diff options
Diffstat (limited to 'docs/reference')
| -rw-r--r-- | docs/reference/index.html | 101 | ||||
| -rw-r--r-- | docs/reference/twa.html | 174 |
2 files changed, 239 insertions, 36 deletions
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 0.9.45</h4> + <h4>version 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 "mkinfit"</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) “Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” 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'><-</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'>#> <span class='error'>Error in eval(expr, envir, enclos): konnte Funktion "twa" 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> |