From 3010c9dcbc7f90f15b55c14919f6688d61d14414 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sat, 4 Mar 2017 09:58:00 +0100
Subject: Mention pkgdown.jrwb.de/mkin in README

Add very small twa vignette, update pkgdown docs
---
 docs/reference/index.html | 101 +++++++++++++++++----------
 docs/reference/twa.html   | 174 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 239 insertions(+), 36 deletions(-)
 create mode 100644 docs/reference/twa.html

(limited to 'docs/reference')

diff --git a/docs/reference/index.html b/docs/reference/index.html
index 26b98f69..2e997ef0 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -96,7 +96,7 @@
   <div class="col-md-9">
     <div class="page-header">
       <h1>Function reference</h1>
-      <h4>version&nbsp;0.9.45</h4>
+      <h4>version&nbsp;0.9.45.1</h4>
     </div>
 
     <div class="contents">
@@ -104,17 +104,20 @@
       <p class="section-desc"><p>Essential functionality</p></p>
 
       
-      <p><a href="mkinmod.html">Function to set up a kinetic model with one or more state variables</a></p>
+      <p><a href="mkinmod.html">
+</a></p>
       <ul>
         <li><code><a href="mkinmod.html">mkinmod</a></code></li>
       </ul>
       
-      <p><a href="mkinfit.html">Fit a kinetic model to data with one or more state variables</a></p>
+      <p><a href="mkinfit.html">
+</a></p>
       <ul>
         <li><code><a href="mkinfit.html">mkinfit</a></code></li>
       </ul>
       
-      <p><a href="mmkin.html">Fit one or more kinetic models with one or more state variables to one or more datasets</a></p>
+      <p><a href="mmkin.html">
+</a></p>
       <ul>
         <li><code><a href="mmkin.html">mmkin</a></code></li>
       </ul>
@@ -122,32 +125,38 @@
       <p class="section-desc"><p>Functions working with mkinfit objects</p></p>
 
       
-      <p><a href="plot.mkinfit.html">Plot the observed data and the fitted model of an mkinfit object</a></p>
+      <p><a href="plot.mkinfit.html">
+</a></p>
       <ul>
         <li><code><a href="plot.mkinfit.html">plot.mkinfit</a></code></li><li><code><a href="plot.mkinfit.html">plot_sep</a></code></li>
       </ul>
       
-      <p><a href="summary.mkinfit.html">Summary method for class &quot;mkinfit&quot;</a></p>
+      <p><a href="summary.mkinfit.html">
+</a></p>
       <ul>
         <li><code><a href="summary.mkinfit.html">summary.mkinfit</a></code></li><li><code><a href="summary.mkinfit.html">print.summary.mkinfit</a></code></li>
       </ul>
       
-      <p><a href="mkinresplot.html">Function to plot residuals stored in an mkin object</a></p>
+      <p><a href="mkinresplot.html">
+</a></p>
       <ul>
         <li><code><a href="mkinresplot.html">mkinresplot</a></code></li>
       </ul>
       
-      <p><a href="mkinparplot.html">Function to plot the confidence intervals obtained using mkinfit</a></p>
+      <p><a href="mkinparplot.html">
+</a></p>
       <ul>
         <li><code><a href="mkinparplot.html">mkinparplot</a></code></li>
       </ul>
       
-      <p><a href="endpoints.html">Function to calculate endpoints for further use from kinetic models fitted with mkinfit</a></p>
+      <p><a href="endpoints.html">
+</a></p>
       <ul>
         <li><code><a href="endpoints.html">endpoints</a></code></li>
       </ul>
       
-      <p><a href="mkinerrmin.html">Calculate the minimum error to assume in order to pass the variance test</a></p>
+      <p><a href="mkinerrmin.html">
+</a></p>
       <ul>
         <li><code><a href="mkinerrmin.html">mkinerrmin</a></code></li>
       </ul>
@@ -160,7 +169,8 @@
         <li><code><a href="Extract.mmkin.html">[.mmkin</a></code></li>
       </ul>
       
-      <p><a href="plot.mmkin.html">Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</a></p>
+      <p><a href="plot.mmkin.html">
+</a></p>
       <ul>
         <li><code><a href="plot.mmkin.html">plot.mmkin</a></code></li>
       </ul>
@@ -168,42 +178,50 @@
       <p class="section-desc"></p>
 
       
-      <p><a href="FOCUS_2006_datasets.html">Datasets A to F from the FOCUS Kinetics report from 2006</a></p>
+      <p><a href="FOCUS_2006_datasets.html">
+</a></p>
       <ul>
         <li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_A</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_B</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_C</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_D</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_E</a></code></li><li><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_F</a></code></li>
       </ul>
       
-      <p><a href="FOCUS_2006_SFO_ref_A_to_F.html">Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</a></p>
+      <p><a href="FOCUS_2006_SFO_ref_A_to_F.html">
+</a></p>
       <ul>
         <li><code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code></li>
       </ul>
       
-      <p><a href="FOCUS_2006_FOMC_ref_A_to_F.html">Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</a></p>
+      <p><a href="FOCUS_2006_FOMC_ref_A_to_F.html">
+</a></p>
       <ul>
         <li><code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">FOCUS_2006_FOMC_ref_A_to_F</a></code></li>
       </ul>
       
-      <p><a href="FOCUS_2006_HS_ref_A_to_F.html">Results of fitting the HS model to Datasets A to F of FOCUS (2006)</a></p>
+      <p><a href="FOCUS_2006_HS_ref_A_to_F.html">
+</a></p>
       <ul>
         <li><code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code></li>
       </ul>
       
-      <p><a href="FOCUS_2006_DFOP_ref_A_to_B.html">Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</a></p>
+      <p><a href="FOCUS_2006_DFOP_ref_A_to_B.html">
+</a></p>
       <ul>
         <li><code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code></li>
       </ul>
       
-      <p><a href="mccall81_245T.html">Datasets on aerobic soil metabolism of 2,4,5-T in six soils</a></p>
+      <p><a href="mccall81_245T.html">
+</a></p>
       <ul>
         <li><code><a href="mccall81_245T.html">mccall81_245T</a></code></li>
       </ul>
       
-      <p><a href="schaefer07_complex_case.html">Metabolism data set used for checking the software quality of KinGUI</a></p>
+      <p><a href="schaefer07_complex_case.html">
+</a></p>
       <ul>
         <li><code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code></li><li><code><a href="schaefer07_complex_case.html">schaefer07_complex_results</a></code></li>
       </ul>
       
-      <p><a href="synthetic_data_for_UBA.html">Synthetic datasets for one parent compound with two metabolites</a></p>
+      <p><a href="synthetic_data_for_UBA.html">
+</a></p>
       <ul>
         <li><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code></li>
       </ul>
@@ -213,7 +231,8 @@
         <li><code><a href="mkinds.html">mkinds</a></code></li>
       </ul>
       
-      <p><a href="print.mkinds.html">Print mkinds objects</a></p>
+      <p><a href="print.mkinds.html">
+</a></p>
       <ul>
         <li><code><a href="print.mkinds.html">print.mkinds</a></code></li>
       </ul>
@@ -221,42 +240,49 @@
       <p class="section-desc"></p>
 
       
-      <p><a href="mkin_wide_to_long.html">Convert a dataframe with observations over time into long format</a></p>
+      <p><a href="mkin_wide_to_long.html">
+</a></p>
       <ul>
         <li><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code></li>
       </ul>
       
-      <p><a href="mkin_long_to_wide.html">Convert a dataframe from long to wide format</a></p>
+      <p><a href="mkin_long_to_wide.html">
+</a></p>
       <ul>
         <li><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code></li>
       </ul>
       
-      <p><a href="mkinsub.html">Function to set up a kinetic submodel for one state variable</a></p>
+      <p><a href="mkinsub.html">
+</a></p>
       <ul>
         <li><code><a href="mkinsub.html">mkinsub</a></code></li>
       </ul>
       
-      <p><a href="print.mkinmod.html">Print mkinmod objects</a></p>
+      <p><a href="print.mkinmod.html">
+</a></p>
       <ul>
         <li><code><a href="print.mkinmod.html">print.mkinmod</a></code></li>
       </ul>
       
-      <p><a href="mkinpredict.html">Produce predictions from a kinetic model using specific parameters</a></p>
+      <p><a href="mkinpredict.html">
+</a></p>
       <ul>
         <li><code><a href="mkinpredict.html">mkinpredict</a></code></li>
       </ul>
       
-      <p><a href="transform_odeparms.html">Functions to transform and backtransform kinetic parameters for fitting</a></p>
+      <p><a href="transform_odeparms.html">
+</a></p>
       <ul>
         <li><code><a href="transform_odeparms.html">transform_odeparms</a></code></li><li><code><a href="transform_odeparms.html">backtransform_odeparms</a></code></li>
       </ul>
       
-      <p><a href="ilr.html">Function to perform isometric log-ratio transformation</a></p>
+      <p><a href="ilr.html">
+</a></p>
       <ul>
         <li><code><a href="ilr.html">ilr</a></code></li><li><code><a href="ilr.html">invilr</a></code></li>
       </ul>
       
-      <p><a href="geometric_mean.html">Calculate the geometric mean</a></p>
+      <p><a href="geometric_mean.html"> Calculate the geometric mean </a></p>
       <ul>
         <li><code><a href="geometric_mean.html">geometric_mean</a></code></li>
       </ul>
@@ -264,32 +290,33 @@
       <p class="section-desc"><p>Parent only model solutions</p></p>
 
       
-      <p><a href="SFO.solution.html">Single First-Order kinetics</a></p>
+      <p><a href="SFO.solution.html"> Single First-Order kinetics </a></p>
       <ul>
         <li><code><a href="SFO.solution.html">SFO.solution</a></code></li>
       </ul>
       
-      <p><a href="FOMC.solution.html">First-Order Multi-Compartment kinetics</a></p>
+      <p><a href="FOMC.solution.html"> First-Order Multi-Compartment kinetics </a></p>
       <ul>
         <li><code><a href="FOMC.solution.html">FOMC.solution</a></code></li>
       </ul>
       
-      <p><a href="DFOP.solution.html">Double First-Order in Parallel kinetics</a></p>
+      <p><a href="DFOP.solution.html">
+</a></p>
       <ul>
         <li><code><a href="DFOP.solution.html">DFOP.solution</a></code></li>
       </ul>
       
-      <p><a href="SFORB.solution.html">Single First-Order Reversible Binding kinetics</a></p>
+      <p><a href="SFORB.solution.html"> Single First-Order Reversible Binding kinetics </a></p>
       <ul>
         <li><code><a href="SFORB.solution.html">SFORB.solution</a></code></li>
       </ul>
       
-      <p><a href="HS.solution.html">Hockey-Stick kinetics</a></p>
+      <p><a href="HS.solution.html"> Hockey-Stick kinetics </a></p>
       <ul>
         <li><code><a href="HS.solution.html">HS.solution</a></code></li>
       </ul>
       
-      <p><a href="IORE.solution.html">Indeterminate order rate equation kinetics</a></p>
+      <p><a href="IORE.solution.html"> Indeterminate order rate equation kinetics </a></p>
       <ul>
         <li><code><a href="IORE.solution.html">IORE.solution</a></code></li>
       </ul>
@@ -297,7 +324,8 @@
       <p class="section-desc"></p>
 
       
-      <p><a href="add_err.html">Add normally distributed errors to simulated kinetic degradation data</a></p>
+      <p><a href="add_err.html">
+</a></p>
       <ul>
         <li><code><a href="add_err.html">add_err</a></code></li>
       </ul>
@@ -305,7 +333,8 @@
       <p class="section-desc"><p>Functions that have been superseeded</p></p>
 
       
-      <p><a href="mkinplot.html">Plot the observed data and the fitted model of an mkinfit object</a></p>
+      <p><a href="mkinplot.html">
+</a></p>
       <ul>
         <li><code><a href="mkinplot.html">mkinplot</a></code></li>
       </ul>
diff --git a/docs/reference/twa.html b/docs/reference/twa.html
new file mode 100644
index 00000000..9c2efd10
--- /dev/null
+++ b/docs/reference/twa.html
@@ -0,0 +1,174 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+  <head>
+  <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>
+ — twa • mkin</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+  </head>
+
+  <body>
+    <div class="container template-reference-topic">
+      <header>
+      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
+      </button>
+      <a class="navbar-brand" href="../index.html">mkin</a>
+    </div>
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+        <li>
+  <a href="../reference/index.html">Functions and data</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/mkin.html">Introduction to mkin</a>
+    </li>
+    <li>
+      <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+    </li>
+    <li>
+      <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+    </li>
+    <li>
+      <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+    </li>
+  </ul>
+</li>
+<li>
+  <a href="../news/index.html">News</a>
+</li>
+      </ul>
+      
+      <ul class="nav navbar-nav navbar-right">
+        <li>
+  <a href="http://github.com/jranke/mkin">
+    <span class="fa fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul>
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+      </header>
+
+      <div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>
+</h1>
+    </div>
+
+    
+    <p>This function calculates maximum moving window time weighted average concentrations
+(TWAs) for kinetic models fitted with <code><a href='mkinfit.html'>mkinfit</a></code>. Currently, only
+calculations for the parent are implemented for the SFO, FOMC and DFOP models,
+using the analytical formulas given in the PEC soil section of the FOCUS
+guidance.</p>
+    
+
+    <pre><span class='fu'>twa</span>(<span class='no'>fit</span>, <span class='no'>windows</span>)</pre>
+    
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+    <dl class="dl-horizontal">
+      <dt>fit</dt>
+      <dd>
+    An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.
+  </dd>
+      <dt>windows</dt>
+      <dd>
+    The width of the time windows for which the TWAs should be calculated.
+  </dd>
+    </dl>
+    
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>A numeric vector, named using the <code>windows</code> argument.</p>
+    
+    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+    <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence and
+  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://http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+    
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'>  <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>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='fu'>twa</span>(<span class='no'>fit</span>, <span class='fu'>c</span>(<span class='fl'>7</span>, <span class='fl'>21</span>))</div><div class='output co'>#&gt; <span class='error'>Error in eval(expr, envir, enclos): konnte Funktion &quot;twa&quot; nicht finden</span></div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <ul class="nav nav-pills nav-stacked">
+      <li><a href="#arguments">Arguments</a></li>
+      
+      <li><a href="#value">Value</a></li>
+
+      <li><a href="#references">References</a></li>
+      
+      <li><a href="#examples">Examples</a></li>
+    </ul>
+
+    <h2>Author</h2>
+    
+  Johannes Ranke
+
+  </div>
+</div>
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+      </footer>
+   </div>
+
+  </body>
+</html>
-- 
cgit v1.2.1