target) {
- var active
- , selector
-
- this.activeTarget = target
-
- $(this.selector)
- .parent('.active')
- .removeClass('active')
-
- selector = this.selector
- + '[data-target="' + target + '"],'
- + this.selector + '[href="' + target + '"]'
-
- active = $(selector)
- .parent('li')
- .addClass('active')
-
- if (active.parent('.dropdown-menu')) {
- active = active.closest('li.dropdown').addClass('active')
- }
-
- active.trigger('activate')
- }
-
- }
-
-
- /* SCROLLSPY PLUGIN DEFINITION
- * =========================== */
-
- $.fn.scrollspy = function ( option ) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('scrollspy')
- , options = typeof option == 'object' && option
- if (!data) $this.data('scrollspy', (data = new ScrollSpy(this, options)))
- if (typeof option == 'string') data[option]()
- })
- }
-
- $.fn.scrollspy.Constructor = ScrollSpy
-
- $.fn.scrollspy.defaults = {
- offset: 10
- }
-
-
- /* SCROLLSPY DATA-API
- * ================== */
-
- $(function () {
- $('[data-spy="scroll"]').each(function () {
- var $spy = $(this)
- $spy.scrollspy($spy.data())
- })
- })
-
-}(window.jQuery);/* ========================================================
- * bootstrap-tab.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#tabs
- * ========================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ======================================================== */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* TAB CLASS DEFINITION
- * ==================== */
-
- var Tab = function ( element ) {
- this.element = $(element)
- }
-
- Tab.prototype = {
-
- constructor: Tab
-
- , show: function () {
- var $this = this.element
- , $ul = $this.closest('ul:not(.dropdown-menu)')
- , selector = $this.attr('data-target')
- , previous
- , $target
- , e
-
- if (!selector) {
- selector = $this.attr('href')
- selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7
- }
-
- if ( $this.parent('li').hasClass('active') ) return
-
- previous = $ul.find('.active a').last()[0]
-
- e = $.Event('show', {
- relatedTarget: previous
- })
-
- $this.trigger(e)
-
- if (e.isDefaultPrevented()) return
-
- $target = $(selector)
-
- this.activate($this.parent('li'), $ul)
- this.activate($target, $target.parent(), function () {
- $this.trigger({
- type: 'shown'
- , relatedTarget: previous
- })
- })
- }
-
- , activate: function ( element, container, callback) {
- var $active = container.find('> .active')
- , transition = callback
- && $.support.transition
- && $active.hasClass('fade')
-
- function next() {
- $active
- .removeClass('active')
- .find('> .dropdown-menu > .active')
- .removeClass('active')
-
- element.addClass('active')
-
- if (transition) {
- element[0].offsetWidth // reflow for transition
- element.addClass('in')
- } else {
- element.removeClass('fade')
- }
-
- if ( element.parent('.dropdown-menu') ) {
- element.closest('li.dropdown').addClass('active')
- }
-
- callback && callback()
- }
-
- transition ?
- $active.one($.support.transition.end, next) :
- next()
-
- $active.removeClass('in')
- }
- }
-
-
- /* TAB PLUGIN DEFINITION
- * ===================== */
-
- $.fn.tab = function ( option ) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('tab')
- if (!data) $this.data('tab', (data = new Tab(this)))
- if (typeof option == 'string') data[option]()
- })
- }
-
- $.fn.tab.Constructor = Tab
-
-
- /* TAB DATA-API
- * ============ */
-
- $(function () {
- $('body').on('click.tab.data-api', '[data-toggle="tab"], [data-toggle="pill"]', function (e) {
- e.preventDefault()
- $(this).tab('show')
- })
- })
-
-}(window.jQuery);/* =============================================================
- * bootstrap-typeahead.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#typeahead
- * =============================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ============================================================ */
-
-
-!function($){
-
- "use strict"; // jshint ;_;
-
-
- /* TYPEAHEAD PUBLIC CLASS DEFINITION
- * ================================= */
-
- var Typeahead = function (element, options) {
- this.$element = $(element)
- this.options = $.extend({}, $.fn.typeahead.defaults, options)
- this.matcher = this.options.matcher || this.matcher
- this.sorter = this.options.sorter || this.sorter
- this.highlighter = this.options.highlighter || this.highlighter
- this.updater = this.options.updater || this.updater
- this.$menu = $(this.options.menu).appendTo('body')
- this.source = this.options.source
- this.shown = false
- this.listen()
- }
-
- Typeahead.prototype = {
-
- constructor: Typeahead
-
- , select: function () {
- var val = this.$menu.find('.active').attr('data-value')
- this.$element
- .val(this.updater(val))
- .change()
- return this.hide()
- }
-
- , updater: function (item) {
- return item
- }
-
- , show: function () {
- var pos = $.extend({}, this.$element.offset(), {
- height: this.$element[0].offsetHeight
- })
-
- this.$menu.css({
- top: pos.top + pos.height
- , left: pos.left
- })
-
- this.$menu.show()
- this.shown = true
- return this
- }
-
- , hide: function () {
- this.$menu.hide()
- this.shown = false
- return this
- }
-
- , lookup: function (event) {
- var that = this
- , items
- , q
-
- this.query = this.$element.val()
-
- if (!this.query) {
- return this.shown ? this.hide() : this
- }
-
- items = $.grep(this.source, function (item) {
- return that.matcher(item)
- })
-
- items = this.sorter(items)
-
- if (!items.length) {
- return this.shown ? this.hide() : this
- }
-
- return this.render(items.slice(0, this.options.items)).show()
- }
-
- , matcher: function (item) {
- return ~item.toLowerCase().indexOf(this.query.toLowerCase())
- }
-
- , sorter: function (items) {
- var beginswith = []
- , caseSensitive = []
- , caseInsensitive = []
- , item
-
- while (item = items.shift()) {
- if (!item.toLowerCase().indexOf(this.query.toLowerCase())) beginswith.push(item)
- else if (~item.indexOf(this.query)) caseSensitive.push(item)
- else caseInsensitive.push(item)
- }
-
- return beginswith.concat(caseSensitive, caseInsensitive)
- }
-
- , highlighter: function (item) {
- var query = this.query.replace(/[\-\[\]{}()*+?.,\\\^$|#\s]/g, '\\$&')
- return item.replace(new RegExp('(' + query + ')', 'ig'), function ($1, match) {
- return '<strong>' + match + '</strong>'
- })
- }
-
- , render: function (items) {
- var that = this
-
- items = $(items).map(function (i, item) {
- i = $(that.options.item).attr('data-value', item)
- i.find('a').html(that.highlighter(item))
- return i[0]
- })
-
- items.first().addClass('active')
- this.$menu.html(items)
- return this
- }
-
- , next: function (event) {
- var active = this.$menu.find('.active').removeClass('active')
- , next = active.next()
-
- if (!next.length) {
- next = $(this.$menu.find('li')[0])
- }
-
- next.addClass('active')
- }
-
- , prev: function (event) {
- var active = this.$menu.find('.active').removeClass('active')
- , prev = active.prev()
-
- if (!prev.length) {
- prev = this.$menu.find('li').last()
- }
-
- prev.addClass('active')
- }
-
- , listen: function () {
- this.$element
- .on('blur', $.proxy(this.blur, this))
- .on('keypress', $.proxy(this.keypress, this))
- .on('keyup', $.proxy(this.keyup, this))
-
- if ($.browser.webkit || $.browser.msie) {
- this.$element.on('keydown', $.proxy(this.keypress, this))
- }
-
- this.$menu
- .on('click', $.proxy(this.click, this))
- .on('mouseenter', 'li', $.proxy(this.mouseenter, this))
- }
-
- , keyup: function (e) {
- switch(e.keyCode) {
- case 40: // down arrow
- case 38: // up arrow
- break
-
- case 9: // tab
- case 13: // enter
- if (!this.shown) return
- this.select()
- break
-
- case 27: // escape
- if (!this.shown) return
- this.hide()
- break
-
- default:
- this.lookup()
- }
-
- e.stopPropagation()
- e.preventDefault()
- }
-
- , keypress: function (e) {
- if (!this.shown) return
-
- switch(e.keyCode) {
- case 9: // tab
- case 13: // enter
- case 27: // escape
- e.preventDefault()
- break
-
- case 38: // up arrow
- if (e.type != 'keydown') break
- e.preventDefault()
- this.prev()
- break
-
- case 40: // down arrow
- if (e.type != 'keydown') break
- e.preventDefault()
- this.next()
- break
- }
-
- e.stopPropagation()
- }
-
- , blur: function (e) {
- var that = this
- setTimeout(function () { that.hide() }, 150)
- }
-
- , click: function (e) {
- e.stopPropagation()
- e.preventDefault()
- this.select()
- }
-
- , mouseenter: function (e) {
- this.$menu.find('.active').removeClass('active')
- $(e.currentTarget).addClass('active')
- }
-
- }
-
-
- /* TYPEAHEAD PLUGIN DEFINITION
- * =========================== */
-
- $.fn.typeahead = function (option) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('typeahead')
- , options = typeof option == 'object' && option
- if (!data) $this.data('typeahead', (data = new Typeahead(this, options)))
- if (typeof option == 'string') data[option]()
- })
- }
-
- $.fn.typeahead.defaults = {
- source: []
- , items: 8
- , menu: '<ul class="typeahead dropdown-menu"></ul>'
- , item: '<li><a href="#"></a></li>'
- }
-
- $.fn.typeahead.Constructor = Typeahead
-
-
- /* TYPEAHEAD DATA-API
- * ================== */
-
- $(function () {
- $('body').on('focus.typeahead.data-api', '[data-provide="typeahead"]', function (e) {
- var $this = $(this)
- if ($this.data('typeahead')) return
- e.preventDefault()
- $this.typeahead($this.data())
- })
- })
-
-}(window.jQuery); \ No newline at end of file
diff --git a/docs/js/bootstrap.min.js b/docs/js/bootstrap.min.js
deleted file mode 100644
index 1435698..0000000
--- a/docs/js/bootstrap.min.js
+++ /dev/null
@@ -1,6 +0,0 @@
-/*!
-* Bootstrap.js by @fat & @mdo
-* Copyright 2012 Twitter, Inc.
-* http://www.apache.org/licenses/LICENSE-2.0.txt
-*/
-!function(a){a(function(){"use strict",a.support.transition=function(){var a=function(){var a=document.createElement("bootstrap"),b={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd",msTransition:"MSTransitionEnd",transition:"transitionend"},c;for(c in b)if(a.style[c]!==undefined)return b[c]}();return a&&{end:a}}()})}(window.jQuery),!function(a){"use strict";var b='[data-dismiss="alert"]',c=function(c){a(c).on("click",b,this.close)};c.prototype.close=function(b){function f(){e.trigger("closed").remove()}var c=a(this),d=c.attr("data-target"),e;d||(d=c.attr("href"),d=d&&d.replace(/.*(?=#[^\s]*$)/,"")),e=a(d),b&&b.preventDefault(),e.length||(e=c.hasClass("alert")?c:c.parent()),e.trigger(b=a.Event("close"));if(b.isDefaultPrevented())return;e.removeClass("in"),a.support.transition&&e.hasClass("fade")?e.on(a.support.transition.end,f):f()},a.fn.alert=function(b){return this.each(function(){var d=a(this),e=d.data("alert");e||d.data("alert",e=new 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+++ /dev/null
@@ -1,123 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>pfm_degradation. pfm 0.3-8</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="
-Johannes Ranke
-">
-
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- }
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- src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
- </head>
-
- <body>
- <div class="navbar">
- <div class="navbar-inner">
- <div class="container">
- <a class="brand" href="index.html">pfm 0.3-8</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html">Home</a></li>
- <li><a href="reference.html">Reference</a></li>
- </ul>
- </div>
- </div>
- </div>
-</div>
-
-
- <div class="container">
- <header>
-
- </header>
-
- <h1>Calculate a time course of relative concentrations based on an mkinmod model</h1>
-
-<div class="row">
- <div class="span8">
- <h2>Usage</h2>
- <pre><span class="functioncall"><a href='pfm_degradation.html'>pfm_degradation</a></span><span class="keyword">(</span><span class="argument">model</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"SFO"</span><span class="keyword">,</span> <span class="argument">DT50</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">1000</span><span class="keyword">,</span> <span class="argument">parms</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">k_parent_sink</span> <span class="argument">=</span>
- <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/Log'>log</a></span><span class="keyword">(</span><span class="number">2</span><span class="keyword">)</span><span class="keyword">/</span><span class="symbol">DT50</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">years</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">1</span><span class="keyword">,</span> <span class="argument">step_days</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">1</span><span class="keyword">,</span> <span class="argument">times</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="symbol">years</span> <span class="keyword">*</span> <span class="number">365</span><span class="keyword">,</span> <span class="argument">by</span> <span class="argument">=</span>
- <span class="symbol">step_days</span><span class="keyword">)</span><span class="keyword">)</span></pre>
-
- <h2>Arguments</h2>
- <dl>
- <dt>model</dt>
- <dd>The degradation model to be used. Either a parent only model like
-&#39;SFO&#39; or &#39;FOMC&#39;, or an mkinmod object</dd>
- <dt>DT50</dt>
- <dd>The half-life. This is only used when simple exponential decline
-is calculated (SFO model).</dd>
- <dt>parms</dt>
- <dd>The parameters used for the degradation model</dd>
- <dt>years</dt>
- <dd>For how many years should the degradation be predicted?</dd>
- <dt>step_days</dt>
- <dd>What step size in days should the output have?</dd>
- <dt>times</dt>
- <dd>The output times</dd>
- </dl>
-
- <div class="Description">
- <h2>Description</h2>
-
- <p>Calculate a time course of relative concentrations based on an mkinmod model</p>
-
- </div>
-
- <h2 id="examples">Examples</h2>
- <pre class="examples"><div class='input'><span class="functioncall"><a href='http://www.rdocumentation.org/packages/utils/topics/head'>head</a></span><span class="keyword">(</span><span class="functioncall"><a href='pfm_degradation.html'>pfm_degradation</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="argument">DT50</span> <span class="argument">=</span> <span class="number">10</span><span class="keyword">)</span><span class="keyword">)</span></div>
-<div class='output'> time parent
-1 0 1.0000000
-2 1 0.9330330
-3 2 0.8705506
-4 3 0.8122524
-5 4 0.7578583
-6 5 0.7071068
-</div></pre>
- </div>
- <div class="span4 sidebar">
- <!-- <ul>
- <li>pfm_degradation</li>
- </ul>
- <ul>
-
- </ul> -->
-
-
-
- <h2>Author</h2>
-
-Johannes Ranke
-
-
- </div>
-</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
- </footer>
- </div>
- </body>
-</html> \ No newline at end of file
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
new file mode 100644
index 0000000..fd7b0ba
--- /dev/null
+++ b/docs/pkgdown.css
@@ -0,0 +1,113 @@
+/* Sticker footer */
+body > .container {
+ display: flex;
+ padding-top: 60px;
+ min-height: calc(100vh);
+ flex-direction: column;
+}
+
+body > .container .row {
+ flex: 1;
+}
+
+footer {
+ margin-top: 45px;
+ padding: 35px 0 36px;
+ border-top: 1px solid #e5e5e5;
+ color: #666;
+ display: flex;
+}
+footer p {
+ margin-bottom: 0;
+}
+footer div {
+ flex: 1;
+}
+footer .pkgdown {
+ text-align: right;
+}
+footer p {
+ margin-bottom: 0;
+}
+
+img.icon {
+ float: right;
+}
+
+/* Section anchors ---------------------------------*/
+
+.hasAnchor {
+ margin-left: -30px;
+}
+
+a.anchor {
+ display:inline-block;
+ width: 30px;
+ height: 30px;
+ visibility: hidden;
+
+ background-image: url(./link.svg);
+ background-repeat: no-repeat;
+ background-size: 20px 20px;
+ background-position: center center;
+}
+
+.hasAnchor:hover a.anchor {
+ visibility: visible;
+}
+
+/* Fixes for fixed navbar --------------------------*/
+
+.contents h1, .contents h2, .contents h3, .contents h4 {
+ padding-top: 60px;
+ margin-top: -60px;
+}
+
+/* Sidebar --------------------------*/
+
+#sidebar {
+ margin-top: 30px;
+}
+#sidebar h2 {
+ font-size: 1.5em;
+ margin-top: 1em;
+}
+
+#sidebar h2:first-child {
+ margin-top: 0;
+}
+
+#sidebar .list-unstyled li {
+ margin-bottom: 0.5em;
+}
+
+/* Syntax highlighting ---------------------------------------------------- */
+
+code {
+ background-color: #f7f7f7;
+ color: #333;
+}
+code a {
+ color: #375f84;
+}
+
+.warning { color: red; }
+.message { font-weight: bolder; }
+.error { color: red; font-weight: bolder; }
+
+.fl,.number {color:rgb(21,20,181);}
+.fu,.functioncall {color:#264D66 ;}
+.ch,.st,.string {color:#375D81 ;}
+.kw,.keyword {color:black;}
+.argument {color:#264D66 ;}
+.co,.comment {color: #777;}
+.formalargs {color: #264D66;}
+.eqformalargs {color:#264D66;}
+.slot {font-style:italic;}
+.symbol {color:black ;}
+.prompt {color:black ;}
+
+pre img {
+ background-color: #fff;
+ display: block;
+}
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
new file mode 100644
index 0000000..c8b38c4
--- /dev/null
+++ b/docs/pkgdown.js
@@ -0,0 +1,8 @@
+$(function() {
+ $("#sidebar").stick_in_parent({offset_top: 40});
+ $('body').scrollspy({
+ target: '#sidebar',
+ offset: 60
+ });
+
+});
diff --git a/docs/plot.TOXSWA_cwa-2.png b/docs/plot.TOXSWA_cwa-2.png
deleted file mode 100644
index 764c7f4..0000000
--- a/docs/plot.TOXSWA_cwa-2.png
+++ /dev/null
Binary files differ
diff --git a/docs/plot.TOXSWA_cwa.html b/docs/plot.TOXSWA_cwa.html
deleted file mode 100644
index 87dae02..0000000
--- a/docs/plot.TOXSWA_cwa.html
+++ /dev/null
@@ -1,124 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>plot.TOXSWA_cwa. pfm 0.3-8</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="
-Johannes Ranke
-">
-
-<link href="css/bootstrap.css" rel="stylesheet">
-<link href="css/bootstrap-responsive.css" rel="stylesheet">
-<link href="css/highlight.css" rel="stylesheet">
-<link href="css/staticdocs.css" rel="stylesheet">
-
-<!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-<![endif]-->
-
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [ ['$','$'], ["\\(","\\)"] ],
- processEscapes: true
- }
- });
-</script>
-<script type="text/javascript"
- src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
- </head>
-
- <body>
- <div class="navbar">
- <div class="navbar-inner">
- <div class="container">
- <a class="brand" href="index.html">pfm 0.3-8</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html">Home</a></li>
- <li><a href="reference.html">Reference</a></li>
- </ul>
- </div>
- </div>
- </div>
-</div>
-
-
- <div class="container">
- <header>
-
- </header>
-
- <h1>Plot TOXSWA surface water concentrations</h1>
-
-<div class="row">
- <div class="span8">
- <h2>Usage</h2>
- <pre><span class="comment"># S3 method for TOXSWA_cwa</span>
-<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">x</span><span class="keyword">,</span> <span class="argument">time_column</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"datetime"</span><span class="keyword">,</span> <span class="string">"t"</span><span class="keyword">,</span> <span class="string">"t_firstjan"</span><span class="keyword">,</span>
- <span class="string">"t_rel_to_max"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">xlab</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"default"</span><span class="keyword">,</span> <span class="argument">ylab</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"default"</span><span class="keyword">,</span> <span class="argument">add</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">,</span>
- <span class="argument">total</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">LC_TIME</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"C"</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span></pre>
-
- <h2>Arguments</h2>
- <dl>
- <dt>x</dt>
- <dd>The TOXSWA_cwa object to be plotted.</dd>
- <dt>time_column</dt>
- <dd>What should be used for the time axis. If &quot;t_firstjan&quot; is chosen,
-the time is given in days relative to the first of January in the first year.</dd>
- <dt>xlab, ylab</dt>
- <dd>Labels for x and y axis.</dd>
- <dt>add</dt>
- <dd>Should we add to an existing plot?</dd>
- <dt>total</dt>
- <dd>Should the total concentration in water be plotted, including substance sorbed
-to suspended matter?</dd>
- <dt>LC_TIME</dt>
- <dd>Specification of the locale used to format dates</dd>
- <dt>...</dt>
- <dd>Further arguments passed to <code>plot</code> if we are not adding to an existing plot</dd>
- </dl>
-
- <div class="Description">
- <h2>Description</h2>
-
- <p>Plot TOXSWA hourly concentrations of a chemical substance in a specific
-segment of a TOXSWA surface water body.</p>
-
- </div>
-
- <h2 id="examples">Examples</h2>
- <pre class="examples"><div class='input'><span class="symbol">H_sw_D4_pond</span> <span class="assignement">&lt;-</span> <span class="functioncall"><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span><span class="keyword">(</span><span class="string">"00001p_pa.cwa"</span><span class="keyword">,</span>
- <span class="argument">basedir</span> <span class="argument">=</span> <span class="string">"SwashProjects/project_H_sw/TOXSWA"</span><span class="keyword">,</span>
- <span class="argument">zipfile</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/devtools/topics/system.file'>system.file</a></span><span class="keyword">(</span><span class="string">"testdata/SwashProjects.zip"</span><span class="keyword">,</span>
- <span class="argument">package</span> <span class="argument">=</span> <span class="string">"pfm"</span><span class="keyword">)</span><span class="keyword">)</span>
-<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">H_sw_D4_pond</span><span class="keyword">)</span></div>
-<p><img src='plot.TOXSWA_cwa-2.png' alt='' width='540' height='400' /></p></pre>
- </div>
- <div class="span4 sidebar">
- <!-- <ul>
- <li>plot.TOXSWA_cwa</li>
- </ul>
- <ul>
-
- </ul> -->
-
-
-
- <h2>Author</h2>
-
-Johannes Ranke
-
-
- </div>
-</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
- </footer>
- </div>
- </body>
-</html> \ No newline at end of file
diff --git a/docs/read.TOXSWA_cwa.html b/docs/read.TOXSWA_cwa.html
deleted file mode 100644
index cc34733..0000000
--- a/docs/read.TOXSWA_cwa.html
+++ /dev/null
@@ -1,142 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>read.TOXSWA_cwa. pfm 0.3-8</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="
-Johannes Ranke
-">
-
-<link href="css/bootstrap.css" rel="stylesheet">
-<link href="css/bootstrap-responsive.css" rel="stylesheet">
-<link href="css/highlight.css" rel="stylesheet">
-<link href="css/staticdocs.css" rel="stylesheet">
-
-<!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-<![endif]-->
-
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [ ['$','$'], ["\\(","\\)"] ],
- processEscapes: true
- }
- });
-</script>
-<script type="text/javascript"
- src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
- </head>
-
- <body>
- <div class="navbar">
- <div class="navbar-inner">
- <div class="container">
- <a class="brand" href="index.html">pfm 0.3-8</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html">Home</a></li>
- <li><a href="reference.html">Reference</a></li>
- </ul>
- </div>
- </div>
- </div>
-</div>
-
-
- <div class="container">
- <header>
-
- </header>
-
- <h1>Read TOXSWA surface water concentrations</h1>
-
-<div class="row">
- <div class="span8">
- <h2>Usage</h2>
- <pre><span class="functioncall"><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span><span class="keyword">(</span><span class="symbol">filename</span><span class="keyword">,</span> <span class="argument">basedir</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"."</span><span class="keyword">,</span> <span class="argument">zipfile</span>&nbsp;<span class="argument">=</span>&nbsp;NULL<span class="keyword">,</span> <span class="argument">segment</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"last"</span><span class="keyword">,</span>
- <span class="argument">substance</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"parent"</span><span class="keyword">,</span> <span class="argument">total</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">windows</span>&nbsp;<span class="argument">=</span>&nbsp;NULL<span class="keyword">,</span>
- <span class="argument">thresholds</span>&nbsp;<span class="argument">=</span>&nbsp;NULL<span class="keyword">)</span></pre>
-
- <h2>Arguments</h2>
- <dl>
- <dt>filename</dt>
- <dd>The filename of the cwa file (TOXSWA 2.x.y or similar) or the
-out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).</dd>
- <dt>basedir</dt>
- <dd>The path to the directory where the cwa file resides.</dd>
- <dt>zipfile</dt>
- <dd>Optional path to a zip file containing the cwa file.</dd>
- <dt>segment</dt>
- <dd>The segment for which the data should be read. Either &quot;last&quot;, or
-the segment number.</dd>
- <dt>substance</dt>
- <dd>For TOXSWA 4 .out files, the default value &quot;parent&quot; leads
-to reading concentrations of the parent compound. Alternatively, the substance
-of interested can be selected by its code name.</dd>
- <dt>total</dt>
- <dd>Set this to TRUE in order to read total concentrations as well. This is
-only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa
-files. For .cwa files, the total concentration is always read as well.</dd>
- <dt>windows</dt>
- <dd>Numeric vector of width of moving windows in days, for calculating
-maximum time weighted average concentrations and areas under the curve.</dd>
- <dt>thresholds</dt>
- <dd>Numeric vector of threshold concentrations in µg/L for
-generating event statistics.</dd>
- </dl>
-
- <div class="Value">
- <h2>Value</h2>
-
- <p><dl>
-An instance of an R6 object of class
-<code><a href='TOXSWA_cwa.html'>TOXSWA_cwa</a></code>.
-</dl></p>
-
- </div>
-
- <div class="Description">
- <h2>Description</h2>
-
- <p>Read TOXSWA hourly concentrations of a chemical substance in a specific
-segment of a TOXSWA surface water body. Per default, the data for the last
-segment are imported. As TOXSWA 4 reports the values at the end of the hour
-(ConLiqWatLayCur) in its summary file, we use this value as well instead
-of the hourly averages (ConLiqWatLay).</p>
-
- </div>
-
- <h2 id="examples">Examples</h2>
- <pre class="examples"><div class='input'><span class="symbol">H_sw_D4_pond</span> <span class="assignement">&lt;-</span> <span class="functioncall"><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span><span class="keyword">(</span><span class="string">"00001p_pa.cwa"</span><span class="keyword">,</span>
- <span class="argument">basedir</span> <span class="argument">=</span> <span class="string">"SwashProjects/project_H_sw/TOXSWA"</span><span class="keyword">,</span>
- <span class="argument">zipfile</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/devtools/topics/system.file'>system.file</a></span><span class="keyword">(</span><span class="string">"testdata/SwashProjects.zip"</span><span class="keyword">,</span>
- <span class="argument">package</span> <span class="argument">=</span> <span class="string">"pfm"</span><span class="keyword">)</span><span class="keyword">)</span></div></pre>
- </div>
- <div class="span4 sidebar">
- <!-- <ul>
- <li>read.TOXSWA_cwa</li>
- </ul>
- <ul>
-
- </ul> -->
-
-
-
- <h2>Author</h2>
-
-Johannes Ranke
-
-
- </div>
-</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
- </footer>
- </div>
- </body>
-</html> \ No newline at end of file
diff --git a/docs/reference.html b/docs/reference.html
deleted file mode 100644
index 83e788a..0000000
--- a/docs/reference.html
+++ /dev/null
@@ -1,164 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>Function reference. pfm 0.3-8</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="">
-
-<link href="css/bootstrap.css" rel="stylesheet">
-<link href="css/bootstrap-responsive.css" rel="stylesheet">
-<link href="css/highlight.css" rel="stylesheet">
-<link href="css/staticdocs.css" rel="stylesheet">
-
-<!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-<![endif]-->
-
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [ ['$','$'], ["\\(","\\)"] ],
- processEscapes: true
- }
- });
-</script>
-<script type="text/javascript"
- src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
- </head>
-
- <body>
- <div class="navbar">
- <div class="navbar-inner">
- <div class="container">
- <a class="brand" href="index.html">pfm 0.3-8</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html">Home</a></li>
- <li><a href="reference.html">Reference</a></li>
- </ul>
- </div>
- </div>
- </div>
-</div>
-
-
- <div class="container">
- <header>
-
- </header>
-
- <div class="row">
- <div class="span8">
- <h2>Function reference</h2>
-
- <h3>Degradation</h3>
- <p>Functions related to degradation</p>
-
-
- <ul class="index">
-
- <li>
- <code><a href="pfm_degradation.html">pfm_degradation</a></code><br />Calculate a time course of relative concentrations based on an mkinmod model</li>
-
- <li>
- <code><a href="SFO_actual_twa.html">SFO_actual_twa</a></code><br />Actual and maximum moving window time average concentrations for SFO kinetics</li>
-
- </ul>
- <h3>Mobility</h3>
- <p>Indicators related to mobility</p>
-
-
- <ul class="index">
-
- <li>
- <code><a href="GUS.html">GUS</a></code>(GUS.chent, GUS.numeric, print.GUS_result)<br />Groundwater ubiquity score based on Gustafson (1989)</li>
-
- <li>
- <code><a href="SSLRC_mobility_classification.html">SSLRC_mobility_classification</a></code><br />Determine the SSLRC mobility classification for a chemical substance from its Koc</li>
-
- </ul>
- <h3>Soil</h3>
- <p>Predicted environmental concentrations in soil</p>
-
-
- <ul class="index">
-
- <li>
- <code><a href="PEC_soil.html">PEC_soil</a></code><br />Calculate predicted environmental concentrations in soil</li>
-
- <li>
- <code><a href="soil_scenario_data_EFSA_2015.html">soil_scenario_data_EFSA_2015</a></code><br />Properties of the predefined scenarios from the EFSA guidance from 2015</li>
-
- </ul>
- <h3>Surface water</h3>
- <p>Predicted environmental concentrations in surface water</p>
-
-
- <ul class="index">
-
- <li>
- <code><a href="PEC_sw_drift.html">PEC_sw_drift</a></code><br />Calculate predicted environmental concentrations in surface water due to drift</li>
-
- <li>
- <code><a href="PEC_sw_sed.html">PEC_sw_sed</a></code><br />Calculate predicted environmental concentrations in sediment from surface
-water concentrations</li>
-
- <li>
- <code><a href="drift_data_JKI.html">drift_data_JKI</a></code><br />Deposition from spray drift expressed as percent of the applied dose as
-published by the JKI</li>
-
- <li>
- <code><a href="PEC_sw_drainage_UK.html">PEC_sw_drainage_UK</a></code><br />Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</li>
-
- <li>
- <code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code><br />R6 class for holding TOXSWA cwa concentration data and associated statistics</li>
-
- <li>
- <code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></code><br />Read TOXSWA surface water concentrations</li>
-
- <li>
- <code><a href="plot.TOXSWA_cwa.html">plot.TOXSWA_cwa</a></code><br />Plot TOXSWA surface water concentrations</li>
-
- </ul>
- <h3>Groundwater</h3>
- <p>Predicted environmental concentrations in groundwater</p>
-
-
- <ul class="index">
-
- <li>
- <code><a href="FOCUS_GW_scenarios_2012.html">FOCUS_GW_scenarios_2012</a></code><br />A very small subset of the FOCUS Groundwater scenario defitions</li>
-
- </ul>
- <h3>Chemical entities</h3>
- <p>Work with input stored in chemical entites as R objects using the chent package</p>
-
-
- <ul class="index">
-
- <li>
- <code><a href="endpoint.html">endpoint</a></code>(soil_DT50, soil_Kfoc, soil_N, soil_sorption)<br />Retrieve endpoint information from the chyaml field of a chent object</li>
-
- </ul>
- <h3>General</h3>
- <p>Utilities that are generally useful</p>
-
-
- <ul class="index">
-
- <li>
- <code><a href="geomean.html">geomean</a></code><br />Calculate the geometric mean</li>
-
- </ul>
- </div>
-</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
- </footer>
- </div>
- </body>
-</html> \ No newline at end of file
diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html
new file mode 100644
index 0000000..64b42e9
--- /dev/null
+++ b/docs/reference/FOCUS_GW_scenarios_2012.html
@@ -0,0 +1,171 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
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+ <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>A very small subset of the FOCUS Groundwater scenario defitions — FOCUS_GW_scenarios_2012 • 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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+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+ </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>
+ <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>
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+
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+
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+ </div><!--/.nav-collapse -->
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+</div><!--/.navbar -->
+
+
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+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>A very small subset of the FOCUS Groundwater scenario defitions</h1>
+ </div>
+
+
+ <p>Currently, only a small subset of the soil definitions are provided.</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.
+ FOrum for the Co-ordination of pesticde fate models and their USe.
+ http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>FOCUS_GW_scenarios_2012</span></div><div class='output co'>#&gt; $names
+#&gt; Cha Ham Jok Kre Oke
+#&gt; &quot;Châteaudun&quot; &quot;Hamburg&quot; &quot;Jokioinen&quot; &quot;Kremsmünster&quot; &quot;Okehampton&quot;
+#&gt; Pia Por Sev Thi
+#&gt; &quot;Piacenza&quot; &quot;Porto&quot; &quot;Sevilla&quot; &quot;Thiva&quot;
+#&gt;
+#&gt; $soils
+#&gt; location horizon number pH_H2O perc_clay perc_oc rel_deg
+#&gt; 1 Cha Ap 1 8.0 30.0 1.39 1.0
+#&gt; 2 Cha B1 2 8.1 31.0 0.93 0.5
+#&gt; 3 Cha B2 3 8.2 25.0 0.70 0.5
+#&gt; 4 Cha II C1 4 8.5 26.0 0.30 0.3
+#&gt; 5 Cha II C1 5 8.5 26.0 0.30 0.0
+#&gt; 6 Cha II C2 6 8.5 24.0 0.27 0.0
+#&gt; 7 Cha M 7 8.3 31.0 0.21 0.0
+#&gt; 8 Ham Ap 1 6.4 7.2 1.50 1.0
+#&gt; 9 Ham BvI 2 5.6 6.7 1.00 0.5
+#&gt; 10 Ham BvII 3 5.6 0.9 0.20 0.3
+#&gt; 11 Ham Bv/Cv 4 5.7 0.0 0.00 0.3
+#&gt; 12 Ham Cv 5 5.5 0.0 0.00 0.3
+#&gt; 13 Ham Cv 6 5.5 0.0 0.00 0.0
+#&gt; 14 Jok Ap 1 6.2 3.6 4.06 1.0
+#&gt; 15 Jok Bs 2 5.6 1.8 0.84 0.5
+#&gt; 16 Jok BC1 3 5.4 1.2 0.36 0.3
+#&gt; 17 Jok BC2 4 5.4 1.7 0.29 0.3
+#&gt; 18 Jok BC2 5 5.4 1.7 0.29 0.0
+#&gt; 19 Jok Cg 6 5.3 1.9 0.21 0.0
+#&gt; 20 Kre &lt;NA&gt; 1 7.7 14.0 3.60 1.0
+#&gt; 21 Kre &lt;NA&gt; 2 7.0 25.0 1.00 0.5
+#&gt; 22 Kre &lt;NA&gt; 3 7.1 27.0 0.50 0.5
+#&gt; 23 Kre &lt;NA&gt; 4 7.1 27.0 0.50 0.3
+#&gt; 24 Kre &lt;NA&gt; 5 7.1 27.0 0.50 0.0
+#&gt; 25 Oke A 1 5.8 18.0 2.20 1.0
+#&gt; 26 Oke Bw1 2 6.3 17.0 0.70 0.5
+#&gt; 27 Oke BC 3 6.5 14.0 0.40 0.3
+#&gt; 28 Oke C 4 6.6 9.0 0.10 0.3
+#&gt; 29 Oke C 5 6.6 9.0 0.10 0.0
+#&gt; 30 Pia Ap 1 7.0 15.0 1.26 1.0
+#&gt; 31 Pia Ap 2 7.0 15.0 1.26 0.5
+#&gt; 32 Pia Bw 3 6.3 7.0 0.47 0.5
+#&gt; 33 Pia Bw 4 6.3 7.0 0.47 0.3
+#&gt; 34 Pia 2C 5 6.4 0.0 0.00 0.3
+#&gt; 35 Pia 2C 6 6.4 0.0 0.00 0.0
+#&gt; 36 Por &lt;NA&gt; 1 4.9 10.0 1.42 1.0
+#&gt; 37 Por &lt;NA&gt; 2 4.8 8.0 0.78 0.5
+#&gt; 38 Por &lt;NA&gt; 3 4.8 8.0 0.78 0.3
+#&gt; 39 Por &lt;NA&gt; 4 4.8 8.0 0.78 0.0
+#&gt; 40 Sev &lt;NA&gt; 1 7.3 14.0 0.93 1.0
+#&gt; 41 Sev &lt;NA&gt; 2 7.3 13.0 0.93 1.0
+#&gt; 42 Sev &lt;NA&gt; 3 7.8 15.0 0.70 0.5
+#&gt; 43 Sev &lt;NA&gt; 4 8.1 16.0 0.58 0.3
+#&gt; 44 Sev &lt;NA&gt; 5 8.1 16.0 0.58 0.0
+#&gt; 45 Sev &lt;NA&gt; 6 8.2 22.0 0.49 0.0
+#&gt; 46 Thi Ap1 1 7.7 25.3 0.74 1.0
+#&gt; 47 Thi Ap2 2 7.7 25.3 0.74 0.5
+#&gt; 48 Thi Bw 3 7.8 29.6 0.57 0.5
+#&gt; 49 Thi Bw 4 7.8 31.9 0.31 0.3
+#&gt; 50 Thi Ck1 5 7.8 32.9 0.18 0.3
+#&gt; 51 Thi Ck1 6 7.8 32.9 0.18 0.0
+#&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="#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://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html
new file mode 100644
index 0000000..f65c6fd
--- /dev/null
+++ b/docs/reference/GUS.html
@@ -0,0 +1,181 @@
+<!-- Generated by pkgdown: do not edit by hand -->
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+<html>
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+
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+ <span class="icon-bar"></span>
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+ <div id="navbar" class="navbar-collapse collapse">
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+</li>
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+
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+</div><!--/.navbar -->
+
+
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+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Groundwater ubiquity score based on Gustafson (1989)</h1>
+ </div>
+
+
+ <p>The groundwater ubiquity score GUS is calculated according to
+the following equation
+$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$</p>
+
+
+ <pre><span class='fu'>GUS</span>(<span class='no'>...</span>)
+
+<span class='co'># S3 method for numeric</span>
+<span class='fu'>GUS</span>(<span class='no'>DT50</span>, <span class='no'>Koc</span>, <span class='no'>...</span>)
+
+<span class='co'># S3 method for chent</span>
+<span class='fu'>GUS</span>(<span class='no'>chent</span>, <span class='kw'>degradation_value</span> <span class='kw'>=</span> <span class='st'>"DT50ref"</span>,
+ <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='st'>"laboratory"</span>, <span class='kw'>redox</span> <span class='kw'>=</span> <span class='st'>"aerobic"</span>, <span class='kw'>sorption_value</span> <span class='kw'>=</span> <span class='st'>"Kfoc"</span>,
+ <span class='kw'>degradation_aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>sorption_aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='no'>...</span>)
+
+<span class='co'># S3 method for GUS_result</span>
+<span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>...</dt>
+ <dd>Included in the generic to allow for further arguments later. Therefore
+this also had to be added to the specific methods.</dd>
+ <dt>DT50</dt>
+ <dd>Half-life of the chemical in soil. Should be a field
+half-life according to Gustafson (1989). However, leaching to the sub-soil
+can not completely be excluded in field dissipation experiments and Gustafson
+did not refer to any normalisation procedure, but says the field study should
+be conducted under use conditions.</dd>
+ <dt>Koc</dt>
+ <dd>The sorption constant normalised to organic carbon. Gustafson
+does not mention the nonlinearity of the sorption constant commonly
+found and usually described by Freundlich sorption, therefore it is
+unclear at which reference concentration the Koc should be observed
+(and if the reference concentration would be in soil or in porewater).</dd>
+ <dt>chent</dt>
+ <dd>If a chent is given with appropriate information present in its
+chyaml field, this information is used, with defaults specified below.</dd>
+ <dt>degradation_value</dt>
+ <dd>Which of the available degradation values should
+be used?</dd>
+ <dt>lab_field</dt>
+ <dd>Should laboratory or field half-lives be used? This
+defaults to lab in this implementation, in order to avoid
+double-accounting for mobility. If comparability with the original GUS
+values given by Gustafson (1989) is desired, non-normalised first-order
+field half-lives obtained under actual use conditions should be used.</dd>
+ <dt>redox</dt>
+ <dd>Aerobic or anaerobic degradation data</dd>
+ <dt>sorption_value</dt>
+ <dd>Which of the available sorption values should be used?
+Defaults to Kfoc as this is what is generally available from the European
+pesticide peer review process. These values generally use a reference
+concentration of 1 mg/L in porewater, that means they would be expected to
+be Koc values at a concentration of 1 mg/L in the water phase.</dd>
+ <dt>degradation_aggregator</dt>
+ <dd>Function for aggregating half-lives</dd>
+ <dt>sorption_aggregator</dt>
+ <dd>Function for aggregation Koc values</dd>
+ <dt>x</dt>
+ <dd>An object of class GUS_result to be printed</dd>
+ <dt>digits</dt>
+ <dd>The number of digits used in the print method</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A list with the DT50 and Koc used as well as the resulting score
+ of class GUS_result</p>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>Gustafson, David I. (1989) Groundwater ubiquity score: a simple
+method for assessing pesticide leachability. <em>Environmental
+toxicology and chemistry</em> <b>8</b>(4) 339–57.</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="#value">Value</a></li>
+
+ <li><a href="#references">References</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+Johannes Ranke
+
+ </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/PEC_soil.html b/docs/reference/PEC_soil.html
new file mode 100644
index 0000000..0449f8e
--- /dev/null
+++ b/docs/reference/PEC_soil.html
@@ -0,0 +1,229 @@
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+<!DOCTYPE html>
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Calculate predicted environmental concentrations in soil — PEC_soil • 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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+ </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 predicted environmental concentrations in soil</h1>
+ </div>
+
+
+ <p>This is a basic calculation of a contaminant concentration in bulk soil
+based on complete, instantaneous mixing. If an interval is given, an
+attempt is made at calculating a long term maximum concentration using
+the concepts layed out for example in the PPR panel opinion (EFSA 2012).</p>
+
+
+ <pre><span class='fu'>PEC_soil</span>(<span class='no'>rate</span>, <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>mixing_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>,
+ <span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"mg/kg"</span>, <span class='kw'>PEC_pw_units</span> <span class='kw'>=</span> <span class='st'>"mg/L"</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+ <span class='kw'>n_periods</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, <span class='kw'>tillage_depth</span> <span class='kw'>=</span> <span class='fl'>20</span>, <span class='kw'>chent</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+ <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='no'>Koc</span>/<span class='fl'>1.724</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"default"</span>,
+ <span class='st'>"EFSA_2015"</span>), <span class='kw'>porewater</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>rate</dt>
+ <dd>Application rate in units specified below</dd>
+ <dt>rate_units</dt>
+ <dd>Defaults to g/ha</dd>
+ <dt>interception</dt>
+ <dd>The fraction of the application rate that does not reach the soil</dd>
+ <dt>mixing_depth</dt>
+ <dd>Mixing depth in cm</dd>
+ <dt>PEC_units</dt>
+ <dd>Requested units for the calculated PEC. Only mg/kg currently supported</dd>
+ <dt>PEC_pw_units</dt>
+ <dd>Only mg/L currently supported</dd>
+ <dt>interval</dt>
+ <dd>Period of the deeper mixing, defaults to 365, which is a year if
+rate units are in days</dd>
+ <dt>n_periods</dt>
+ <dd>Number of periods to be considered for long term PEC calculations</dd>
+ <dt>tillage_depth</dt>
+ <dd>Periodic (see interval) deeper mixing in cm</dd>
+ <dt>chent</dt>
+ <dd>An optional chent object holding substance specific information. Can
+also be a name for the substance as a character string</dd>
+ <dt>DT50</dt>
+ <dd>If specified, overrides soil DT50 endpoints from a chent object
+If DT50 is not specified here and not available from the chent object, zero
+degradation is assumed</dd>
+ <dt>Koc</dt>
+ <dd>If specified, overrides Koc endpoints from a chent object</dd>
+ <dt>Kom</dt>
+ <dd>Calculated from Koc by default, but can explicitly be specified
+as Kom here</dd>
+ <dt>t_avg</dt>
+ <dd>Averaging times for time weighted average concentrations</dd>
+ <dt>scenarios</dt>
+ <dd>If this is &#39;default&#39;, the DT50 will be used without correction
+and soil properties as specified in the REACH guidance (R.16, Table
+R.16-9) are used for porewater PEC calculations. If this is &quot;EFSA_2015&quot;,
+the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when
+&#39;chents&#39; is specified, the DegT50 with destination &#39;PECgw&#39; will be used),
+and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also
+model and scenario adjustment factors from the EFSA guidance are used.</dd>
+ <dt>porewater</dt>
+ <dd>Should equilibrium porewater concentrations be estimated
+based on Kom and the organic carbon fraction of the soil instead of total
+soil concentrations? Based on equation (7) given in the PPR panel opinion
+(EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015,
+p. 13).</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The predicted concentration in soil</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>This assumes that the complete load to soil during the time specified by
+&#39;interval&#39; (typically 365 days) is dosed at once. As in the PPR panel
+opinion cited below (PPR panel 2012), only temperature correction using the
+Arrhenius equation is performed.</p>
+ <p>Total soil and porewater PEC values for the scenarios as defined in the EFSA
+guidance (2015, p. 13) can easily be calculated.</p>
+
+ <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
+
+ <p>If temperature information is available in the selected scenarios, as
+ e.g. in the EFSA scenarios, the DT50 for groundwater modelling
+ (destination &#39;PECgw&#39;) is taken from the chent object, otherwise the DT50
+ with destination &#39;PECsoil&#39;.</p>
+
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>EFSA Panel on Plant Protection Products and their Residues (2012)
+ Scientific Opinion on the science behind the guidance for scenario
+ selection and scenario parameterisation for predicting environmental
+ concentrations of plant protection products in soil. <em>EFSA Journal</em>
+ <b>10</b>(2) 2562, doi:10.2903/j.efsa.2012.2562</p>
+ <p>EFSA (European Food Safety Authority) (2015) EFSA guidance document for
+ predicting environmental concentrations of active substances of plant
+ protection products and transformation products of these active substances
+ in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093
+ doi:10.2903/j.efsa.2015.4093</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='fu'>PEC_soil</span>(<span class='fl'>100</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0.25</span>)</div><div class='output co'>#&gt; scenario
+#&gt; t_avg default
+#&gt; 0 0.1</div><div class='input'>
+<span class='co'># This is example 1 starting at p. 79 of the EFSA guidance (2015)</span>
+<span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
+ <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>)</div><div class='output co'>#&gt; scenario
+#&gt; t_avg CTN CTC CTS
+#&gt; 0 21.96827 11.53750 9.145259
+#&gt; 21 21.78517 11.40701 9.017370</div><div class='input'><span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
+ <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; scenario
+#&gt; t_avg CLN CLC CLS
+#&gt; 0 0.7589401 0.6674322 0.9147861
+#&gt; 21 0.7506036 0.6590345 0.8987279</div><div class='input'>
+<span class='co'># The following is from example 4 starting at p. 85 of the EFSA guidance (2015)</span>
+<span class='co'># Metabolite M2</span>
+<span class='co'># Calculate total and porewater soil concentrations for tier 1 scenarios</span>
+<span class='co'># Relative molar mass is 100/300, formation fraction is 0.7 * 1</span>
+<span class='no'>results_pfm</span> <span class='kw'>&lt;-</span> <span class='fu'>PEC_soil</span>(<span class='fl'>100</span>/<span class='fl'>300</span> * <span class='fl'>0.7</span> * <span class='fl'>1</span> * <span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
+ <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>)
+<span class='no'>results_pfm_pw</span> <span class='kw'>&lt;-</span> <span class='fu'>PEC_soil</span>(<span class='fl'>100</span>/<span class='fl'>300</span> * <span class='fl'>0.7</span> * <span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>21</span>),
+ <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</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="#note">Note</a></li>
+
+ <li><a href="#references">References</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+Johannes Ranke
+
+ </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>
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diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html
new file mode 100644
index 0000000..db0f85f
--- /dev/null
+++ b/docs/reference/PEC_sw_drainage_UK.html
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+ <h1>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</h1>
+ </div>
+
+
+ <p>This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet
+published on the CRC website</p>
+
+
+ <pre><span class='fu'>PEC_sw_drainage_UK</span>(<span class='no'>rate</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='no'>Koc</span>, <span class='kw'>latest_application</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+ <span class='kw'>soil_DT50</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>model_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>rate</dt>
+ <dd>Application rate in g/ha</dd>
+ <dt>interception</dt>
+ <dd>The fraction of the application rate that does not reach the soil</dd>
+ <dt>Koc</dt>
+ <dd>The sorption coefficient normalised to organic carbon in L/kg</dd>
+ <dt>latest_application</dt>
+ <dd>Latest application date, formatted as e.g. &quot;01 July&quot;</dd>
+ <dt>soil_DT50</dt>
+ <dd>Soil degradation half-life, if SFO kinetics are to be used</dd>
+ <dt>model</dt>
+ <dd>The soil degradation model to be used. Either one of &quot;FOMC&quot;,
+&quot;DFOP&quot;, &quot;HS&quot;, or &quot;IORE&quot;, or an mkinmod object</dd>
+ <dt>model_parms</dt>
+ <dd>A named numeric vector containing the model parameters</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The predicted concentration in surface water in µg/L</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>
+ </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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+Johannes Ranke
+
+ </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>
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diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html
new file mode 100644
index 0000000..a168de3
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@@ -0,0 +1,144 @@
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+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Calculate predicted environmental concentrations in surface water due to drift</h1>
+ </div>
+
+
+ <p>This is a basic, vectorised form of a simple calculation of a contaminant
+concentration in surface water based on complete, instantaneous mixing
+with input via spray drift.</p>
+
+
+ <pre><span class='fu'>PEC_sw_drift</span>(<span class='no'>rate</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>water_depth</span> <span class='kw'>=</span> <span class='fl'>30</span>,
+ <span class='kw'>drift_percentages</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>drift_data</span> <span class='kw'>=</span> <span class='st'>"JKI"</span>, <span class='kw'>crop</span> <span class='kw'>=</span> <span class='st'>"Ackerbau"</span>,
+ <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</span>), <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>, <span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"µg/L"</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>rate</dt>
+ <dd>Application rate in units specified below</dd>
+ <dt>applications</dt>
+ <dd>Number of applications for selection of drift percentile</dd>
+ <dt>water_depth</dt>
+ <dd>Depth of the water body in cm</dd>
+ <dt>drift_percentages</dt>
+ <dd>Percentage drift values for which to calculate PECsw.
+&#39;drift_data&#39; and &#39;distances&#39; if not NULL.</dd>
+ <dt>drift_data</dt>
+ <dd>Source of drift percentage data</dd>
+ <dt>crop</dt>
+ <dd>Crop name (use German names for JKI data), defaults to &quot;Ackerbau&quot;</dd>
+ <dt>distances</dt>
+ <dd>The distances in m for which to get PEC values</dd>
+ <dt>rate_units</dt>
+ <dd>Defaults to g/ha</dd>
+ <dt>PEC_units</dt>
+ <dd>Requested units for the calculated PEC. Only µg/L currently supported</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The predicted concentration in surface water</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_drift</span>(<span class='fl'>100</span>)</div><div class='output co'>#&gt; 1 m 5 m 10 m 20 m
+#&gt; 0.92333333 0.19000000 0.09666667 0.05000000 </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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+Johannes Ranke
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
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+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
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diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html
new file mode 100644
index 0000000..6ede4c7
--- /dev/null
+++ b/docs/reference/PEC_sw_sed.html
@@ -0,0 +1,142 @@
+<!-- Generated by pkgdown: do not edit by hand -->
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+ — PEC_sw_sed • pfm</title>
+
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+ </head>
+
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+ <div class="container template-reference-topic">
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+ <div class="container">
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+
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+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Calculate predicted environmental concentrations in sediment from surface
+</h1>
+ </div>
+
+
+ <p>The method &#39;percentage&#39; is equivalent to what is used in the CRD spreadsheet
+PEC calculator</p>
+
+
+ <pre><span class='fu'>PEC_sw_sed</span>(<span class='no'>PEC_sw</span>, <span class='kw'>percentage</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"percentage"</span>,
+ <span class='kw'>sediment_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>water_depth</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>sediment_density</span> <span class='kw'>=</span> <span class='fl'>1.3</span>,
+ <span class='kw'>PEC_sed_units</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"µg/kg"</span>, <span class='st'>"mg/kg"</span>))</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>PEC_sw</dt>
+ <dd>Numeric vector or matrix of surface water concentrations in µg/L for
+which the corresponding sediment concentration is to be estimated</dd>
+ <dt>percentage</dt>
+ <dd>The percentage in sediment, used for the percentage method</dd>
+ <dt>method</dt>
+ <dd>The method used for the calculation</dd>
+ <dt>sediment_depth</dt>
+ <dd>Depth of the sediment layer</dd>
+ <dt>water_depth</dt>
+ <dd>Depth of the water body in cm</dd>
+ <dt>sediment_density</dt>
+ <dd>The density of the sediment in L/kg (equivalent to
+g/cm3)</dd>
+ <dt>PEC_sed_units</dt>
+ <dd>The units of the estimated sediment PEC value</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The predicted concentration in sediment</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_sed</span>(<span class='fu'><a href='PEC_sw_drift.html'>PEC_sw_drift</a></span>(<span class='fl'>100</span>, <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fl'>1</span>), <span class='kw'>percentage</span> <span class='kw'>=</span> <span class='fl'>50</span>)</div><div class='output co'>#&gt; 1 m
+#&gt; 2.130769 </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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+Johannes Ranke
+
+ </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/SFO_actual_twa.html b/docs/reference/SFO_actual_twa.html
new file mode 100644
index 0000000..4285191
--- /dev/null
+++ b/docs/reference/SFO_actual_twa.html
@@ -0,0 +1,138 @@
+<!-- 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>Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa • 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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+
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
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+
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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>
+ <a class="navbar-brand" href="../index.html">pfm</a>
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+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
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+
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+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Actual and maximum moving window time average concentrations for SFO kinetics</h1>
+ </div>
+
+
+ <p>Actual and maximum moving window time average concentrations for SFO kinetics</p>
+
+
+ <pre><span class='fu'>SFO_actual_twa</span>(<span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>21</span>, <span class='fl'>28</span>, <span class='fl'>42</span>, <span class='fl'>50</span>,
+ <span class='fl'>100</span>))</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>DT50</dt>
+ <dd>The half-life.</dd>
+ <dt>times</dt>
+ <dd>The output times, and window sizes for time weighted average concentrations</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+
+ <p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation
+ Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1,
+ 18 December 2014, p. 251</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='fu'>SFO_actual_twa</span>(<span class='fl'>10</span>)</div><div class='output co'>#&gt; actual twa
+#&gt; 0 1.0000000000 NaN
+#&gt; 1 0.9330329915 0.9661297
+#&gt; 2 0.8705505633 0.9337803
+#&gt; 4 0.7578582833 0.8733416
+#&gt; 7 0.6155722067 0.7923030
+#&gt; 14 0.3789291416 0.6400113
+#&gt; 21 0.2332582479 0.5267498
+#&gt; 28 0.1435872944 0.4412651
+#&gt; 42 0.0544094102 0.3248093
+#&gt; 50 0.0312500000 0.2795222
+#&gt; 100 0.0009765625 0.1441286</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="#source">Source</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+Johannes Ranke
+
+ </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/SSLRC_mobility_classification.html b/docs/reference/SSLRC_mobility_classification.html
new file mode 100644
index 0000000..f207a7a
--- /dev/null
+++ b/docs/reference/SSLRC_mobility_classification.html
@@ -0,0 +1,129 @@
+<!-- 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>Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification • 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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+
+<!-- Font Awesome icons -->
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+
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
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+
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+ <header>
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+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">pfm</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Determine the SSLRC mobility classification for a chemical substance from its Koc</h1>
+ </div>
+
+
+ <p>This implements the method specified in the UK data requirements handbook and was
+checked against the spreadsheet published on the CRC website</p>
+
+
+ <pre><span class='fu'>SSLRC_mobility_classification</span>(<span class='no'>Koc</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>Koc</dt>
+ <dd>The sorption coefficient normalised to organic carbon in L/kg</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A list containing the classification and the percentage of the
+ compound transported per 10 mm drain water</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`
+#&gt; [1] &quot;Moderately mobile&quot;
+#&gt;
+#&gt; $`Percentage drained per mm of drain water`
+#&gt; [1] 0.7
+#&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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+Johannes Ranke
+
+ </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/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html
new file mode 100644
index 0000000..3f9310a
--- /dev/null
+++ b/docs/reference/TOXSWA_cwa.html
@@ -0,0 +1,178 @@
+<!-- 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>R6 class for holding TOXSWA cwa concentration data and associated statistics — TOXSWA_cwa • 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">
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+<script src="../pkgdown.js"></script>
+
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+
+<!--[if lt IE 9]>
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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>R6 class for holding TOXSWA cwa concentration data and associated statistics</h1>
+ </div>
+
+
+ <p>An R6 class for holding TOXSWA cwa concentration data and some associated statistics.
+Usually, an instance of this class will be generated by <code><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></code>.</p>
+
+
+ <pre><span class='no'>TOXSWA_cwa</span></pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>An <code>R6Class</code> generator object.</p>
+
+ <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2>
+
+ <p></p>
+ <p><dl class='dl-horizontal'>
+<dt><code>filename</code></dt><dd>Length one character vector.</dd></p>
+ <p><dt><code>basedir</code></dt><dd>Length one character vector.</dd></p>
+ <p><dt><code>segment</code></dt><dd>Length one integer, specifying for which segment the cwa data were read.</dd></p>
+ <p><dt><code>cwas</code></dt><dd>Dataframe holding the concentrations.</dd></p>
+ <p><dt><code>events</code></dt><dd>List of dataframes holding the event statistics for each threshold.</dd></p>
+ <p><dt><code>windows</code></dt><dd>Matrix of maximum time weighted average concentrations (TWAC_max)
+and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d)
+for the requested moving window sizes in days.</dd>
+</dl></p>
+
+ <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
+
+ <p></p>
+ <p><dl class='dl-horizontal'>
+ <dt><code>get_events(threshold, total = FALSE)</code></dt><dd>
+ Populate a datataframe with event information for the specified threshold value
+ in µg/L. If <code>total = TRUE</code>, the total concentration including the amount
+ adsorbed to suspended matter will be used. The resulting dataframe is stored in the
+ <code>events</code> field of the object.
+ </dd>
+ <dt><code>moving_windows(windows, total = FALSE)</code></dt><dd>
+ Add to the <code>windows</code> field described above.
+ Again, if <code>total = TRUE</code>, the total concentration including the amount
+ adsorbed to suspended matter will be used.
+ </dd>
+</dl></p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>H_sw_R1_stream</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00003s_pa.cwa"</span>,
+ <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>,
+ <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata/SwashProjects.zip"</span>,
+ <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>))
+<span class='no'>H_sw_R1_stream</span>$<span class='fu'>get_events</span>(<span class='fu'>c</span>(<span class='fl'>2</span>, <span class='fl'>10</span>))
+<span class='no'>H_sw_R1_stream</span>$<span class='fu'>moving_windows</span>(<span class='fu'>c</span>(<span class='fl'>7</span>, <span class='fl'>21</span>))
+<span class='fu'>print</span>(<span class='no'>H_sw_R1_stream</span>)</div><div class='output co'>#&gt; &lt;TOXSWA_cwa&gt; data from file 00003s_pa.cwa segment 20
+#&gt; datetime t t_firstjan t_rel_to_max cwa_mug_per_L
+#&gt; 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0
+#&gt; 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0
+#&gt; 60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0
+#&gt; 80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0
+#&gt; 100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0
+#&gt; 120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0
+#&gt; cwa_tot_mug_per_L
+#&gt; 20 0
+#&gt; 40 0
+#&gt; 60 0
+#&gt; 80 0
+#&gt; 100 0
+#&gt; 120 0
+#&gt; Moving window analysis
+#&gt; window max_TWAC max_AUC_h max_AUC_d
+#&gt; 1 7 days 2.3926551 401.9660 16.74859
+#&gt; 2 21 days 0.8369248 421.8101 17.57542
+#&gt; Event statistics for threshold 2
+#&gt; t_start cwa_max duration pre_interval AUC_h AUC_d
+#&gt; 1 44.375 4.167238 0.208 44.375 17.77202 0.740501
+#&gt; 2 55.042 40.584010 0.583 10.459 398.21189 16.592162
+#&gt; Event statistics for threshold 10
+#&gt; t_start cwa_max duration pre_interval AUC_h AUC_d
+#&gt; 1 55.083 40.58401 0.459 55.083 379.433 15.80971</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="#fields">Fields</a></li>
+
+ <li><a href="#methods">Methods</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>
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diff --git a/docs/reference/drift_data_JKI.html b/docs/reference/drift_data_JKI.html
new file mode 100644
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+ <h1>Deposition from spray drift expressed as percent of the applied dose as
+</h1>
+ </div>
+
+
+ <p>Deposition from spray drift expressed as percent of the applied dose as
+published by the German Julius-Kühn Institute (JKI).</p>
+
+
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>A list currently containing matrices with spray drift percentage
+data for field crops (Ackerbau), and Pome/stone fruit, early and late
+(Obstbau frueh, spaet).</p>
+
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+
+ <p>JKI (2010) Spreadsheet &#39;Tabelle der Abdrifteckwerte.xls&#39;, retrieved
+from
+http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html
+on 2015-06-11</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The data were extracted from the spreadsheet cited below using the R code
+given in the example section. The spreadsheet is not included in the package
+as its licence is not clear.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'>
+<span class='co'>## Not run: ------------------------------------</span>
+<span class='co'># # This is the code that was used to extract the data</span>
+<span class='co'># library(readxl)</span>
+<span class='co'># abdrift_path &lt;- "inst/extdata/Tabelle der Abdrifteckwerte.xls"</span>
+<span class='co'># JKI_crops &lt;- c("Ackerbau", "Obstbau frueh", "Obstbau spaet")</span>
+<span class='co'># names(JKI_crops) &lt;- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late")</span>
+<span class='co'># drift_data_JKI &lt;- list()</span>
+<span class='co'># </span>
+<span class='co'># for (n in 1:8) {</span>
+<span class='co'># drift_data_raw &lt;- read_excel(abdrift_path, sheet = n + 1, skip = 2)</span>
+<span class='co'># drift_data &lt;- as.matrix(drift_data_raw[1:9, 2:4]) </span>
+<span class='co'># dimnames(drift_data) &lt;- list(distance = as.integer(drift_data_raw[1:9, 1]),</span>
+<span class='co'># crop = JKI_crops)</span>
+<span class='co'># drift_data_JKI[[n]] &lt;- drift_data</span>
+<span class='co'># }</span>
+<span class='co'># save(drift_data_JKI, file = "data/drift_data_JKI.RData")</span>
+<span class='co'>## ---------------------------------------------</span>
+
+<span class='co'># And this is the resulting data</span>
+<span class='no'>drift_data_JKI</span></div><div class='output co'>#&gt; [[1]]
+#&gt; crop
+#&gt; distance Ackerbau Obstbau frueh Obstbau spaet
+#&gt; 1 2.77 NA NA
+#&gt; 3 NA 29.20 15.73
+#&gt; 5 0.57 19.89 8.41
+#&gt; 10 0.29 11.81 3.60
+#&gt; 15 0.20 5.55 1.81
+#&gt; 20 0.15 2.77 1.09
+#&gt; 30 0.10 1.04 0.54
+#&gt; 40 0.07 0.52 0.32
+#&gt; 50 0.06 0.30 0.22
+#&gt;
+#&gt; [[2]]
+#&gt; crop
+#&gt; distance Ackerbau Obstbau frueh Obstbau spaet
+#&gt; 1 2.38 NA NA
+#&gt; 3 NA 25.53 12.13
+#&gt; 5 0.47 16.87 6.81
+#&gt; 10 0.24 9.61 3.11
+#&gt; 15 0.16 5.61 1.58
+#&gt; 20 0.12 2.59 0.90
+#&gt; 30 0.08 0.87 0.40
+#&gt; 40 0.06 0.40 0.23
+#&gt; 50 0.05 0.22 0.15
+#&gt;
+#&gt; [[3]]
+#&gt; crop
+#&gt; distance Ackerbau Obstbau frueh Obstbau spaet
+#&gt; 1 2.01 NA NA
+#&gt; 3 NA 23.96 11.01
+#&gt; 5 0.41 15.79 6.04
+#&gt; 10 0.20 8.96 2.67
+#&gt; 15 0.14 4.24 1.39
+#&gt; 20 0.10 2.01 0.80
+#&gt; 30 0.07 0.70 0.36
+#&gt; 40 0.05 0.33 0.21
+#&gt; 50 0.04 0.19 0.13
+#&gt;
+#&gt; [[4]]
+#&gt; crop
+#&gt; distance Ackerbau Obstbau frueh Obstbau spaet
+#&gt; 1 1.85 NA NA
+#&gt; 3 NA 23.61 10.12
+#&gt; 5 0.38 15.42 5.60
+#&gt; 10 0.19 8.66 2.50
+#&gt; 15 0.13 4.01 1.28
+#&gt; 20 0.10 1.89 0.75
+#&gt; 30 0.06 0.66 0.35
+#&gt; 40 0.05 0.31 0.20
+#&gt; 50 0.04 0.17 0.13
+#&gt;
+#&gt; [[5]]
+#&gt; crop
+#&gt; distance Ackerbau Obstbau frueh Obstbau spaet
+#&gt; 1 1.75 NA NA
+#&gt; 3 NA 23.12 9.74
+#&gt; 5 0.36 15.06 5.41
+#&gt; 10 0.18 8.42 2.43
+#&gt; 15 0.12 3.83 1.24
+#&gt; 20 0.09 1.81 0.72
+#&gt; 30 0.06 0.63 0.34
+#&gt; 40 0.05 0.30 0.20
+#&gt; 50 0.04 0.17 0.13
+#&gt;
+#&gt; [[6]]
+#&gt; crop
+#&gt; distance Ackerbau Obstbau frueh Obstbau spaet
+#&gt; 1 1.64 NA NA
+#&gt; 3 NA 22.76 9.21
+#&gt; 5 0.34 14.64 5.18
+#&gt; 10 0.17 8.04 2.38
+#&gt; 15 0.11 3.71 1.20
+#&gt; 20 0.09 1.75 0.68
+#&gt; 30 0.06 0.61 0.31
+#&gt; 40 0.04 0.29 0.17
+#&gt; 50 0.03 0.16 0.11
+#&gt;
+#&gt; [[7]]
+#&gt; crop
+#&gt; distance Ackerbau Obstbau frueh Obstbau spaet
+#&gt; 1 1.61 NA NA
+#&gt; 3 NA 22.69 9.10
+#&gt; 5 0.33 14.45 5.11
+#&gt; 10 0.17 7.83 2.33
+#&gt; 15 0.11 3.62 1.20
+#&gt; 20 0.08 1.71 0.67
+#&gt; 30 0.06 0.60 0.30
+#&gt; 40 0.04 0.28 0.17
+#&gt; 50 0.03 0.16 0.11
+#&gt;
+#&gt; [[8]]
+#&gt; crop
+#&gt; distance Ackerbau Obstbau frueh Obstbau spaet
+#&gt; 1 1.52 NA NA
+#&gt; 3 NA 22.24 8.66
+#&gt; 5 0.31 14.09 4.92
+#&gt; 10 0.16 7.58 2.29
+#&gt; 15 0.11 3.48 1.14
+#&gt; 20 0.08 1.65 0.65
+#&gt; 30 0.05 0.57 0.29
+#&gt; 40 0.04 0.27 0.16
+#&gt; 50 0.03 0.15 0.11
+#&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="#details">Details</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/endpoint.html b/docs/reference/endpoint.html
new file mode 100644
index 0000000..57a7652
--- /dev/null
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@@ -0,0 +1,170 @@
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+ <h1>Retrieve endpoint information from the chyaml field of a chent object</h1>
+ </div>
+
+
+ <p>R6 class objects of class chent represent chemical entities
+and can hold a list of information loaded from a chemical yaml file in their
+chyaml field. Such information is extracted and optionally aggregated by
+this function.</p>
+
+
+ <pre><span class='fu'>endpoint</span>(<span class='no'>chent</span>, <span class='kw'>medium</span> <span class='kw'>=</span> <span class='st'>"soil"</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"degradation"</span>, <span class='st'>"sorption"</span>),
+ <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>NA</span>, <span class='st'>"laboratory"</span>, <span class='st'>"field"</span>), <span class='kw'>redox</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>NA</span>, <span class='st'>"aerobic"</span>,
+ <span class='st'>"anaerobic"</span>), <span class='kw'>value</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"DT50ref"</span>, <span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>), <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>,
+ <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>)
+
+<span class='fu'>soil_DT50</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>,
+ <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='st'>"laboratory"</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='st'>"DT50ref"</span>, <span class='kw'>redox</span> <span class='kw'>=</span> <span class='st'>"aerobic"</span>,
+ <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
+
+<span class='fu'>soil_Kfoc</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='st'>"Kfoc"</span>,
+ <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
+
+<span class='fu'>soil_N</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>mean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
+
+<span class='fu'>soil_sorption</span>(<span class='no'>chent</span>, <span class='kw'>values</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>), <span class='kw'>aggregators</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>Kfoc</span> <span class='kw'>=</span>
+ <span class='no'>geomean</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='no'>mean</span>), <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>Kfoc</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='fl'>3</span>),
+ <span class='kw'>raw</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>chent</dt>
+ <dd>The chent object to get the information from</dd>
+ <dt>medium</dt>
+ <dd>The medium for which information is sought</dd>
+ <dt>type</dt>
+ <dd>The information type</dd>
+ <dt>lab_field</dt>
+ <dd>If not NA, do we want laboratory or field endpoints</dd>
+ <dt>redox</dt>
+ <dd>If not NA, are we looking for aerobic or anaerobic data</dd>
+ <dt>value</dt>
+ <dd>The name of the value we want. The list given in the
+usage section is not exclusive</dd>
+ <dt>aggregator</dt>
+ <dd>The aggregator function. Can be mean,
+<code><a href='geomean.html'>geomean</a></code>, or identity, for example.</dd>
+ <dt>raw</dt>
+ <dd>Should the number(s) be returned as stored in the chent
+object (could be a character value) to retain original information
+about precision?</dd>
+ <dt>signif</dt>
+ <dd>How many significant digits do we want</dd>
+ <dt>values</dt>
+ <dd>The values to be returned</dd>
+ <dt>aggregators</dt>
+ <dd>A named vector of aggregator functions to be used</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The result from applying the aggregator function to
+ the values converted to a numeric vector, rounded to the
+ given number of significant digits, or, if raw = TRUE,
+ the values as a character value, retaining any implicit
+ information on precision that may be present.</p>
+
+ <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+ <p>The functions <code>soil_*</code> are functions to extract soil specific endpoints.
+For the Freundlich exponent, the capital letter <code>N</code> is used in order to
+facilitate dealing with such data in R. In pesticide fate modelling, this
+exponent is often called 1/n.</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="#value">Value</a></li>
+
+ <li><a href="#details">Details</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/geomean.html b/docs/reference/geomean.html
new file mode 100644
index 0000000..4634f99
--- /dev/null
+++ b/docs/reference/geomean.html
@@ -0,0 +1,127 @@
+<!-- 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 geometric mean — geomean • 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 geometric mean</h1>
+ </div>
+
+
+ <p>Based on some posts in a thread on Stackoverflow
+<a href = 'http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in'>http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in</a>
+This function checks for negative values, removes NA values per default and
+returns 0 if at least one element of the vector is 0.</p>
+
+
+ <pre><span class='fu'>geomean</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>x</dt>
+ <dd>Vector of numbers</dd>
+ <dt>na.rm</dt>
+ <dd>Should NA values be omitted?</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>The geometric mean</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='fu'>geomean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>9</span>))</div><div class='output co'>#&gt; [1] 3</div><div class='input'><span class='fu'>geomean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>NA</span>, <span class='fl'>9</span>))</div><div class='output co'>#&gt; [1] 3</div><div class='input'><span class='co'>## Not run: geomean(c(1, -3, 9)) # returns an error</span></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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+Johannes Ranke
+
+ </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
new file mode 100644
index 0000000..e458048
--- /dev/null
+++ b/docs/reference/index.html
@@ -0,0 +1,195 @@
+<!-- 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>Function reference • 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-index">
+ <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">
+ <div class="page-header">
+ <h1>Function reference</h1>
+ <h4>version&nbsp;0.4-1</h4>
+ </div>
+
+ <div class="contents">
+ <h2 id="section-general-utility-functions" class="hasAnchor"><a href="#section-general-utility-functions" class="anchor"></a>General utility functions</h2>
+ <p class="section-desc"><p>Functions that are independent of specific fate modelling areas</p></p>
+
+
+ <p><a href="geomean.html">Calculate the geometric mean</a></p>
+ <ul>
+ <li><code><a href="geomean.html">geomean</a></code></li>
+ </ul>
+
+ <p><a href="one_box.html">Create a time series of decline data</a></p>
+ <ul>
+ <li><code><a href="one_box.html">one_box</a></code></li><li><code><a href="one_box.html">one_box.numeric</a></code></li><li><code><a href="one_box.html">one_box.mkinfit</a></code></li>
+ </ul>
+
+ <p><a href="plot.one_box.html">Plot time series of decline data</a></p>
+ <ul>
+ <li><code><a href="plot.one_box.html">plot.one_box</a></code></li>
+ </ul>
+
+ <p><a href="sawtooth.html">Create decline time series for multiple applications</a></p>
+ <ul>
+ <li><code><a href="sawtooth.html">sawtooth</a></code></li>
+ </ul>
+
+ <p><a href="twa.html">Calculate a time weighted average concentration</a></p>
+ <ul>
+ <li><code><a href="twa.html">twa</a></code></li><li><code><a href="twa.html">twa.one_box</a></code></li>
+ </ul>
+
+ <p><a href="max_twa.html">The maximum time weighted average concentration for a moving window</a></p>
+ <ul>
+ <li><code><a href="max_twa.html">max_twa</a></code></li>
+ </ul>
+ <h2 id="section-predicted-environmental-concentrations-in-soil" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-soil" class="anchor"></a>Predicted environmental concentrations in soil</h2>
+ <p class="section-desc"></p>
+
+
+ <p><a href="PEC_soil.html">Calculate predicted environmental concentrations in soil</a></p>
+ <ul>
+ <li><code><a href="PEC_soil.html">PEC_soil</a></code></li>
+ </ul>
+
+ <p><a href="soil_scenario_data_EFSA_2015.html">Properties of the predefined scenarios from the EFSA guidance from 2015</a></p>
+ <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-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>
+
+
+ <p><a href="PEC_sw_drift.html">Calculate predicted environmental concentrations in surface water due to drift</a></p>
+ <ul>
+ <li><code><a href="PEC_sw_drift.html">PEC_sw_drift</a></code></li>
+ </ul>
+
+ <p><a href="drift_data_JKI.html">Deposition from spray drift expressed as percent of the applied dose as
+</a></p>
+ <ul>
+ <li><code><a href="drift_data_JKI.html">drift_data_JKI</a></code></li>
+ </ul>
+
+ <p><a href="PEC_sw_drainage_UK.html">Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</a></p>
+ <ul>
+ <li><code><a href="PEC_sw_drainage_UK.html">PEC_sw_drainage_UK</a></code></li>
+ </ul>
+
+ <p><a href="TOXSWA_cwa.html">R6 class for holding TOXSWA cwa concentration data and associated statistics</a></p>
+ <ul>
+ <li><code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code></li>
+ </ul>
+
+ <p><a href="read.TOXSWA_cwa.html">Read TOXSWA surface water concentrations</a></p>
+ <ul>
+ <li><code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></code></li>
+ </ul>
+
+ <p><a href="plot.TOXSWA_cwa.html">Plot TOXSWA surface water concentrations</a></p>
+ <ul>
+ <li><code><a href="plot.TOXSWA_cwa.html">plot.TOXSWA_cwa</a></code></li>
+ </ul>
+ <h2 id="section-classifications-and-indicators" class="hasAnchor"><a href="#section-classifications-and-indicators" class="anchor"></a>Classifications and indicators</h2>
+ <p class="section-desc"><p>Evaluating environmental fate properties</p></p>
+
+
+ <p><a href="SSLRC_mobility_classification.html">Determine the SSLRC mobility classification for a chemical substance from its Koc</a></p>
+ <ul>
+ <li><code><a href="SSLRC_mobility_classification.html">SSLRC_mobility_classification</a></code></li>
+ </ul>
+
+ <p><a href="GUS.html">Groundwater ubiquity score based on Gustafson (1989)</a></p>
+ <ul>
+ <li><code><a href="GUS.html">GUS</a></code></li><li><code><a href="GUS.html">GUS.numeric</a></code></li><li><code><a href="GUS.html">GUS.chent</a></code></li><li><code><a href="GUS.html">print.GUS_result</a></code></li>
+ </ul>
+
+ </div>
+ </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="#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-surface-water">Predicted environmental concentrations in surface water</a></li>
+ <li><a href="#section-classifications-and-indicators">Classifications and indicators</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/max_twa.html b/docs/reference/max_twa.html
new file mode 100644
index 0000000..4bb1be9
--- /dev/null
+++ b/docs/reference/max_twa.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>The maximum time weighted average concentration for a moving window — max_twa • 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>The maximum time weighted average concentration for a moving window</h1>
+ </div>
+
+
+ <p>The maximum time weighted average concentration for a moving window</p>
+
+
+ <pre><span class='fu'>max_twa</span>(<span class='no'>x</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>21</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>x</dt>
+ <dd>An object of type <code><a href='one_box.html'>one_box</a></code></dd>
+ <dt>window</dt>
+ <dd>The size of the moving window</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <p><code><a href='twa.html'>twa</a></code></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="#see-also">See also</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>
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+++ b/docs/reference/one_box.html
@@ -0,0 +1,137 @@
+<!-- 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 time series of decline data — one_box • 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 time series of decline data</h1>
+ </div>
+
+
+ <p>The time series starts with the amount specified for the first application.
+This does not create objects of type <code>ts</code>.</p>
+
+
+ <pre><span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='no'>...</span>)
+
+<span class='co'># S3 method for numeric</span>
+<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='no'>...</span>)
+
+<span class='co'># S3 method for mkinfit</span>
+<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>x</dt>
+ <dd>When numeric, this is the half-life to be used for an exponential
+decline. If x is an mkinfit object, the decline is calculated from this object</dd>
+ <dt>t_end</dt>
+ <dd>End of the time series</dd>
+ <dt>res</dt>
+ <dd>Resolution of the time series</dd>
+ <dt>...</dt>
+ <dd>Further arguments passed to methods</dd>
+ </dl>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='co'># Only use a half-life</span>
+<span class='no'>pred_0</span> <span class='kw'>&lt;-</span> <span class='fu'>one_box</span>(<span class='fl'>10</span>)
+<span class='fu'>plot</span>(<span class='no'>pred_0</span>)</div><img src='one_box-2.png' alt='' width='540' height='400' /><div class='input'>
+<span class='co'># Use a fitted mkinfit model</span>
+<span class='fu'>require</span>(<span class='no'>mkin</span>)
+<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='no'>pred_1</span> <span class='kw'>&lt;-</span> <span class='fu'>one_box</span>(<span class='no'>fit</span>)
+<span class='fu'>plot</span>(<span class='no'>pred_1</span>)</div><img src='one_box-4.png' alt='' width='540' height='400' /><div class='input'>
+<span class='co'># Use a model with more than one observed variable</span>
+<span class='no'>m_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='no'>pred_2</span> <span class='kw'>&lt;-</span> <span class='fu'>one_box</span>(<span class='no'>fit_2</span>)
+<span class='fu'>plot</span>(<span class='no'>pred_2</span>)</div><img src='one_box-8.png' alt='' width='540' height='400' /></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="#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/pfm_degradation.html b/docs/reference/pfm_degradation.html
new file mode 100644
index 0000000..d98778b
--- /dev/null
+++ b/docs/reference/pfm_degradation.html
@@ -0,0 +1,136 @@
+<!-- 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 a time course of relative concentrations based on an mkinmod model — pfm_degradation • 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 a time course of relative concentrations based on an mkinmod model</h1>
+ </div>
+
+
+ <p>Calculate a time course of relative concentrations based on an mkinmod model</p>
+
+
+ <pre><span class='fu'>pfm_degradation</span>(<span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span>
+ <span class='fu'>log</span>(<span class='fl'>2</span>)/<span class='no'>DT50</span>), <span class='kw'>years</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>step_days</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='no'>years</span> * <span class='fl'>365</span>, <span class='kw'>by</span> <span class='kw'>=</span>
+ <span class='no'>step_days</span>))</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>model</dt>
+ <dd>The degradation model to be used. Either a parent only model like
+&#39;SFO&#39; or &#39;FOMC&#39;, or an mkinmod object</dd>
+ <dt>DT50</dt>
+ <dd>The half-life. This is only used when simple exponential decline
+is calculated (SFO model).</dd>
+ <dt>parms</dt>
+ <dd>The parameters used for the degradation model</dd>
+ <dt>years</dt>
+ <dd>For how many years should the degradation be predicted?</dd>
+ <dt>step_days</dt>
+ <dd>What step size in days should the output have?</dd>
+ <dt>times</dt>
+ <dd>The output times</dd>
+ </dl>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='fu'>head</span>(<span class='fu'>pfm_degradation</span>(<span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>10</span>))</div><div class='output co'>#&gt; time parent
+#&gt; 1 0 1.0000000
+#&gt; 2 1 0.9330330
+#&gt; 3 2 0.8705506
+#&gt; 4 3 0.8122524
+#&gt; 5 4 0.7578583
+#&gt; 6 5 0.7071068</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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+Johannes Ranke
+
+ </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/plot.TOXSWA_cwa-2.png b/docs/reference/plot.TOXSWA_cwa-2.png
new file mode 100644
index 0000000..6f9de30
--- /dev/null
+++ b/docs/reference/plot.TOXSWA_cwa-2.png
Binary files differ
diff --git a/docs/reference/plot.TOXSWA_cwa.html b/docs/reference/plot.TOXSWA_cwa.html
new file mode 100644
index 0000000..7cbe238
--- /dev/null
+++ b/docs/reference/plot.TOXSWA_cwa.html
@@ -0,0 +1,138 @@
+<!-- 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>Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa • 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>Plot TOXSWA surface water concentrations</h1>
+ </div>
+
+
+ <p>Plot TOXSWA hourly concentrations of a chemical substance in a specific
+segment of a TOXSWA surface water body.</p>
+
+
+ <pre><span class='co'># S3 method for TOXSWA_cwa</span>
+<span class='fu'>plot</span>(<span class='no'>x</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"datetime"</span>, <span class='st'>"t"</span>, <span class='st'>"t_firstjan"</span>,
+ <span class='st'>"t_rel_to_max"</span>), <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+ <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>LC_TIME</span> <span class='kw'>=</span> <span class='st'>"C"</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>x</dt>
+ <dd>The TOXSWA_cwa object to be plotted.</dd>
+ <dt>time_column</dt>
+ <dd>What should be used for the time axis. If &quot;t_firstjan&quot; is chosen,
+the time is given in days relative to the first of January in the first year.</dd>
+ <dt>xlab, ylab</dt>
+ <dd>Labels for x and y axis.</dd>
+ <dt>add</dt>
+ <dd>Should we add to an existing plot?</dd>
+ <dt>total</dt>
+ <dd>Should the total concentration in water be plotted, including substance sorbed
+to suspended matter?</dd>
+ <dt>LC_TIME</dt>
+ <dd>Specification of the locale used to format dates</dd>
+ <dt>...</dt>
+ <dd>Further arguments passed to <code>plot</code> if we are not adding to an existing plot</dd>
+ </dl>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>H_sw_D4_pond</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00001p_pa.cwa"</span>,
+ <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>,
+ <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata/SwashProjects.zip"</span>,
+ <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>))
+<span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>)</div><img src='plot.TOXSWA_cwa-2.png' alt='' width='540' height='400' /></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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+Johannes Ranke
+
+ </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/plot.one_box-2.png b/docs/reference/plot.one_box-2.png
new file mode 100644
index 0000000..4007876
--- /dev/null
+++ b/docs/reference/plot.one_box-2.png
Binary files differ
diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html
new file mode 100644
index 0000000..1870a55
--- /dev/null
+++ b/docs/reference/plot.one_box.html
@@ -0,0 +1,131 @@
+<!-- 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>Plot time series of decline data — plot.one_box • 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>
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+
+ <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>Plot time series of decline data</h1>
+ </div>
+
+
+ <p>Plot time series of decline data</p>
+
+
+ <pre><span class='co'># S3 method for one_box</span>
+<span class='fu'>plot</span>(<span class='no'>x</span>, <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'>range</span>(<span class='fu'>time</span>(<span class='no'>x</span>)), <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fu'>max</span>(<span class='no'>x</span>)),
+ <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Fraction of initial"</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+ <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='fu'>dimnames</span>(<span class='no'>x</span>)<span class='kw'>[[</span><span class='fl'>2</span>]][<span class='fl'>1</span>], <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>x</dt>
+ <dd>The object of type <code><a href='one_box.html'>one_box</a></code> to be plotted</dd>
+ <dt>xlim</dt>
+ <dd>Limits for the x axis</dd>
+ <dt>ylim</dt>
+ <dd>Limits for the y axis</dd>
+ <dt>xlab</dt>
+ <dd>Label for the x axis</dd>
+ <dt>ylab</dt>
+ <dd>Label for the y axis</dd>
+ <dt>max_twa</dt>
+ <dd>If a numeric value is given, the maximum time weighted
+average concentration(s) is/are shown in the graph.</dd>
+ <dt>max_twa_var</dt>
+ <dd>Variable for which the maximum time weighted average should
+be shown if max_twa is not NULL.</dd>
+ <dt>...</dt>
+ <dd>Further arguments passed to methods</dd>
+ </dl>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='fu'>plot</span>(<span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>), <span class='fl'>3</span>, <span class='fl'>7</span>), <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>)</div><img src='plot.one_box-2.png' alt='' width='540' height='400' /></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="#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/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html
new file mode 100644
index 0000000..3afec9c
--- /dev/null
+++ b/docs/reference/read.TOXSWA_cwa.html
@@ -0,0 +1,154 @@
+<!-- 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>Read TOXSWA surface water concentrations — read.TOXSWA_cwa • 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 -->
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+
+<!--[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>Read TOXSWA surface water concentrations</h1>
+ </div>
+
+
+ <p>Read TOXSWA hourly concentrations of a chemical substance in a specific
+segment of a TOXSWA surface water body. Per default, the data for the last
+segment are imported. As TOXSWA 4 reports the values at the end of the hour
+(ConLiqWatLayCur) in its summary file, we use this value as well instead
+of the hourly averages (ConLiqWatLay).</p>
+
+
+ <pre><span class='fu'>read.TOXSWA_cwa</span>(<span class='no'>filename</span>, <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>segment</span> <span class='kw'>=</span> <span class='st'>"last"</span>,
+ <span class='kw'>substance</span> <span class='kw'>=</span> <span class='st'>"parent"</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>windows</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
+ <span class='kw'>thresholds</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>filename</dt>
+ <dd>The filename of the cwa file (TOXSWA 2.x.y or similar) or the
+out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).</dd>
+ <dt>basedir</dt>
+ <dd>The path to the directory where the cwa file resides.</dd>
+ <dt>zipfile</dt>
+ <dd>Optional path to a zip file containing the cwa file.</dd>
+ <dt>segment</dt>
+ <dd>The segment for which the data should be read. Either &quot;last&quot;, or
+the segment number.</dd>
+ <dt>substance</dt>
+ <dd>For TOXSWA 4 .out files, the default value &quot;parent&quot; leads
+to reading concentrations of the parent compound. Alternatively, the substance
+of interested can be selected by its code name.</dd>
+ <dt>total</dt>
+ <dd>Set this to TRUE in order to read total concentrations as well. This is
+only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa
+files. For .cwa files, the total concentration is always read as well.</dd>
+ <dt>windows</dt>
+ <dd>Numeric vector of width of moving windows in days, for calculating
+maximum time weighted average concentrations and areas under the curve.</dd>
+ <dt>thresholds</dt>
+ <dd>Numeric vector of threshold concentrations in µg/L for
+generating event statistics.</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>An instance of an R6 object of class
+<code><a href='TOXSWA_cwa.html'>TOXSWA_cwa</a></code>.</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>H_sw_D4_pond</span> <span class='kw'>&lt;-</span> <span class='fu'>read.TOXSWA_cwa</span>(<span class='st'>"00001p_pa.cwa"</span>,
+ <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>,
+ <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata/SwashProjects.zip"</span>,
+ <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>))</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="#examples">Examples</a></li>
+ </ul>
+
+ <h2>Author</h2>
+
+Johannes Ranke
+
+ </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/sawtooth-2.png b/docs/reference/sawtooth-2.png
new file mode 100644
index 0000000..e6ff97d
--- /dev/null
+++ b/docs/reference/sawtooth-2.png
Binary files differ
diff --git a/docs/reference/sawtooth-6.png b/docs/reference/sawtooth-6.png
new file mode 100644
index 0000000..161ecb4
--- /dev/null
+++ b/docs/reference/sawtooth-6.png
Binary files differ
diff --git a/docs/reference/sawtooth-8.png b/docs/reference/sawtooth-8.png
new file mode 100644
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--- /dev/null
+++ b/docs/reference/sawtooth-8.png
Binary files differ
diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html
new file mode 100644
index 0000000..e24186e
--- /dev/null
+++ b/docs/reference/sawtooth.html
@@ -0,0 +1,142 @@
+<!-- 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 decline time series for multiple applications — sawtooth • 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 decline time series for multiple applications</h1>
+ </div>
+
+
+ <p>If the number of application cycles <code>n</code> is greater than 1, the
+application pattern specified in <code>applications</code> is repeated <code>n</code>
+times, with an interval <code>i</code>.</p>
+
+
+ <pre><span class='fu'>sawtooth</span>(<span class='no'>x</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>0</span> + <span class='no'>n</span>
+ * <span class='no'>i</span>, <span class='kw'>length.out</span> <span class='kw'>=</span> <span class='no'>n</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fl'>1</span>))</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>x</dt>
+ <dd>A <code><a href='one_box.html'>one_box</a></code> object</dd>
+ <dt>n</dt>
+ <dd>The number of applications. If <code>applications</code> is specified, <code>n</code> is not used</dd>
+ <dt>i</dt>
+ <dd>The interval between applications. If <code>applications</code> is specified, <code>i</code>
+is not used</dd>
+ <dt>applications</dt>
+ <dd>A data frame holding the application times in the first column and
+the corresponding amounts applied in the second column for each application cycle.
+If <code>n</code> is one, the application pattern specified here is used only once.</dd>
+ </dl>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>applications</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>14</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>3</span>))
+<span class='no'>pred</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>)
+<span class='fu'>plot</span>(<span class='fu'>sawtooth</span>(<span class='no'>pred</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='no'>applications</span>))</div><img src='sawtooth-2.png' alt='' width='540' height='400' /><div class='input'>
+<span class='no'>m_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='no'>pred_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>)
+<span class='no'>pred_2_saw</span> <span class='kw'>&lt;-</span> <span class='fu'>sawtooth</span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>)
+<span class='fu'>plot</span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><img src='sawtooth-6.png' alt='' width='540' height='400' /><div class='input'>
+<span class='fu'><a href='max_twa.html'>max_twa</a></span>(<span class='no'>pred_2_saw</span>)</div><div class='output co'>#&gt; $max
+#&gt; parent m1
+#&gt; 0.6627707 0.8542785
+#&gt;
+#&gt; $window_start
+#&gt; parent m1
+#&gt; 0.00 32.09
+#&gt;
+#&gt; $window_end
+#&gt; parent m1
+#&gt; 21.00 53.09
+#&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="#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/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html
new file mode 100644
index 0000000..f842d08
--- /dev/null
+++ b/docs/reference/soil_scenario_data_EFSA_2015.html
@@ -0,0 +1,157 @@
+<!-- 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>Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015 • 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">
+<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 -->
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+<script src="../pkgdown.js"></script>
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+
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+ <a href="../reference/index.html">Reference</a>
+</li>
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+
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+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Properties of the predefined scenarios from the EFSA guidance from 2015</h1>
+ </div>
+
+
+ <p>Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the
+concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the
+scenario and model adjustment factors from p. 15 and p. 17 are included.</p>
+
+
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>A data frame with one row for each scenario. Row names are the scenario codes,
+ e.g. CTN for the Northern scenario for the total concentration in soil. Columns are
+ mostly self-explanatory. <code>rho</code> is the dry bulk density of the top soil.</p>
+
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+
+ <p>EFSA (European Food Safety Authority) (2015)
+EFSA guidance document for predicting environmental concentrations
+of active substances of plant protection products and transformation products of these
+active substances in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093
+doi:10.2903/j.efsa.2015.4093</p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span>
+<span class='co'># # This is the code that was used to define the data</span>
+<span class='co'># soil_scenario_data_EFSA_2015 &lt;- data.frame(</span>
+<span class='co'># Zone = rep(c("North", "Central", "South"), 2),</span>
+<span class='co'># Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"),</span>
+<span class='co'># T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8),</span>
+<span class='co'># T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7),</span>
+<span class='co'># Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"),</span>
+<span class='co'># f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011),</span>
+<span class='co'># theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347),</span>
+<span class='co'># rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51),</span>
+<span class='co'># f_sce = c(3, 2, 2, 2, 1.5, 1.5),</span>
+<span class='co'># f_mod = c(2, 2, 2, 4, 4, 4),</span>
+<span class='co'># stringsAsFactors = FALSE,</span>
+<span class='co'># row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS")</span>
+<span class='co'># )</span>
+<span class='co'># save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData')</span>
+<span class='co'>## ---------------------------------------------</span>
+
+<span class='co'># And this is the resulting dataframe</span>
+<span class='no'>soil_scenario_data_EFSA_2015</span></div><div class='output co'>#&gt; Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce
+#&gt; CTN North Estonia 4.7 7.0 Coarse 0.118 0.244 0.95 3.0
+#&gt; CTC Central Germany 8.0 10.1 Coarse 0.086 0.244 1.05 2.0
+#&gt; CTS South France 11.0 12.3 Medium fine 0.048 0.385 1.22 2.0
+#&gt; CLN North Denmark 8.2 9.8 Medium 0.023 0.347 1.39 2.0
+#&gt; CLC Central Czech Republik 9.1 11.2 Medium 0.018 0.347 1.43 1.5
+#&gt; CLS South Spain 12.8 14.7 Medium 0.011 0.347 1.51 1.5
+#&gt; f_mod
+#&gt; CTN 2
+#&gt; CTC 2
+#&gt; CTS 2
+#&gt; CLN 4
+#&gt; CLC 4
+#&gt; CLS 4</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/twa.html b/docs/reference/twa.html
new file mode 100644
index 0000000..414b372
--- /dev/null
+++ b/docs/reference/twa.html
@@ -0,0 +1,138 @@
+<!-- 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 a time weighted average concentration — twa • 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 a time weighted average concentration</h1>
+ </div>
+
+
+ <p>The moving average is built only using the values in the past, so
+the earliest possible time for the maximum in the time series returned
+is after one window has passed.</p>
+
+
+ <pre><span class='fu'>twa</span>(<span class='no'>x</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>21</span>)
+
+<span class='co'># S3 method for one_box</span>
+<span class='fu'>twa</span>(<span class='no'>x</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>21</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+ <dl class="dl-horizontal">
+ <dt>x</dt>
+ <dd>An object of type <code><a href='one_box.html'>one_box</a></code></dd>
+ <dt>window</dt>
+ <dd>The size of the moving window</dd>
+ </dl>
+
+ <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <p><code><a href='max_twa.html'>max_twa</a></code></p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>pred</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>),
+ <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>1</span>)))
+<span class='fu'><a href='max_twa.html'>max_twa</a></span>(<span class='no'>pred</span>)</div><div class='output co'>#&gt; $max
+#&gt; parent
+#&gt; 0.9537545
+#&gt;
+#&gt; $window_start
+#&gt; parent
+#&gt; 0
+#&gt;
+#&gt; $window_end
+#&gt; parent
+#&gt; 21
+#&gt; </div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+
+ <li><a href="#see-also">See also</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/soil_scenario_data_EFSA_2015.html b/docs/soil_scenario_data_EFSA_2015.html
deleted file mode 100644
index 405e5b0..0000000
--- a/docs/soil_scenario_data_EFSA_2015.html
+++ /dev/null
@@ -1,144 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>soil_scenario_data_EFSA_2015. pfm 0.3-8</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="">
-
-<link href="css/bootstrap.css" rel="stylesheet">
-<link href="css/bootstrap-responsive.css" rel="stylesheet">
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-
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- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-<![endif]-->
-
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [ ['$','$'], ["\\(","\\)"] ],
- processEscapes: true
- }
- });
-</script>
-<script type="text/javascript"
- src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
- </head>
-
- <body>
- <div class="navbar">
- <div class="navbar-inner">
- <div class="container">
- <a class="brand" href="index.html">pfm 0.3-8</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html">Home</a></li>
- <li><a href="reference.html">Reference</a></li>
- </ul>
- </div>
- </div>
- </div>
-</div>
-
-
- <div class="container">
- <header>
-
- </header>
-
- <h1>Properties of the predefined scenarios from the EFSA guidance from 2015</h1>
-
-<div class="row">
- <div class="span8">
-
- <div class="Format">
- <h2>Format</h2>
-
- <p>A data frame with one row for each scenario. Row names are the scenario codes,
- e.g. CTN for the Northern scenario for the total concentration in soil. Columns are
- mostly self-explanatory. <code>rho</code> is the dry bulk density of the top soil.</p>
-
- </div>
-
- <div class="Source">
- <h2>Source</h2>
-
- <p>EFSA (European Food Safety Authority) (2015)
-EFSA guidance document for predicting environmental concentrations
-of active substances of plant protection products and transformation products of these
-active substances in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093
-doi:10.2903/j.efsa.2015.4093</p>
-
- </div>
-
- <div class="Description">
- <h2>Description</h2>
-
- <p>Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the
-concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the
-scenario and model adjustment factors from p. 15 and p. 17 are included.</p>
-
- </div>
-
- <h2 id="examples">Examples</h2>
- <pre class="examples"><div class='input'><span class="comment">## Not run: ------------------------------------</span>
-<span class="comment"># # This is the code that was used to define the data</span>
-<span class="comment"># soil_scenario_data_EFSA_2015 &lt;- data.frame(</span>
-<span class="comment"># Zone = rep(c("North", "Central", "South"), 2),</span>
-<span class="comment"># Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"),</span>
-<span class="comment"># T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8),</span>
-<span class="comment"># T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7),</span>
-<span class="comment"># Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"),</span>
-<span class="comment"># f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011),</span>
-<span class="comment"># theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347),</span>
-<span class="comment"># rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51),</span>
-<span class="comment"># f_sce = c(3, 2, 2, 2, 1.5, 1.5),</span>
-<span class="comment"># f_mod = c(2, 2, 2, 4, 4, 4),</span>
-<span class="comment"># stringsAsFactors = FALSE,</span>
-<span class="comment"># row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS")</span>
-<span class="comment"># )</span>
-<span class="comment"># save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData')</span>
-<span class="comment">## ---------------------------------------------</span>
-
-<span class="comment"># And this is the resulting dataframe</span>
-<span class="symbol">soil_scenario_data_EFSA_2015</span></div>
-<div class='output'> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce
-CTN North Estonia 4.7 7.0 Coarse 0.118 0.244 0.95 3.0
-CTC Central Germany 8.0 10.1 Coarse 0.086 0.244 1.05 2.0
-CTS South France 11.0 12.3 Medium fine 0.048 0.385 1.22 2.0
-CLN North Denmark 8.2 9.8 Medium 0.023 0.347 1.39 2.0
-CLC Central Czech Republik 9.1 11.2 Medium 0.018 0.347 1.43 1.5
-CLS South Spain 12.8 14.7 Medium 0.011 0.347 1.51 1.5
- f_mod
-CTN 2
-CTC 2
-CTS 2
-CLN 4
-CLC 4
-CLS 4
-</div></pre>
- </div>
- <div class="span4 sidebar">
- <!-- <ul>
- <li>soil_scenario_data_EFSA_2015</li>
- </ul>
- <ul>
- <li>datasets</li>
- </ul> -->
-
-
-
-
- </div>
-</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
- </footer>
- </div>
- </body>
-</html> \ No newline at end of file
diff --git a/man/max_twa.Rd b/man/max_twa.Rd
index 13e7bbf..86cc174 100644
--- a/man/max_twa.Rd
+++ b/man/max_twa.Rd
@@ -15,5 +15,5 @@ max_twa(x, window = 21)
The maximum time weighted average concentration for a moving window
}
\seealso{
-twa
+\code{\link{twa}}
}
diff --git a/man/one_box.Rd b/man/one_box.Rd
index 86440ce..0085f3f 100644
--- a/man/one_box.Rd
+++ b/man/one_box.Rd
@@ -33,13 +33,13 @@ plot(pred_0)
# Use a fitted mkinfit model
require(mkin)
-fit <- mkinfit("FOMC", FOCUS_2006_C)
+fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
pred_1 <- one_box(fit)
plot(pred_1)
# Use a model with more than one observed variable
m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
-fit_2 <- mkinfit(m_2, FOCUS_2006_D)
+fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE)
pred_2 <- one_box(fit_2)
plot(pred_2)
}
diff --git a/man/sawtooth.Rd b/man/sawtooth.Rd
index 4576c8b..d26c0bf 100644
--- a/man/sawtooth.Rd
+++ b/man/sawtooth.Rd
@@ -30,7 +30,7 @@ pred <- one_box(10)
plot(sawtooth(pred, applications = applications))
m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
-fit_2 <- mkinfit(m_2, FOCUS_2006_D)
+fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE)
pred_2 <- one_box(fit_2)
pred_2_saw <- sawtooth(pred_2, 2, 7)
plot(pred_2_saw, max_twa = 21, max_twa_var = "m1")
diff --git a/man/twa.Rd b/man/twa.Rd
index a6afa87..a3509cd 100644
--- a/man/twa.Rd
+++ b/man/twa.Rd
@@ -25,5 +25,5 @@ pred <- sawtooth(one_box(10),
max_twa(pred)
}
\seealso{
-max_twa
+\code{\link{max_twa}}
}

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