Rebuild static docs using current pkdown

Process PELMO runs in example using 15 (hyperthreading) cores and show processor info.
author: Johannes Ranke <jranke@uni-bremen.de> 2018-03-01 10:10:08 +0100
committer: Johannes Ranke <jranke@uni-bremen.de> 2018-03-01 10:10:08 +0100
commit: 6d8de73e68f2c0349e618af35ce4a8f095ca0ed5 (patch)
tree: 3f4b574934ce0bcb1ed0f167b4daab81accc5a38
parent: 3c39bba4af013b099ec013bddcc92407058026e0 (diff)
60 files changed, 855 insertions, 134 deletions
diff --git a/ChangeLog b/ChangeLog
index 017af3a..ea7b134 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,15 @@
+commit ffeec05d913f2e987da362c05df2afc2a8a23965
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2018-01-29 10:11:27 +0100
+
+    Documentation fixes and updates
+
+commit 8423df9693c5cd2f2d36ee3131c7b6fcefa4d0ca
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2018-01-29 10:11:27 +0100
+
+    Documentation fixes and updates
+
 commit b9ce44748f2795ae1f35fe5a510e88635f247a7f
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2018-01-29 09:22:42 +0100
diff --git a/DESCRIPTION b/DESCRIPTION
index 35c29dc..deb08cc 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: pfm
 Type: Package
 Title: Utilities for Pesticide Fate Modelling
 Version: 0.4-5
-Date: 2018-01-29
+Date: 2018-02-27
 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de",
                   role = c("aut", "cre", "cph"),
                   comment = c(ORCID = "0000-0003-4371-6538"))
diff --git a/R/PELMO_runs.R b/R/PELMO_runs.R
index 432231e..2768205 100644
--- a/R/PELMO_runs.R
+++ b/R/PELMO_runs.R
@@ -42,11 +42,14 @@
 #'        pot = c("Cha", "Ham", "Jok", "Kre", "Oke", "Pia", "Por", "Sev", "Thi")))
 #' time_1 <- system.time(
 #'   PECgw_1 <- PELMO_runs(runs_1, psm_dir = system.file("testdata", package = "pfm"),
-#'     cores = 6, overwrite = TRUE)
+#'     cores = 15, overwrite = TRUE)
 #' )
 #' print(PECgw_1)
 #' # We get exactly the same PECgw values (on Linux, calling PELMO using Wine).
 #' print(time_1)
+#' if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) {
+#'   cat(gsub("model name\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[1]]))
+#' }
 #'
 #' # Demonstrate some results with metabolites.
 #' runs_2 <- list(list(psm = 'Pesticide_D_1_May_every_other_year_mets',
diff --git a/docs/authors.html b/docs/authors.html
index d2ef54f..d08c687 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -18,12 +18,16 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="pkgdown.css" rel="stylesheet">
 <script src="jquery.sticky-kit.min.js"></script>
 <script src="pkgdown.js"></script>
-
+  
+  
+<meta property="og:title" content="Authors" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +55,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="reference/index.html">Reference</a>
 </li>
       </ul>
@@ -73,8 +83,8 @@
 
     <ul class="list-unstyled">
       <li>
-        <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright&nbsp;holder.
-        <br /><small>0000-0003-4371-6538</small></p>
+        <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. <a href='https://orcid.org/0000-0003-4371-6538' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid'></a>
+        </p>
       </li>
     </ul>
 
@@ -89,7 +99,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/index.html b/docs/index.html
index 66f3304..5b977a6 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -8,8 +8,13 @@
 <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">
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-<!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
+<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><meta property="og:title" content="Utilities for Pesticide Fate Modelling">
+<meta property="og:description" content="Utilities for simple calculations of predicted environmental
+    concentrations ('PEC' values) and for dealing with data from some FOCUS
+    pesticide fate modelling software packages.">
+<meta name="twitter:card" content="summary">
+<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
@@ -29,6 +34,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
 <li>
+  <a href="index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="reference/index.html">Reference</a>
 </li>
       </ul>
@@ -64,7 +75,7 @@ this program. If not, see &lt;http:<span class="er">//</span>www.gnu.org/license
 <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">quick =</span> <span class="ot">TRUE</span>)</code></pre></div>
+<span class="kw"><a href="http://www.rdocumentation.org/packages/devtools/topics/install_github">install_github</a></span>(<span class="st">"jranke/pfm"</span>, <span class="dt">quick =</span> <span class="ot">TRUE</span>)</code></pre></div>
 </div>
 <div id="use" class="section level2">
 <h2 class="hasAnchor">
@@ -85,8 +96,7 @@ this program. If not, see &lt;http:<span class="er">//</span>www.gnu.org/license
 <p>GPL</p>
 <h2>Developers</h2>
 <ul class="list-unstyled">
-<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> <br><small>(0000-0003-4371-6538)</small>
-</li>
+<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid"></a> </li>
 </ul>
 </div>
 </div>
@@ -97,7 +107,7 @@ this program. If not, see &lt;http:<span class="er">//</span>www.gnu.org/license
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
index 9c437c7..181fe63 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -34,6 +34,10 @@ img.icon {
   float: right;
 }
 
+img {
+  max-width: 100%;
+}
+
 /* Section anchors ---------------------------------*/
 
 a.anchor {
@@ -96,6 +100,11 @@ a.anchor {
   margin-bottom: 0.5em;
 }
 
+.orcid {
+  height: 16px;
+  vertical-align: middle;
+}
+
 /* Reference index & topics ----------------------------------------------- */
 
 .ref-index th {font-weight: normal;}
@@ -133,15 +142,30 @@ pre, code {
   color: #333;
 }
 
-pre img {
+pre code {
+  overflow: auto;
+  word-wrap: normal;
+  white-space: pre;
+}
+
+pre .img {
+  margin: 5px 0;
+}
+
+pre .img img {
   background-color: #fff;
   display: block;
+  height: auto;
 }
 
 code a, pre a {
   color: #375f84;
 }
 
+a.sourceLine:hover {
+  text-decoration: none;
+}
+
 .fl      {color: #1514b5;}
 .fu      {color: #000000;} /* function */
 .ch,.st  {color: #036a07;} /* string */
@@ -152,3 +176,19 @@ code a, pre a {
 .error   { color: orange;  font-weight: bolder;}
 .warning { color: #6A0366; font-weight: bolder;}
 
+/* Clipboard --------------------------*/
+
+.hasCopyButton {
+  position: relative;
+}
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+  position: absolute;
+  right: 0;
+  top: 0;
+  visibility: hidden;
+}
+
+.hasCopyButton:hover button.btn-copy-ex {
+  visibility: visible;
+}
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
index c8b38c4..64b20df 100644
--- a/docs/pkgdown.js
+++ b/docs/pkgdown.js
@@ -1,8 +1,94 @@
 $(function() {
-  $("#sidebar").stick_in_parent({offset_top: 40});
+
+  $("#sidebar")
+    .stick_in_parent({offset_top: 40})
+    .on('sticky_kit:bottom', function(e) {
+      $(this).parent().css('position', 'static');
+    })
+    .on('sticky_kit:unbottom', function(e) {
+      $(this).parent().css('position', 'relative');
+    });
+
   $('body').scrollspy({
     target: '#sidebar',
     offset: 60
   });
 
+  var cur_path = paths(location.pathname);
+  $("#navbar ul li a").each(function(index, value) {
+    if (value.text == "Home")
+      return;
+    if (value.getAttribute("href") === "#")
+      return;
+
+    var path = paths(value.pathname);
+    if (is_prefix(cur_path, path)) {
+      // Add class to parent <li>, and enclosing <li> if in dropdown
+      var menu_anchor = $(value);
+      menu_anchor.parent().addClass("active");
+      menu_anchor.closest("li.dropdown").addClass("active");
+    }
+  });
 });
+
+function paths(pathname) {
+  var pieces = pathname.split("/");
+  pieces.shift(); // always starts with /
+
+  var end = pieces[pieces.length - 1];
+  if (end === "index.html" || end === "")
+    pieces.pop();
+  return(pieces);
+}
+
+function is_prefix(needle, haystack) {
+  if (needle.length > haystack.lengh)
+    return(false);
+
+  for (var i = 0; i < haystack.length; i++) {
+    if (needle[i] != haystack[i])
+      return(false);
+  }
+
+  return(true);
+}
+
+/* Clipboard --------------------------*/
+
+function changeTooltipMessage(element, msg) {
+  var tooltipOriginalTitle=element.getAttribute('data-original-title');
+  element.setAttribute('data-original-title', msg);
+  $(element).tooltip('show');
+  element.setAttribute('data-original-title', tooltipOriginalTitle);
+}
+
+if(Clipboard.isSupported()) {
+  $(document).ready(function() {
+    var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+
+    $(".examples").addClass("hasCopyButton");
+
+    // Insert copy buttons:
+    $(copyButton).prependTo(".hasCopyButton");
+
+    // Initialize tooltips:
+    $('.btn-copy-ex').tooltip({container: 'body'});
+
+    // Initialize clipboard:
+    var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      text: function(trigger) {
+        return trigger.parentNode.textContent;
+      }
+    });
+
+    clipboardBtnCopies.on('success', function(e) {
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+
diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html
index 97bdebf..8b3ee87 100644
--- a/docs/reference/FOCUS_GW_scenarios_2012.html
+++ b/docs/reference/FOCUS_GW_scenarios_2012.html
@@ -18,12 +18,20 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012" />
 
+<meta property="og:description" content="Currently, only scenario names with acronyms and a small subset of the soil definitions are provided. The 
+soil definitions are from page 46ff. from FOCUS (2012)." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +59,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -171,7 +185,7 @@ soil definitions are from page 46ff. from FOCUS (2012).</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/FOCUS_PELMO_crop_sze_names.html b/docs/reference/FOCUS_PELMO_crop_sze_names.html
index 16c0dc6..954a707 100644
--- a/docs/reference/FOCUS_PELMO_crop_sze_names.html
+++ b/docs/reference/FOCUS_PELMO_crop_sze_names.html
@@ -18,12 +18,22 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="FOCUS PELMO crop acronyms used for naming sceneario files — FOCUS_PELMO_crop_sze_names" />
 
+<meta property="og:description" content="A named character vector with the crop acronyms used in FOCUS PELMO 5.5.3
+for naming the .sze files located in the FOCUS directory. The crop acronyms
+in the file names are sometimes capitalized, sometimes not. The scenario
+files used for Beans (field) and Beans (vegetable) are the same." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +61,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -113,7 +129,7 @@ files used for Beans (field) and Beans (vegetable) are the same.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/FOCUS_PELMO_crops.html b/docs/reference/FOCUS_PELMO_crops.html
index ed02c04..81783ba 100644
--- a/docs/reference/FOCUS_PELMO_crops.html
+++ b/docs/reference/FOCUS_PELMO_crops.html
@@ -18,12 +18,23 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="FOCUS PELMO crop names — FOCUS_PELMO_crops" />
 
+<meta property="og:description" content="A named character vector with the crop names used in the PELMO 5.5.3 GUI.
+For the names, three letter codes were constructed by generally taking the
+first three letters in lower case. Only when there is an expression in
+parentheses, the first letter of this expression becomes the first letter
+in the three letter code, i.e. 'Peas (animals)' has the code ape." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +62,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -124,7 +141,7 @@ in the three letter code, i.e. 'Peas (animals)' has the code <code>ape</code>.</
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/FOCUS_PELMO_location_codes.html b/docs/reference/FOCUS_PELMO_location_codes.html
index 7f4003d..31084b8 100644
--- a/docs/reference/FOCUS_PELMO_location_codes.html
+++ b/docs/reference/FOCUS_PELMO_location_codes.html
@@ -18,12 +18,20 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Location codes in FOCUS PELMO — FOCUS_PELMO_location_codes" />
 
+<meta property="og:description" content="A named character vector of one letter location codes used in FOCUS PELMO,
+indexed by three letter acronyms." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +59,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -105,7 +119,7 @@ indexed by three letter acronyms.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html
index 37bb2fd..9bd7165 100644
--- a/docs/reference/FOCUS_Step_12_scenarios.html
+++ b/docs/reference/FOCUS_Step_12_scenarios.html
@@ -18,12 +18,20 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios" />
 
+<meta property="og:description" content="The data were extracted from the scenario.txt file using the R code shown below.
+The text file is not included in the package as its licence is not clear." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +59,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -87,26 +101,25 @@ The text file 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='fu'>not_run</span>({
-    <span class='co'># This is the code that was used to extract the data</span>
-    <span class='no'>scenario_path</span> <span class='kw'>&lt;-</span> <span class='st'>"inst/extdata/FOCUS_Step_12_scenarios.txt"</span>
-    <span class='no'>scenarios</span> <span class='kw'>&lt;-</span> <span class='fu'>readLines</span>(<span class='no'>scenario_path</span>)[<span class='fl'>9</span>:<span class='fl'>38</span>]
-    <span class='no'>FOCUS_Step_12_scenarios</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>()
-    <span class='no'>sce</span> <span class='kw'>&lt;-</span> <span class='fu'>read.table</span>(<span class='kw'>text</span> <span class='kw'>=</span> <span class='no'>scenarios</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>, <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>check.names</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-      <span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-    <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span> <span class='kw'>=</span> <span class='no'>sce</span>$<span class='no'>Crop</span>
-    <span class='fu'>rownames</span>(<span class='no'>sce</span>) <span class='kw'>&lt;-</span> <span class='no'>sce</span>$<span class='no'>Crop</span>
-    <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>drift</span> <span class='kw'>=</span> <span class='no'>sce</span>[, <span class='fl'>3</span>:<span class='fl'>11</span>]
-    <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>interception</span> <span class='kw'>=</span> <span class='no'>sce</span>[, <span class='fl'>12</span>:<span class='fl'>15</span>]
-    <span class='no'>sce_2</span> <span class='kw'>&lt;-</span> <span class='fu'>readLines</span>(<span class='no'>scenario_path</span>)[<span class='fl'>41</span>:<span class='fl'>46</span>]
-    <span class='no'>rd</span> <span class='kw'>&lt;-</span> <span class='fu'>read.table</span>(<span class='kw'>text</span> <span class='kw'>=</span> <span class='no'>sce_2</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>)[<span class='fl'>1</span>:<span class='fl'>2</span>]
-    <span class='no'>rd_mat</span> <span class='kw'>&lt;-</span> <span class='fu'>matrix</span>(<span class='no'>rd</span>$<span class='no'>V2</span>, <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>byrow</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
-    <span class='fu'>dimnames</span>(<span class='no'>rd_mat</span>) <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>Time</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Oct-Feb"</span>, <span class='st'>"Mar-May"</span>, <span class='st'>"Jun-Sep"</span>),
-                            <span class='kw'>Region</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"North"</span>, <span class='st'>"South"</span>))
-    <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>rd</span> <span class='kw'>=</span> <span class='no'>rd_mat</span>
-    <span class='fu'>save</span>(<span class='no'>FOCUS_Step_12_scenarios</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"data/FOCUS_Step_12_scenarios.RData"</span>)
-})
-
+</div><span class='co'># NOT RUN {</span>
+  <span class='co'># This is the code that was used to extract the data</span>
+  <span class='no'>scenario_path</span> <span class='kw'>&lt;-</span> <span class='st'>"inst/extdata/FOCUS_Step_12_scenarios.txt"</span>
+  <span class='no'>scenarios</span> <span class='kw'>&lt;-</span> <span class='fu'>readLines</span>(<span class='no'>scenario_path</span>)[<span class='fl'>9</span>:<span class='fl'>38</span>]
+  <span class='no'>FOCUS_Step_12_scenarios</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>()
+  <span class='no'>sce</span> <span class='kw'>&lt;-</span> <span class='fu'>read.table</span>(<span class='kw'>text</span> <span class='kw'>=</span> <span class='no'>scenarios</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>, <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>check.names</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+    <span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
+  <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span> <span class='kw'>=</span> <span class='no'>sce</span>$<span class='no'>Crop</span>
+  <span class='fu'>rownames</span>(<span class='no'>sce</span>) <span class='kw'>&lt;-</span> <span class='no'>sce</span>$<span class='no'>Crop</span>
+  <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>drift</span> <span class='kw'>=</span> <span class='no'>sce</span>[, <span class='fl'>3</span>:<span class='fl'>11</span>]
+  <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>interception</span> <span class='kw'>=</span> <span class='no'>sce</span>[, <span class='fl'>12</span>:<span class='fl'>15</span>]
+  <span class='no'>sce_2</span> <span class='kw'>&lt;-</span> <span class='fu'>readLines</span>(<span class='no'>scenario_path</span>)[<span class='fl'>41</span>:<span class='fl'>46</span>]
+  <span class='no'>rd</span> <span class='kw'>&lt;-</span> <span class='fu'>read.table</span>(<span class='kw'>text</span> <span class='kw'>=</span> <span class='no'>sce_2</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>"\t"</span>)[<span class='fl'>1</span>:<span class='fl'>2</span>]
+  <span class='no'>rd_mat</span> <span class='kw'>&lt;-</span> <span class='fu'>matrix</span>(<span class='no'>rd</span>$<span class='no'>V2</span>, <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>byrow</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
+  <span class='fu'>dimnames</span>(<span class='no'>rd_mat</span>) <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>Time</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Oct-Feb"</span>, <span class='st'>"Mar-May"</span>, <span class='st'>"Jun-Sep"</span>),
+                          <span class='kw'>Region</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"North"</span>, <span class='st'>"South"</span>))
+  <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>rd</span> <span class='kw'>=</span> <span class='no'>rd_mat</span>
+  <span class='fu'>save</span>(<span class='no'>FOCUS_Step_12_scenarios</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"data/FOCUS_Step_12_scenarios.RData"</span>)
+<span class='co'># }</span><div class='input'>
 <span class='co'># And this is the resulting data</span>
 <span class='no'>FOCUS_Step_12_scenarios</span></div><div class='output co'>#&gt; $names
 #&gt;  [1] "cereals, spring"                  "cereals, winter"                 
@@ -275,7 +288,7 @@ The text file is not included in the package as its licence is not clear.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html
index 6f29e72..98bed51 100644
--- a/docs/reference/GUS.html
+++ b/docs/reference/GUS.html
@@ -18,12 +18,21 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Groundwater ubiquity score based on Gustafson (1989) — GUS" />
 
+<meta property="og:description" content="The groundwater ubiquity score GUS is calculated according to
+the following equation
+$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +60,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -198,7 +213,7 @@ Johannes Ranke
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html
index 4b1b7b9..a706729 100644
--- a/docs/reference/PEC_soil.html
+++ b/docs/reference/PEC_soil.html
@@ -18,12 +18,22 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Calculate predicted environmental concentrations in soil — PEC_soil" />
 
+<meta property="og:description" content="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)." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +61,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -254,7 +270,7 @@ Johannes Ranke
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html
index e52eeb8..7ad2c12 100644
--- a/docs/reference/PEC_sw_drainage_UK.html
+++ b/docs/reference/PEC_sw_drainage_UK.html
@@ -18,12 +18,20 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK" />
 
+<meta property="og:description" content="This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet
+published on the CRC website" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +59,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -144,7 +158,7 @@ Johannes Ranke
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html
index e52546b..6a567fe 100644
--- a/docs/reference/PEC_sw_drift.html
+++ b/docs/reference/PEC_sw_drift.html
@@ -18,12 +18,21 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift" />
 
+<meta property="og:description" content="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." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +60,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -155,7 +170,7 @@ Johannes Ranke
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/PEC_sw_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html
index 5539dc6..a99821d 100644
--- a/docs/reference/PEC_sw_exposit_runoff.html
+++ b/docs/reference/PEC_sw_exposit_runoff.html
@@ -18,12 +18,20 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff" />
 
+<meta property="og:description" content="This is a reimplementation of the calculation described in the Exposit 3.01 spreadsheet file,
+in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not implemented." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +59,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -116,7 +130,7 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not imp
     <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
 
     <p>Excel 3.01 spreadsheet available from
-  <a href = 'https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3'>https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3</a></p>
+  <a href='https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3'>https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3</a></p>
     
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
@@ -176,7 +190,7 @@ in the worksheet "Konzept Runoff". Calculation of sediment PEC values is not imp
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html
index 2250795..0c9516d 100644
--- a/docs/reference/PEC_sw_focus.html
+++ b/docs/reference/PEC_sw_focus.html
@@ -18,12 +18,25 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus" />
 
+<meta property="og:description" content="This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2,
+authored by Michael Klein, in R. Note that results for multiple
+applications should be compared to the corresponding results for a
+single application. At current, this is not done automatically in
+this implementation. Only Step 1 PECs are calculated. However,
+input files are generated that are suitable as input also for Step 2
+to be used with the FOCUS calculator." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +64,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -314,7 +333,7 @@ should be written</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html
index ceb8ea3..ee1e275 100644
--- a/docs/reference/PEC_sw_sed.html
+++ b/docs/reference/PEC_sw_sed.html
@@ -19,12 +19,21 @@ water concentrations — PEC_sw_sed • pfm</title>
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-
+  
+  
+<meta property="og:title" content="Calculate predicted environmental concentrations in sediment from surface
+water concentrations — PEC_sw_sed" />
+
+<meta property="og:description" content="The method 'percentage' is equivalent to what is used in the CRD spreadsheet
+PEC calculator" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -52,6 +61,12 @@ water concentrations — PEC_sw_sed • pfm</title>
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -149,7 +164,7 @@ Johannes Ranke
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/PELMO_path.html b/docs/reference/PELMO_path.html
index d19d640..fbe643d 100644
--- a/docs/reference/PELMO_path.html
+++ b/docs/reference/PELMO_path.html
@@ -18,12 +18,19 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Create a path of run directories as the PELMO GUI does — PELMO_path" />
 
+<meta property="og:description" content="Create a path of run directories as the PELMO GUI does" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +58,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -111,7 +124,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html
index 3d70c32..1c2aabe 100644
--- a/docs/reference/PELMO_runs.html
+++ b/docs/reference/PELMO_runs.html
@@ -18,12 +18,25 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Set up runs for FOCUS PELMO — PELMO_runs" />
 
+<meta property="og:description" content="Per default, the runs are not only set up but also executed with FOCUS
+PELMO, the results are processed and returned. Currently, only FOCUS PELMO
+as installed on Linux (or other Unix systems)
+using the install_PELMO from the PELMO.installeR package
+maintained on github is supported. In such installations, FOCUS PELMO is
+installed into the package installation directory of PELMO.installeR
+and run using wine." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +64,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -144,9 +163,9 @@ the period.plm file generated by the FOCUS PELMO GUI.</p>
     
     <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
 
-    <p>PELMO.installeR <a href = 'https://pkgdown.jrwb.de/PELMO.installeR'>https://pkgdown.jrwb.de/PELMO.installeR</a></p>
-<p>Wine <a href = 'https://winehq.org'>https://winehq.org</a></p>
-<p>PELMO test results <a href = 'http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc'>http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc</a></p>
+    <p>PELMO.installeR <a href='https://pkgdown.jrwb.de/PELMO.installeR'>https://pkgdown.jrwb.de/PELMO.installeR</a></p>
+<p>Wine <a href='https://winehq.org'>https://winehq.org</a></p>
+<p>PELMO test results <a href='http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc'>http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc</a></p>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -159,7 +178,7 @@ the period.plm file generated by the FOCUS PELMO GUI.</p>
        <span class='kw'>pot</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Cha"</span>, <span class='st'>"Ham"</span>, <span class='st'>"Jok"</span>, <span class='st'>"Kre"</span>, <span class='st'>"Oke"</span>, <span class='st'>"Pia"</span>, <span class='st'>"Por"</span>, <span class='st'>"Sev"</span>, <span class='st'>"Thi"</span>)))
 <span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'>system.time</span>(
   <span class='no'>PECgw_1</span> <span class='kw'>&lt;-</span> <span class='fu'>PELMO_runs</span>(<span class='no'>runs_1</span>, <span class='kw'>psm_dir</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>),
-    <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>6</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+    <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>15</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
 )
 <span class='fu'>print</span>(<span class='no'>PECgw_1</span>)</div><div class='output co'>#&gt; $Pesticide_D
 #&gt; $Pesticide_D$win
@@ -190,7 +209,9 @@ the period.plm file generated by the FOCUS PELMO GUI.</p>
 #&gt; 
 #&gt; </div><div class='input'><span class='co'># We get exactly the same PECgw values (on Linux, calling PELMO using Wine).</span>
 <span class='fu'>print</span>(<span class='no'>time_1</span>)</div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;     218.536       1.056      55.555 </div><div class='input'>
+#&gt;     220.760       1.509      30.234 </div><div class='input'><span class='kw'>if</span>(!<span class='fu'>inherits</span>(<span class='fu'>try</span>(<span class='no'>cpuinfo</span> <span class='kw'>&lt;-</span> <span class='fu'>readLines</span>(<span class='st'>"/proc/cpuinfo"</span>)), <span class='st'>"try-error"</span>)) {
+  <span class='fu'>cat</span>(<span class='fu'>gsub</span>(<span class='st'>"model name\t: "</span>, <span class='st'>"CPU model: "</span>, <span class='no'>cpuinfo</span>[<span class='fu'>grep</span>(<span class='st'>"model name"</span>, <span class='no'>cpuinfo</span>)[<span class='fl'>1</span>]]))
+}</div><div class='output co'>#&gt; CPU model: AMD Ryzen 7 1700 Eight-Core Processor</div><div class='input'>
 <span class='co'># Demonstrate some results with metabolites.</span>
 <span class='no'>runs_2</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>(<span class='fu'>list</span>(<span class='kw'>psm</span> <span class='kw'>=</span> <span class='st'>'Pesticide_D_1_May_every_other_year_mets'</span>,
                     <span class='kw'>win</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Cha"</span>, <span class='st'>"Ham"</span>, <span class='st'>"Kre"</span>)))
@@ -228,7 +249,7 @@ the period.plm file generated by the FOCUS PELMO GUI.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/SFO_actual_twa.html b/docs/reference/SFO_actual_twa.html
index 98a2ea3..2c7c5bf 100644
--- a/docs/reference/SFO_actual_twa.html
+++ b/docs/reference/SFO_actual_twa.html
@@ -18,12 +18,19 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa" />
 
+<meta property="og:description" content="Actual and maximum moving window time average concentrations for SFO kinetics" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +58,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -135,7 +148,7 @@ Johannes Ranke
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/SSLRC_mobility_classification.html b/docs/reference/SSLRC_mobility_classification.html
index b6c6c2d..5310a3f 100644
--- a/docs/reference/SSLRC_mobility_classification.html
+++ b/docs/reference/SSLRC_mobility_classification.html
@@ -18,12 +18,20 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification" />
 
+<meta property="og:description" content="This implements the method specified in the UK data requirements handbook and was 
+checked against the spreadsheet published on the CRC website" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +59,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -124,7 +138,7 @@ Johannes Ranke
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html
index f29951b..3bd0533 100644
--- a/docs/reference/TOXSWA_cwa.html
+++ b/docs/reference/TOXSWA_cwa.html
@@ -18,12 +18,20 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="R6 class for holding TOXSWA cwa concentration data and associated statistics — TOXSWA_cwa" />
 
+<meta property="og:description" content="An R6 class for holding TOXSWA cwa concentration data and some associated statistics.
+Usually, an instance of this class will be generated by read.TOXSWA_cwa." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +59,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -166,7 +180,7 @@ for the requested moving window sizes in days.</p></dd>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html
index 8e95618..0c03fff 100644
--- a/docs/reference/chent_focus_sw.html
+++ b/docs/reference/chent_focus_sw.html
@@ -18,12 +18,19 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw" />
 
+<meta property="og:description" content="Create a chemical compound object for FOCUS Step 1 calculations" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +58,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -148,7 +161,7 @@ systems</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/create_run_list.html b/docs/reference/create_run_list.html
index dfd7ca5..8cefafb 100644
--- a/docs/reference/create_run_list.html
+++ b/docs/reference/create_run_list.html
@@ -18,12 +18,19 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Create a list of runs that we can traverse — create_run_list" />
 
+<meta property="og:description" content="Create a list of runs that we can traverse" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +58,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -115,7 +128,7 @@ as used in <code><a href='FOCUS_GW_scenarios_2012.html'>FOCUS_GW_scenarios_2012<
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/drift_data_JKI.html b/docs/reference/drift_data_JKI.html
index b85dae6..159f662 100644
--- a/docs/reference/drift_data_JKI.html
+++ b/docs/reference/drift_data_JKI.html
@@ -19,12 +19,21 @@ published by the JKI — drift_data_JKI • pfm</title>
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Deposition from spray drift expressed as percent of the applied dose as
+published by the JKI — drift_data_JKI" />
 
+<meta property="og:description" content="Deposition from spray drift expressed as percent of the applied dose as
+published by the German Julius-Kühn Institute (JKI)." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -52,6 +61,12 @@ published by the JKI — drift_data_JKI • pfm</title>
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -101,24 +116,23 @@ 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='fu'>not_run</span>({
-    <span class='co'># This is the code that was used to extract the data</span>
-    <span class='fu'>library</span>(<span class='no'>readxl</span>)
-    <span class='no'>abdrift_path</span> <span class='kw'>&lt;-</span> <span class='st'>"inst/extdata/Tabelle der Abdrifteckwerte.xls"</span>
-    <span class='no'>JKI_crops</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='st'>"Ackerbau"</span>, <span class='st'>"Obstbau frueh"</span>, <span class='st'>"Obstbau spaet"</span>)
-    <span class='fu'>names</span>(<span class='no'>JKI_crops</span>) <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='st'>"Field crops"</span>, <span class='st'>"Pome/stone fruit, early"</span>, <span class='st'>"Pome/stone fruit, late"</span>)
-    <span class='no'>drift_data_JKI</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>()
-
-    <span class='kw'>for</span> (<span class='no'>n</span> <span class='kw'>in</span> <span class='fl'>1</span>:<span class='fl'>8</span>) {
-      <span class='no'>drift_data_raw</span> <span class='kw'>&lt;-</span> <span class='fu'>read_excel</span>(<span class='no'>abdrift_path</span>, <span class='kw'>sheet</span> <span class='kw'>=</span> <span class='no'>n</span> + <span class='fl'>1</span>, <span class='kw'>skip</span> <span class='kw'>=</span> <span class='fl'>2</span>)
-      <span class='no'>drift_data</span> <span class='kw'>&lt;-</span> <span class='fu'>as.matrix</span>(<span class='no'>drift_data_raw</span>[<span class='fl'>1</span>:<span class='fl'>9</span>, <span class='fl'>2</span>:<span class='fl'>4</span>])
-      <span class='fu'>dimnames</span>(<span class='no'>drift_data</span>) <span class='kw'>&lt;-</span> <span class='fu'>list</span>(<span class='kw'>distance</span> <span class='kw'>=</span> <span class='fu'>as.integer</span>(<span class='no'>drift_data_raw</span>[<span class='fl'>1</span>:<span class='fl'>9</span>, <span class='fl'>1</span>]),
-                                              <span class='kw'>crop</span> <span class='kw'>=</span> <span class='no'>JKI_crops</span>)
-      <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='no'>n</span>]] <span class='kw'>&lt;-</span> <span class='no'>drift_data</span>
-    }
-    <span class='fu'>save</span>(<span class='no'>drift_data_JKI</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"data/drift_data_JKI.RData"</span>)
-})
+</div><span class='co'># NOT RUN {</span>
+  <span class='co'># This is the code that was used to extract the data</span>
+  <span class='fu'>library</span>(<span class='no'>readxl</span>)
+  <span class='no'>abdrift_path</span> <span class='kw'>&lt;-</span> <span class='st'>"inst/extdata/Tabelle der Abdrifteckwerte.xls"</span>
+  <span class='no'>JKI_crops</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='st'>"Ackerbau"</span>, <span class='st'>"Obstbau frueh"</span>, <span class='st'>"Obstbau spaet"</span>)
+  <span class='fu'>names</span>(<span class='no'>JKI_crops</span>) <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='st'>"Field crops"</span>, <span class='st'>"Pome/stone fruit, early"</span>, <span class='st'>"Pome/stone fruit, late"</span>)
+  <span class='no'>drift_data_JKI</span> <span class='kw'>&lt;-</span> <span class='fu'>list</span>()
 
+  <span class='kw'>for</span> (<span class='no'>n</span> <span class='kw'>in</span> <span class='fl'>1</span>:<span class='fl'>8</span>) {
+    <span class='no'>drift_data_raw</span> <span class='kw'>&lt;-</span> <span class='fu'>read_excel</span>(<span class='no'>abdrift_path</span>, <span class='kw'>sheet</span> <span class='kw'>=</span> <span class='no'>n</span> + <span class='fl'>1</span>, <span class='kw'>skip</span> <span class='kw'>=</span> <span class='fl'>2</span>)
+    <span class='no'>drift_data</span> <span class='kw'>&lt;-</span> <span class='fu'>as.matrix</span>(<span class='no'>drift_data_raw</span>[<span class='fl'>1</span>:<span class='fl'>9</span>, <span class='fl'>2</span>:<span class='fl'>4</span>])
+    <span class='fu'>dimnames</span>(<span class='no'>drift_data</span>) <span class='kw'>&lt;-</span> <span class='fu'>list</span>(<span class='kw'>distance</span> <span class='kw'>=</span> <span class='fu'>as.integer</span>(<span class='no'>drift_data_raw</span>[<span class='fl'>1</span>:<span class='fl'>9</span>, <span class='fl'>1</span>]),
+                                            <span class='kw'>crop</span> <span class='kw'>=</span> <span class='no'>JKI_crops</span>)
+    <span class='no'>drift_data_JKI</span><span class='kw'>[[</span><span class='no'>n</span>]] <span class='kw'>&lt;-</span> <span class='no'>drift_data</span>
+  }
+  <span class='fu'>save</span>(<span class='no'>drift_data_JKI</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"data/drift_data_JKI.RData"</span>)
+<span class='co'># }</span><div class='input'>
 <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
@@ -247,7 +261,7 @@ as its licence is not clear.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html
index 1cc4da4..2b6e77d 100644
--- a/docs/reference/endpoint.html
+++ b/docs/reference/endpoint.html
@@ -18,12 +18,22 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Retrieve endpoint information from the chyaml field of a chent object — endpoint" />
 
+<meta property="og:description" content="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." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +61,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -185,7 +201,7 @@ exponent is often called 1/n.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/focus_80th.html b/docs/reference/focus_80th.html
index 6b0dcc5..e743986 100644
--- a/docs/reference/focus_80th.html
+++ b/docs/reference/focus_80th.html
@@ -18,12 +18,22 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Calculate the 80th percentile according to FOCUS guidance — focus_80th" />
 
+<meta property="og:description" content="This is nowadays defined as the mean of the 16th and the 17th
+highest value. Previously, the 17th highest values was used (FOCUS 2014, p.
+18). NaN values need to be set to zero in order to reproduce the
+values obtained by PELMO." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +61,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -110,7 +126,7 @@ values obtained by PELMO.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html
index 70fb98d..b1c283d 100644
--- a/docs/reference/geomean.html
+++ b/docs/reference/geomean.html
@@ -18,12 +18,22 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Calculate the geometric mean — geomean" />
 
+<meta property="og:description" content="Based on some posts in a thread on Stackoverflow
+http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in
+This function checks for negative values, removes NA values per default and
+returns 0 if at least one element of the vector is 0." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +61,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -73,7 +89,7 @@
 
     
     <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>
+<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>
     
@@ -99,7 +115,9 @@ returns 0 if at least one element of the vector is 0.</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>
+    <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><span class='co'># NOT RUN {</span>
+<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>)) <span class='co'># returns an error</span>
+<span class='co'># }</span></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
@@ -124,7 +142,7 @@ Johannes Ranke
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/get_flux.html b/docs/reference/get_flux.html
index 8de8b14..9c3a659 100644
--- a/docs/reference/get_flux.html
+++ b/docs/reference/get_flux.html
@@ -18,12 +18,19 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file — get_flux" />
 
+<meta property="og:description" content="Get the flux of a chemical out of the FOCUS layer from a CHEM*.PLM file" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +58,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -103,7 +116,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/get_interval.html b/docs/reference/get_interval.html
index a716b23..a55306d 100644
--- a/docs/reference/get_interval.html
+++ b/docs/reference/get_interval.html
@@ -18,12 +18,19 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Get the application interval in years from a psm file — get_interval" />
 
+<meta property="og:description" content="Get the application interval in years from a psm file" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +58,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -107,7 +120,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 47f495a..8aaa938 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -18,12 +18,16 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-
+  
+  
+<meta property="og:title" content="Function reference" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +55,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -260,7 +270,7 @@ published by the JKI</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html
index 431bbd7..a596d60 100644
--- a/docs/reference/max_twa.html
+++ b/docs/reference/max_twa.html
@@ -18,12 +18,23 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="The maximum time weighted average concentration for a moving window — max_twa" />
 
+<meta property="og:description" content="If you generate your time series using sawtooth,
+you need to make sure that the length of the time series allows
+for finding the maximum. It is therefore recommended to check this using
+plot.one_box using the window size for the argument
+max_twa." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +62,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -106,7 +123,7 @@ SFO, FOMC and DFOP models and to the parent compound</p>
   Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
   Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
   EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-  <a href = 'http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+  <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
     
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
@@ -154,7 +171,7 @@ SFO, FOMC and DFOP models and to the parent compound</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/one_box-1.png b/docs/reference/one_box-1.png
new file mode 100644
index 0000000..eeccb4c
--- /dev/null
+++ b/docs/reference/one_box-1.png
diff --git a/docs/reference/one_box-2.png b/docs/reference/one_box-2.png
index 4788607..89fa0b9 100644
--- a/docs/reference/one_box-2.png
+++ b/docs/reference/one_box-2.png
diff --git a/docs/reference/one_box-3.png b/docs/reference/one_box-3.png
new file mode 100644
index 0000000..0af2c7b
--- /dev/null
+++ b/docs/reference/one_box-3.png
diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html
index 931e722..bfed3a1 100644
--- a/docs/reference/one_box.html
+++ b/docs/reference/one_box.html
@@ -18,12 +18,19 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Create a time series of decline data — one_box" />
 
+<meta property="og:description" content="Create a time series of decline data" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +58,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -132,16 +145,16 @@ all observed variables.</p></td>
     <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='fu'>plot</span>(<span class='no'>pred_0</span>)</div><div class='img'><img src='one_box-1.png' alt='' width='700' height='432.632880098887' /></div><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'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='http://www.rdocumentation.org/packages/mkin/topics/mkinfit'>mkinfit</a></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='fu'>plot</span>(<span class='no'>pred_1</span>)</div><div class='img'><img src='one_box-2.png' alt='' width='700' height='432.632880098887' /></div><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'>m_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='http://www.rdocumentation.org/packages/mkin/topics/mkinmod'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='http://www.rdocumentation.org/packages/mkin/topics/mkinsub'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='http://www.rdocumentation.org/packages/mkin/topics/mkinsub'>mkinsub</a></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'><a href='http://www.rdocumentation.org/packages/mkin/topics/mkinfit'>mkinfit</a></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='kw'>ini</span> <span class='kw'>=</span> <span class='st'>"model"</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>
+<span class='fu'>plot</span>(<span class='no'>pred_2</span>)</div><div class='img'><img src='one_box-3.png' alt='' width='700' height='432.632880098887' /></div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
@@ -162,7 +175,7 @@ all observed variables.</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/perc_runoff_exposit.html b/docs/reference/perc_runoff_exposit.html
index 6feed2c..1098378 100644
--- a/docs/reference/perc_runoff_exposit.html
+++ b/docs/reference/perc_runoff_exposit.html
@@ -18,12 +18,19 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit" />
 
+<meta property="og:description" content="A table of the loss percentages used in Exposit 3 for the twelve different Koc classes" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +58,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -89,7 +102,7 @@
     <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
 
     <p>Excel 3.01 spreadsheet available from
-  <a href = 'https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3'>https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3</a></p>
+  <a href='https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3'>https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3</a></p>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -127,7 +140,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/perc_runoff_reduction_exposit.html b/docs/reference/perc_runoff_reduction_exposit.html
index fba910b..10d7f24 100644
--- a/docs/reference/perc_runoff_reduction_exposit.html
+++ b/docs/reference/perc_runoff_reduction_exposit.html
@@ -18,12 +18,19 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit" />
 
+<meta property="og:description" content="A table of the runoff reduction percentages used in Exposit 3 for different vegetated buffer widths" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +58,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -90,7 +103,7 @@ from which the values were taken.</p><dl class='dl-horizontal'>
     <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
 
     <p>Excel 3.01 spreadsheet available from
-  <a href = 'https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3'>https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3</a></p>
+  <a href='https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3'>https://www.bvl.bund.de/DE/04_Pflanzenschutzmittel/03_Antragsteller/04_Zulassungsverfahren/07_Naturhaushalt/psm_naturhaush_node.html#doc1400590bodyText3</a></p>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -127,7 +140,7 @@ from which the values were taken.</p><dl class='dl-horizontal'>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt
index e8743b0..da01e3f 100644
--- a/docs/reference/pesticide.txt
+++ b/docs/reference/pesticide.txt
@@ -17,3 +17,7 @@ Dummy 1 cereals, spring n NA	Dummy 1 cereals, winter s of	Dummy 1 citrus n mm	Du
 M1 cereals, winter n NA	M1 cereals, winter s of	M1 cereals, winter n mm	M1 cereals, winter s js	M1 cereals, winter n NA	M1 cereals, winter s of	M1 cereals, winter n mm	M1 cereals, winter s js		  250.00	  100.00	  100.00	   50.00	  100.00	  100.00	0.00E+00	   50.00	 1000.00	    1.00	0.00E+00	    1.00	  -99.00	  -99.00	  -99.00	  -99.00	0.00E+00	    1.00
 Dummy 1 cereals, spring n NA	Dummy 1 cereals, winter s of	Dummy 1 citrus n mm	Dummy 1 cotton s js	Dummy 1 field beans n NA	Dummy 1 grass / alfalfa s of	Dummy 1 hops n mm	Dummy 1 legumes s js	Dummy 1 maize n NA	Dummy 1 oil seed rape, spring s of	Dummy 1 oil seed rape, winter n mm	Dummy 1 olives s js	Dummy 1 pome / stone fruit, early applns n NA	Dummy 1 pome / stone fruit, late applns s of	Dummy 1 potatoes n mm	Dummy 1 soybeans s js	Dummy 1 sugar beets n NA	Dummy 1 sunflowers s of	Dummy 1 tobacco n mm	Dummy 1 vegetables, bulb s js	Dummy 1 vegetables, fruiting n NA	Dummy 1 vegetables, leafy s of	Dummy 1 vegetables, root n mm	Dummy 1 vines, early applns s js	Dummy 1 vines, late applns n NA	Dummy 1 appln, aerial s of	Dummy 1 appln, hand (crop < 50 cm) n mm	Dummy 1 appln, hand (crop > 50 cm) s js	Dummy 1 no drift (incorp or seed trtmt) n NA	Dummy 1 cereals, spring n NA	Dummy 1 cereals, winter s of	Dummy 1 citrus n mm	Dummy 1 cotton s js	Dummy 1 field beans n NA	Dummy 1 grass / alfalfa s of	Dummy 1 hops n mm	Dummy 1 legumes s js	Dummy 1 maize n NA	Dummy 1 oil seed rape, spring s of	Dummy 1 oil seed rape, winter n mm	Dummy 1 olives s js	Dummy 1 pome / stone fruit, early applns n NA	Dummy 1 pome / stone fruit, late applns s of	Dummy 1 potatoes n mm	Dummy 1 soybeans s js	Dummy 1 sugar beets n NA	Dummy 1 sunflowers s of	Dummy 1 tobacco n mm	Dummy 1 vegetables, bulb s js	Dummy 1 vegetables, fruiting n NA	Dummy 1 vegetables, leafy s of	Dummy 1 vegetables, root n mm	Dummy 1 vines, early applns s js	Dummy 1 vines, late applns n NA	Dummy 1 appln, aerial s of	Dummy 1 appln, hand (crop < 50 cm) n mm	Dummy 1 appln, hand (crop > 50 cm) s js	Dummy 1 no drift (incorp or seed trtmt) n NA		  -99.00	  -99.00	 6000.00	  344.80	0.00E+00	    6.00	0.00E+00	0.00E+00	 3000.00	    1.00	0.00E+00	0.00E+00	    1.00	    2.00	    3.00	    4.00	    5.00	    6.00	    7.00	    8.00	    9.00	   10.00	   11.00	   12.00	   13.00	   14.00	   15.00	   16.00	   17.00	   18.00	   19.00	   20.00	   21.00	   22.00	   23.00	   24.00	   25.00	   26.00	   27.00	   28.00	0.00E+00	  -99.00	  -99.00	  -99.00	0.00E+00	    1.00
 M1 cereals, winter n NA	M1 cereals, winter s of	M1 cereals, winter n mm	M1 cereals, winter s js	M1 cereals, winter n NA	M1 cereals, winter s of	M1 cereals, winter n mm	M1 cereals, winter s js		  250.00	  100.00	  100.00	   50.00	  100.00	  100.00	0.00E+00	   50.00	 1000.00	    1.00	0.00E+00	    1.00	  -99.00	  -99.00	  -99.00	  -99.00	0.00E+00	    1.00
+Dummy 1 cereals, spring n NA	Dummy 1 cereals, winter s of	Dummy 1 citrus n mm	Dummy 1 cotton s js	Dummy 1 field beans n NA	Dummy 1 grass / alfalfa s of	Dummy 1 hops n mm	Dummy 1 legumes s js	Dummy 1 maize n NA	Dummy 1 oil seed rape, spring s of	Dummy 1 oil seed rape, winter n mm	Dummy 1 olives s js	Dummy 1 pome / stone fruit, early applns n NA	Dummy 1 pome / stone fruit, late applns s of	Dummy 1 potatoes n mm	Dummy 1 soybeans s js	Dummy 1 sugar beets n NA	Dummy 1 sunflowers s of	Dummy 1 tobacco n mm	Dummy 1 vegetables, bulb s js	Dummy 1 vegetables, fruiting n NA	Dummy 1 vegetables, leafy s of	Dummy 1 vegetables, root n mm	Dummy 1 vines, early applns s js	Dummy 1 vines, late applns n NA	Dummy 1 appln, aerial s of	Dummy 1 appln, hand (crop < 50 cm) n mm	Dummy 1 appln, hand (crop > 50 cm) s js	Dummy 1 no drift (incorp or seed trtmt) n NA	Dummy 1 cereals, spring n NA	Dummy 1 cereals, winter s of	Dummy 1 citrus n mm	Dummy 1 cotton s js	Dummy 1 field beans n NA	Dummy 1 grass / alfalfa s of	Dummy 1 hops n mm	Dummy 1 legumes s js	Dummy 1 maize n NA	Dummy 1 oil seed rape, spring s of	Dummy 1 oil seed rape, winter n mm	Dummy 1 olives s js	Dummy 1 pome / stone fruit, early applns n NA	Dummy 1 pome / stone fruit, late applns s of	Dummy 1 potatoes n mm	Dummy 1 soybeans s js	Dummy 1 sugar beets n NA	Dummy 1 sunflowers s of	Dummy 1 tobacco n mm	Dummy 1 vegetables, bulb s js	Dummy 1 vegetables, fruiting n NA	Dummy 1 vegetables, leafy s of	Dummy 1 vegetables, root n mm	Dummy 1 vines, early applns s js	Dummy 1 vines, late applns n NA	Dummy 1 appln, aerial s of	Dummy 1 appln, hand (crop < 50 cm) n mm	Dummy 1 appln, hand (crop > 50 cm) s js	Dummy 1 no drift (incorp or seed trtmt) n NA		  -99.00	  -99.00	 6000.00	  344.80	0.00E+00	    6.00	0.00E+00	0.00E+00	 3000.00	    1.00	0.00E+00	0.00E+00	    1.00	    2.00	    3.00	    4.00	    5.00	    6.00	    7.00	    8.00	    9.00	   10.00	   11.00	   12.00	   13.00	   14.00	   15.00	   16.00	   17.00	   18.00	   19.00	   20.00	   21.00	   22.00	   23.00	   24.00	   25.00	   26.00	   27.00	   28.00	0.00E+00	  -99.00	  -99.00	  -99.00	0.00E+00	    1.00
+M1 cereals, winter n NA	M1 cereals, winter s of	M1 cereals, winter n mm	M1 cereals, winter s js	M1 cereals, winter n NA	M1 cereals, winter s of	M1 cereals, winter n mm	M1 cereals, winter s js		  250.00	  100.00	  100.00	   50.00	  100.00	  100.00	0.00E+00	   50.00	 1000.00	    1.00	0.00E+00	    1.00	  -99.00	  -99.00	  -99.00	  -99.00	0.00E+00	    1.00
+Dummy 1 cereals, spring n NA	Dummy 1 cereals, winter s of	Dummy 1 citrus n mm	Dummy 1 cotton s js	Dummy 1 field beans n NA	Dummy 1 grass / alfalfa s of	Dummy 1 hops n mm	Dummy 1 legumes s js	Dummy 1 maize n NA	Dummy 1 oil seed rape, spring s of	Dummy 1 oil seed rape, winter n mm	Dummy 1 olives s js	Dummy 1 pome / stone fruit, early applns n NA	Dummy 1 pome / stone fruit, late applns s of	Dummy 1 potatoes n mm	Dummy 1 soybeans s js	Dummy 1 sugar beets n NA	Dummy 1 sunflowers s of	Dummy 1 tobacco n mm	Dummy 1 vegetables, bulb s js	Dummy 1 vegetables, fruiting n NA	Dummy 1 vegetables, leafy s of	Dummy 1 vegetables, root n mm	Dummy 1 vines, early applns s js	Dummy 1 vines, late applns n NA	Dummy 1 appln, aerial s of	Dummy 1 appln, hand (crop < 50 cm) n mm	Dummy 1 appln, hand (crop > 50 cm) s js	Dummy 1 no drift (incorp or seed trtmt) n NA	Dummy 1 cereals, spring n NA	Dummy 1 cereals, winter s of	Dummy 1 citrus n mm	Dummy 1 cotton s js	Dummy 1 field beans n NA	Dummy 1 grass / alfalfa s of	Dummy 1 hops n mm	Dummy 1 legumes s js	Dummy 1 maize n NA	Dummy 1 oil seed rape, spring s of	Dummy 1 oil seed rape, winter n mm	Dummy 1 olives s js	Dummy 1 pome / stone fruit, early applns n NA	Dummy 1 pome / stone fruit, late applns s of	Dummy 1 potatoes n mm	Dummy 1 soybeans s js	Dummy 1 sugar beets n NA	Dummy 1 sunflowers s of	Dummy 1 tobacco n mm	Dummy 1 vegetables, bulb s js	Dummy 1 vegetables, fruiting n NA	Dummy 1 vegetables, leafy s of	Dummy 1 vegetables, root n mm	Dummy 1 vines, early applns s js	Dummy 1 vines, late applns n NA	Dummy 1 appln, aerial s of	Dummy 1 appln, hand (crop < 50 cm) n mm	Dummy 1 appln, hand (crop > 50 cm) s js	Dummy 1 no drift (incorp or seed trtmt) n NA		  -99.00	  -99.00	 6000.00	  344.80	0.00E+00	    6.00	0.00E+00	0.00E+00	 3000.00	    1.00	0.00E+00	0.00E+00	    1.00	    2.00	    3.00	    4.00	    5.00	    6.00	    7.00	    8.00	    9.00	   10.00	   11.00	   12.00	   13.00	   14.00	   15.00	   16.00	   17.00	   18.00	   19.00	   20.00	   21.00	   22.00	   23.00	   24.00	   25.00	   26.00	   27.00	   28.00	0.00E+00	  -99.00	  -99.00	  -99.00	0.00E+00	    1.00
+M1 cereals, winter n NA	M1 cereals, winter s of	M1 cereals, winter n mm	M1 cereals, winter s js	M1 cereals, winter n NA	M1 cereals, winter s of	M1 cereals, winter n mm	M1 cereals, winter s js		  250.00	  100.00	  100.00	   50.00	  100.00	  100.00	0.00E+00	   50.00	 1000.00	    1.00	0.00E+00	    1.00	  -99.00	  -99.00	  -99.00	  -99.00	0.00E+00	    1.00
diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html
index 9198f6b..828c500 100644
--- a/docs/reference/pfm_degradation.html
+++ b/docs/reference/pfm_degradation.html
@@ -18,12 +18,19 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation" />
 
+<meta property="og:description" content="Calculate a time course of relative concentrations based on an mkinmod model" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +58,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -141,7 +154,7 @@ Johannes Ranke
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/plot.TOXSWA_cwa-1.png b/docs/reference/plot.TOXSWA_cwa-1.png
new file mode 100644
index 0000000..9fabca9
--- /dev/null
+++ b/docs/reference/plot.TOXSWA_cwa-1.png
diff --git a/docs/reference/plot.TOXSWA_cwa-2.png b/docs/reference/plot.TOXSWA_cwa-2.png
index b36bf11..57a655f 100644
--- a/docs/reference/plot.TOXSWA_cwa-2.png
+++ b/docs/reference/plot.TOXSWA_cwa-2.png
diff --git a/docs/reference/plot.TOXSWA_cwa-3.png b/docs/reference/plot.TOXSWA_cwa-3.png
new file mode 100644
index 0000000..5dc1f37
--- /dev/null
+++ b/docs/reference/plot.TOXSWA_cwa-3.png
diff --git a/docs/reference/plot.TOXSWA_cwa-4.png b/docs/reference/plot.TOXSWA_cwa-4.png
index cb1189b..55f08fe 100644
--- a/docs/reference/plot.TOXSWA_cwa-4.png
+++ b/docs/reference/plot.TOXSWA_cwa-4.png
diff --git a/docs/reference/plot.TOXSWA_cwa-5.png b/docs/reference/plot.TOXSWA_cwa-5.png
new file mode 100644
index 0000000..a46c66c
--- /dev/null
+++ b/docs/reference/plot.TOXSWA_cwa-5.png
diff --git a/docs/reference/plot.TOXSWA_cwa.html b/docs/reference/plot.TOXSWA_cwa.html
index f2088f2..1ff489a 100644
--- a/docs/reference/plot.TOXSWA_cwa.html
+++ b/docs/reference/plot.TOXSWA_cwa.html
@@ -18,12 +18,20 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa" />
 
+<meta property="og:description" content="Plot TOXSWA hourly concentrations of a chemical substance in a specific
+segment of a TOXSWA surface water body." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +59,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -133,11 +147,11 @@ to suspended matter?</p></td>
     <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' /><div class='input'><span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t"</span>)</div><img src='plot.TOXSWA_cwa-4.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_firstjan"</span>)</div><img src='plot.TOXSWA_cwa-6.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><img src='plot.TOXSWA_cwa-8.png' alt='' width='540' height='400' /><div class='input'>
+<span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-1.png' alt='' width='700' height='432.632880098887' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-2.png' alt='' width='700' height='432.632880098887' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_firstjan"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-3.png' alt='' width='700' height='432.632880098887' /></div><div class='input'><span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-4.png' alt='' width='700' height='432.632880098887' /></div><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='fu'>plot</span>(<span class='no'>H_sw_R1_stream</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><img src='plot.TOXSWA_cwa-10.png' alt='' width='540' height='400' /></pre>
+<span class='fu'>plot</span>(<span class='no'>H_sw_R1_stream</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='st'>"t_rel_to_max"</span>)</div><div class='img'><img src='plot.TOXSWA_cwa-5.png' alt='' width='700' height='432.632880098887' /></div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
@@ -160,7 +174,7 @@ Johannes Ranke
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/plot.one_box-1.png b/docs/reference/plot.one_box-1.png
new file mode 100644
index 0000000..7bd9555
--- /dev/null
+++ b/docs/reference/plot.one_box-1.png
diff --git a/docs/reference/plot.one_box-2.png b/docs/reference/plot.one_box-2.png
index 4c6cb92..1a489d6 100644
--- a/docs/reference/plot.one_box-2.png
+++ b/docs/reference/plot.one_box-2.png
diff --git a/docs/reference/plot.one_box-3.png b/docs/reference/plot.one_box-3.png
new file mode 100644
index 0000000..ef78a0e
--- /dev/null
+++ b/docs/reference/plot.one_box-3.png
diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html
index 0a876e3..63e351a 100644
--- a/docs/reference/plot.one_box.html
+++ b/docs/reference/plot.one_box.html
@@ -18,12 +18,19 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Plot time series of decline data — plot.one_box" />
 
+<meta property="og:description" content="Plot time series of decline data" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +58,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -126,12 +139,12 @@ be shown if max_twa is not NULL.</p></td>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='no'>dfop_pred</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='st'>"DFOP"</span>, <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k1</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>, <span class='kw'>g</span> <span class='kw'>=</span> <span class='fl'>0.7</span>))
-<span class='fu'>plot</span>(<span class='no'>dfop_pred</span>)</div><img src='plot.one_box-2.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>dfop_pred</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-4.png' alt='' width='540' height='400' /><div class='input'>
+<span class='fu'>plot</span>(<span class='no'>dfop_pred</span>)</div><div class='img'><img src='plot.one_box-1.png' alt='' width='700' height='432.632880098887' /></div><div class='input'><span class='fu'>plot</span>(<span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>dfop_pred</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><div class='img'><img src='plot.one_box-2.png' alt='' width='700' height='432.632880098887' /></div><div class='input'>
 <span class='co'># Use a fitted mkinfit model</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'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>)
 <span class='no'>pred_2_saw</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></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='plot.one_box-8.png' alt='' width='540' height='400' /></pre>
+<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><div class='img'><img src='plot.one_box-3.png' alt='' width='700' height='432.632880098887' /></div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
@@ -152,7 +165,7 @@ be shown if max_twa is not NULL.</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html
index 25452c5..6afdaa7 100644
--- a/docs/reference/read.TOXSWA_cwa.html
+++ b/docs/reference/read.TOXSWA_cwa.html
@@ -18,12 +18,23 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Read TOXSWA surface water concentrations — read.TOXSWA_cwa" />
 
+<meta property="og:description" content="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)." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +62,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -163,7 +180,7 @@ Johannes Ranke
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/sawtooth-1.png b/docs/reference/sawtooth-1.png
new file mode 100644
index 0000000..448d0c4
--- /dev/null
+++ b/docs/reference/sawtooth-1.png
diff --git a/docs/reference/sawtooth-2.png b/docs/reference/sawtooth-2.png
index 548c87d..ef78a0e 100644
--- a/docs/reference/sawtooth-2.png
+++ b/docs/reference/sawtooth-2.png
diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html
index ce528e6..cfd62f5 100644
--- a/docs/reference/sawtooth.html
+++ b/docs/reference/sawtooth.html
@@ -18,12 +18,21 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-
+  
+  
+<meta property="og:title" content="Create decline time series for multiple applications — sawtooth" />
+
+<meta property="og:description" content="If the number of application cycles n is greater than 1, the
+application pattern specified in applications is repeated n
+times, with an interval i." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +60,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -107,11 +122,11 @@ the corresponding amounts applied in the second column.</p></td>
     <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='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><div class='img'><img src='sawtooth-1.png' alt='' width='700' height='432.632880098887' /></div><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='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</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'>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><div class='img'><img src='sawtooth-2.png' alt='' width='700' height='432.632880098887' /></div><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; 0.7834480 0.8617048 
@@ -142,7 +157,7 @@ the corresponding amounts applied in the second column.</p></td>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html
index 39841ed..e7f209a 100644
--- a/docs/reference/soil_scenario_data_EFSA_2015.html
+++ b/docs/reference/soil_scenario_data_EFSA_2015.html
@@ -18,12 +18,21 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015" />
 
+<meta property="og:description" content="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." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +60,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -94,25 +109,24 @@ 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'>not_run</span>({
-    <span class='co'># This is the code that was used to define the data</span>
-    <span class='no'>soil_scenario_data_EFSA_2015</span> <span class='kw'>&lt;-</span> <span class='fu'>data.frame</span>(
-      <span class='kw'>Zone</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fu'>c</span>(<span class='st'>"North"</span>, <span class='st'>"Central"</span>, <span class='st'>"South"</span>), <span class='fl'>2</span>),
-      <span class='kw'>Country</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Estonia"</span>, <span class='st'>"Germany"</span>, <span class='st'>"France"</span>, <span class='st'>"Denmark"</span>, <span class='st'>"Czech Republik"</span>, <span class='st'>"Spain"</span>),
-      <span class='kw'>T_arit</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>4.7</span>, <span class='fl'>8.0</span>, <span class='fl'>11.0</span>, <span class='fl'>8.2</span>, <span class='fl'>9.1</span>, <span class='fl'>12.8</span>),
-      <span class='kw'>T_arr</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>7.0</span>, <span class='fl'>10.1</span>, <span class='fl'>12.3</span>, <span class='fl'>9.8</span>, <span class='fl'>11.2</span>, <span class='fl'>14.7</span>),
-      <span class='kw'>Texture</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Coarse"</span>, <span class='st'>"Coarse"</span>, <span class='st'>"Medium fine"</span>, <span class='st'>"Medium"</span>, <span class='st'>"Medium"</span>, <span class='st'>"Medium"</span>),
-      <span class='kw'>f_om</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0.118</span>, <span class='fl'>0.086</span>, <span class='fl'>0.048</span>, <span class='fl'>0.023</span>, <span class='fl'>0.018</span>, <span class='fl'>0.011</span>),
-      <span class='kw'>theta_fc</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0.244</span>, <span class='fl'>0.244</span>, <span class='fl'>0.385</span>, <span class='fl'>0.347</span>, <span class='fl'>0.347</span>, <span class='fl'>0.347</span>),
-      <span class='kw'>rho</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0.95</span>, <span class='fl'>1.05</span>, <span class='fl'>1.22</span>, <span class='fl'>1.39</span>, <span class='fl'>1.43</span>, <span class='fl'>1.51</span>),
-      <span class='kw'>f_sce</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>3</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>1.5</span>, <span class='fl'>1.5</span>),
-      <span class='kw'>f_mod</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>4</span>, <span class='fl'>4</span>),
-      <span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
-      <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"CTN"</span>, <span class='st'>"CTC"</span>, <span class='st'>"CTS"</span>, <span class='st'>"CLN"</span>, <span class='st'>"CLC"</span>, <span class='st'>"CLS"</span>)
-    )
-    <span class='fu'>save</span>(<span class='no'>soil_scenario_data_EFSA_2015</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>'../data/soil_scenario_data_EFSA_2015.RData'</span>)
-})
-
+    <pre class="examples"><span class='co'># NOT RUN {</span>
+  <span class='co'># This is the code that was used to define the data</span>
+  <span class='no'>soil_scenario_data_EFSA_2015</span> <span class='kw'>&lt;-</span> <span class='fu'>data.frame</span>(
+    <span class='kw'>Zone</span> <span class='kw'>=</span> <span class='fu'>rep</span>(<span class='fu'>c</span>(<span class='st'>"North"</span>, <span class='st'>"Central"</span>, <span class='st'>"South"</span>), <span class='fl'>2</span>),
+    <span class='kw'>Country</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Estonia"</span>, <span class='st'>"Germany"</span>, <span class='st'>"France"</span>, <span class='st'>"Denmark"</span>, <span class='st'>"Czech Republik"</span>, <span class='st'>"Spain"</span>),
+    <span class='kw'>T_arit</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>4.7</span>, <span class='fl'>8.0</span>, <span class='fl'>11.0</span>, <span class='fl'>8.2</span>, <span class='fl'>9.1</span>, <span class='fl'>12.8</span>),
+    <span class='kw'>T_arr</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>7.0</span>, <span class='fl'>10.1</span>, <span class='fl'>12.3</span>, <span class='fl'>9.8</span>, <span class='fl'>11.2</span>, <span class='fl'>14.7</span>),
+    <span class='kw'>Texture</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Coarse"</span>, <span class='st'>"Coarse"</span>, <span class='st'>"Medium fine"</span>, <span class='st'>"Medium"</span>, <span class='st'>"Medium"</span>, <span class='st'>"Medium"</span>),
+    <span class='kw'>f_om</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0.118</span>, <span class='fl'>0.086</span>, <span class='fl'>0.048</span>, <span class='fl'>0.023</span>, <span class='fl'>0.018</span>, <span class='fl'>0.011</span>),
+    <span class='kw'>theta_fc</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0.244</span>, <span class='fl'>0.244</span>, <span class='fl'>0.385</span>, <span class='fl'>0.347</span>, <span class='fl'>0.347</span>, <span class='fl'>0.347</span>),
+    <span class='kw'>rho</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0.95</span>, <span class='fl'>1.05</span>, <span class='fl'>1.22</span>, <span class='fl'>1.39</span>, <span class='fl'>1.43</span>, <span class='fl'>1.51</span>),
+    <span class='kw'>f_sce</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>3</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>1.5</span>, <span class='fl'>1.5</span>),
+    <span class='kw'>f_mod</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>4</span>, <span class='fl'>4</span>),
+    <span class='kw'>stringsAsFactors</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+    <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"CTN"</span>, <span class='st'>"CTC"</span>, <span class='st'>"CTS"</span>, <span class='st'>"CLN"</span>, <span class='st'>"CLC"</span>, <span class='st'>"CLS"</span>)
+  )
+  <span class='fu'>save</span>(<span class='no'>soil_scenario_data_EFSA_2015</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>'../data/soil_scenario_data_EFSA_2015.RData'</span>)
+<span class='co'># }</span><div class='input'>
 <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
@@ -149,7 +163,7 @@ doi:10.2903/j.efsa.2015.4093</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/sum_periods.html b/docs/reference/sum_periods.html
index 147a698..51ed429 100644
--- a/docs/reference/sum_periods.html
+++ b/docs/reference/sum_periods.html
@@ -18,12 +18,19 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Sum up values according to FOCUS periods — sum_periods" />
 
+<meta property="og:description" content="Sum up values according to FOCUS periods" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +58,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -107,7 +120,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/twa.html b/docs/reference/twa.html
index 32fa459..fad5fd9 100644
--- a/docs/reference/twa.html
+++ b/docs/reference/twa.html
@@ -18,12 +18,21 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Calculate a time weighted average concentration — twa" />
 
+<meta property="og:description" content="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." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,6 +60,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -135,7 +150,7 @@ is after one window has passed.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/man/PELMO_runs.Rd b/man/PELMO_runs.Rd
index f936d8c..6021613 100644
--- a/man/PELMO_runs.Rd
+++ b/man/PELMO_runs.Rd
@@ -64,11 +64,14 @@ runs_1 <- list(
        pot = c("Cha", "Ham", "Jok", "Kre", "Oke", "Pia", "Por", "Sev", "Thi")))
 time_1 <- system.time(
   PECgw_1 <- PELMO_runs(runs_1, psm_dir = system.file("testdata", package = "pfm"),
-    cores = 6, overwrite = TRUE)
+    cores = 15, overwrite = TRUE)
 )
 print(PECgw_1)
 # We get exactly the same PECgw values (on Linux, calling PELMO using Wine).
 print(time_1)
+if(!inherits(try(cpuinfo <- readLines("/proc/cpuinfo")), "try-error")) {
+  cat(gsub("model name\\t: ", "CPU model: ", cpuinfo[grep("model name", cpuinfo)[1]]))
+}
 
 # Demonstrate some results with metabolites.
 runs_2 <- list(list(psm = 'Pesticide_D_1_May_every_other_year_mets',
author	Johannes Ranke <jranke@uni-bremen.de>	2018-03-01 10:10:08 +0100
committer	Johannes Ranke <jranke@uni-bremen.de>	2018-03-01 10:10:08 +0100
commit	6d8de73e68f2c0349e618af35ce4a8f095ca0ed5 (patch)
tree	3f4b574934ce0bcb1ed0f167b4daab81accc5a38
parent	3c39bba4af013b099ec013bddcc92407058026e0 (diff)