aboutsummaryrefslogtreecommitdiff
path: root/inst/web/index.html
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2016-10-06 08:56:45 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-10-06 08:56:45 +0200
commitec1487f0f2cef32d44b0c6ce94a6f1b4f65a79d3 (patch)
tree10820a2fa5ae6b51115c2d2f40e40bcc8f0b8d5e /inst/web/index.html
parent6b7c2049d4feb9dd76dd532830adba23b8a5007f (diff)
Remove staticdocs from old location
Diffstat (limited to 'inst/web/index.html')
-rw-r--r--inst/web/index.html447
1 files changed, 0 insertions, 447 deletions
diff --git a/inst/web/index.html b/inst/web/index.html
deleted file mode 100644
index a78e5877..00000000
--- a/inst/web/index.html
+++ /dev/null
@@ -1,447 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>Index. mkin 0.9.44.9000</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="">
-
-<link href="css/bootstrap.css" rel="stylesheet">
-<link href="css/bootstrap-responsive.css" rel="stylesheet">
-<link href="css/highlight.css" rel="stylesheet">
-<link href="css/staticdocs.css" rel="stylesheet">
-
-<!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-<![endif]-->
-
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [ ['$','$'], ["\\(","\\)"] ],
- processEscapes: true
- }
- });
-</script>
-<script type="text/javascript"
- src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
- </head>
-
- <body>
- <div class="navbar">
- <div class="navbar-inner">
- <div class="container">
- <a class="brand" href="#">mkin 0.9.44.9000</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li>
- </ul>
- </div>
- </div>
- </div>
-</div>
-
- <div class="container">
- <header>
-
- </header>
-
- <div class="row">
- <div class="span8">
- <h1>mkin</h1>
-
-<p><a href="http://cran.r-project.org/package=mkin"><img src="http://www.r-pkg.org/badges/version/mkin" alt=""/></a></p>
-
-<p>The R package <strong>mkin</strong> provides calculation routines for the analysis of
-chemical degradation data, including <b>m</b>ulticompartment <b>kin</b>etics as
-needed for modelling the formation and decline of transformation products, or
-if several compartments are involved.</p>
-
-<h2>Installation</h2>
-
-<p>You can install the latest released version from
-<a href="http://cran.r-project.org/package=mkin">CRAN</a> from within R:</p>
-
-<pre><code class="r">install.packages(&quot;mkin&quot;)
-</code></pre>
-
-<h2>Background</h2>
-
-<p>In the regulatory evaluation of chemical substances like plant protection
-products (pesticides), biocides and other chemicals, degradation data play an
-important role. For the evaluation of pesticide degradation experiments,
-detailed guidance and helpful tools have been developed as detailed in
-&#39;Credits and historical remarks&#39; below.</p>
-
-<h2>Usage</h2>
-
-<p>For a start, have a look a the code examples provided for
-<a href="http://kinfit.r-forge.r-project.org/mkin_static/plot.mkinfit.html"><code>plot.mkinfit</code></a>
-and
-<a href="http://kinfit.r-forge.r-project.org/mkin_static/plot.mmkin.html"><code>plot.mmkin</code></a>, and
-at the package vignettes
-<a href="http://kinfit.r-forge.r-project.org/mkin_static/vignettes/FOCUS_L.html"><code>FOCUS L</code></a> and
-<a href="http://kinfit.r-forge.r-project.org/mkin_static/vignettes/FOCUS_D.html"><code>FOCUS D</code></a>.</p>
-
-<h2>Documentation</h2>
-
-<p>The <a href="http://kinfit.r-forge.r-project.org/mkin_static">HTML documentation</a> is
-maintained at the R-Forge project site.</p>
-
-<h2>Features</h2>
-
-<ul>
-<li>Highly flexible model specification using
-<a href="http://kinfit.r-forge.r-project.org/mkin_static/mkinmod.html"><code>mkinmod</code></a>,
-including equilibrium reactions and using the single first-order
-reversible binding (SFORB) model, which will automatically create
-two latent state variables for the observed variable.</li>
-<li>As of version 0.9-39, fitting of several models to several datasets, optionally in
-parallel, is supported, see for example
-<a href="http://kinfit.r-forge.r-project.org/mkin_static/plot.mmkin.html"><code>plot.mmkin</code></a>.</li>
-<li>Model solution (forward modelling) in the function
-<a href="http://kinfit.r-forge.r-project.org/mkin_static/mkinpredict.html"><code>mkinpredict</code></a>
-is performed either using the analytical solution for the case of
-parent only degradation, an eigenvalue based solution if only simple
-first-order (SFO) or SFORB kinetics are used in the model, or
-using a numeric solver from the <code>deSolve</code> package (default is <code>lsoda</code>).</li>
-<li>If a C compiler is installed, the kinetic models are compiled from automatically
-generated C code, see<br/>
-<a href="http://kinfit.r-forge.r-project.org/mkin_static/vignettes/compiled_models.html">vignette <code>compiled_models</code></a>.
-The autogeneration of C code was
-inspired by the <a href="https://github.com/karlines/ccSolve"><code>ccSolve</code></a> package. Thanks
-to Karline Soetaert for her work on that.</li>
-<li>By default, kinetic rate constants and kinetic formation fractions are
-transformed internally using
-<a href="http://kinfit.r-forge.r-project.org/mkin_static/transform_odeparms.html"><code>transform_odeparms</code></a>
-so their estimators can more reasonably be expected to follow
-a normal distribution. This has the side effect that no constraints
-are needed in the optimisation. Thanks to René Lehmann for the nice
-cooperation on this, especially the isometric logration transformation
-that is now used for the formation fractions.</li>
-<li>A side effect of this is that when parameter estimates are backtransformed
-to match the model definition, confidence intervals calculated from
-standard errors are also backtransformed to the correct scale, and will
-not include meaningless values like negative rate constants or
-formation fractions adding up to more than 1, which can not occur in
-a single experiment with a single defined radiolabel position.</li>
-<li>The usual one-sided t-test for significant difference from zero is nevertheless
-shown based on estimators for the untransformed parameters.</li>
-<li>Summary and plotting functions. The <code>summary</code> of an <code>mkinfit</code> object is in
-fact a full report that should give enough information to be able to
-approximately reproduce the fit with other tools.</li>
-<li>The chi-squared error level as defined in the FOCUS kinetics guidance
-(see below) is calculated for each observed variable.</li>
-<li>Iteratively reweighted least squares fitting is implemented in a similar way
-as in KinGUII and CAKE (see below). Simply add the argument
-<code>reweight = &quot;obs&quot;</code> to your call to <code>mkinfit</code> and a separate variance
-componenent for each of the observed variables will be optimised
-in a second stage after the primary optimisation algorithm has converged.</li>
-<li>When a metabolite decline phase is not described well by SFO kinetics,
-SFORB kinetics can be used for the metabolite.</li>
-</ul>
-
-<h2>GUI</h2>
-
-<p>There is a graphical user interface that I consider useful for real work. Please
-refer to its <a href="http://kinfit.r-forge.r-project.org/gmkin_static">documentation page</a>
-for installation instructions and a manual.</p>
-
-<h2>News</h2>
-
-<p>Yes, there is a ChangeLog, for the latest <a href="http://cran.r-project.org/web/packages/mkin/news.html">CRAN release</a>
-and one for the <a href="https://github.com/jranke/mkin/blob/master/NEWS.md">github master branch</a>.</p>
-
-<h2>Credits and historical remarks</h2>
-
-<p><code>mkin</code> would not be possible without the underlying software stack consisting
-of R and the packages <a href="http://cran.r-project.org/package=deSolve">deSolve</a>
-and <a href="http://cran.r-project.org/package=FME">FME</a>, to say the least.</p>
-
-<p>It could not have been written without me being introduced to regulatory fate
-modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories
-Ltd (formerly RCC Ltd). <code>mkin</code> greatly profits from and largely follows
-the work done by the
-<a href="http://focus.jrc.ec.europa.eu/dk">FOCUS Degradation Kinetics Workgroup</a>,
-as detailed in their guidance document from 2006, slightly updated in 2011 and
-2014.</p>
-
-<p>Also, it was inspired by the first version of KinGUI developed by
-BayerCropScience, which is based on the MatLab runtime environment.</p>
-
-<p>The companion package
-<a href="http://kinfit.r-forge.r-project.org/kinfit_static/index.html">kinfit</a> (now deprecated) was
-<a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&amp;root=kinfit&amp;revision=2">started in 2008</a> and
-<a href="http://cran.r-project.org/src/contrib/Archive/kinfit/">first published</a> on
-CRAN on 01 May 2010.</p>
-
-<p>The first <code>mkin</code> code was
-<a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&amp;root=kinfit&amp;revision=8">published on 11 May 2010</a> and the
-<a href="http://cran.r-project.org/src/contrib/Archive/mkin">first CRAN version</a>
-on 18 May 2010.</p>
-
-<p>In 2011, Bayer Crop Science started to distribute an R based successor to KinGUI named
-KinGUII whose R code is based on <code>mkin</code>, but which added, amongst other
-refinements, a closed source graphical user interface (GUI), iteratively
-reweighted least squares (IRLS) optimisation of the variance for each of the
-observed variables, and Markov Chain Monte Carlo (MCMC) simulation
-functionality, similar to what is available e.g. in the <code>FME</code> package.</p>
-
-<p>Somewhat in parallel, Syngenta has sponsored the development of an <code>mkin</code> and
-KinGUII based GUI application called CAKE, which also adds IRLS and MCMC, is
-more limited in the model formulation, but puts more weight on usability.
-CAKE is available for download from the <a href="http://projects.tessella.com/cake">CAKE
-website</a>, where you can also
-find a zip archive of the R scripts derived from <code>mkin</code>, published under the GPL
-license.</p>
-
-<p>Finally, there is
-<a href="http://github.com/zhenglei-gao/KineticEval">KineticEval</a>, which contains
-a further development of the scripts used for KinGUII, so the different tools
-will hopefully be able to learn from each other in the future as well.</p>
-
-<h2>Development</h2>
-
-<p>Contributions are welcome! Your
-<a href="https://help.github.com/articles/fork-a-repo">mkin fork</a> is just a mouse click
-away&hellip; The master branch on github should always be in good shape, I implement
-new features in separate branches now. If you prefer subversion, project
-members for the
-<a href="http://r-forge.r-project.org/R/?group_id=615">r-forge project</a> are welcome as well.
-Generally, the source code of the latest CRAN version should be available there.
-You can also browse the source code at <a href="http://cgit.jrwb.de/mkin">cgit.jrwb.de/mkin</a>.</p>
-
-
- <h2>Help topics</h2>
-
- <h3>Main functions</h3>
- <p>Essential functionality</p>
-
-
- <ul class="index">
-
- <li>
- <code><a href="mkinmod.html">mkinmod</a></code><br /> Function to set up a kinetic model with one or more state variables
-</li>
-
- <li>
- <code><a href="mkinfit.html">mkinfit</a></code><br /> Fit a kinetic model to data with one or more state variables
-</li>
-
- <li>
- <code><a href="mmkin.html">mmkin</a></code><br /> Fit one or more kinetic models with one or more state variables to one or more datasets
-</li>
-
- </ul>
- <h3>Show results</h3>
- <p>Functions working on mkinfit objects</p>
-
-
- <ul class="index">
-
- <li>
- <code><a href="plot.mkinfit.html">plot.mkinfit</a></code>(plot_sep)<br /> Plot the observed data and the fitted model of an mkinfit object
-</li>
-
- <li>
- <code><a href="summary.mkinfit.html">summary.mkinfit</a></code>(print.summary.mkinfit)<br /> Summary method for class "mkinfit"
-</li>
-
- <li>
- <code><a href="mkinresplot.html">mkinresplot</a></code><br /> Function to plot residuals stored in an mkin object
-</li>
-
- <li>
- <code><a href="mkinparplot.html">mkinparplot</a></code><br /> Function to plot the confidence intervals obtained using
-</li>
-
- <li>
- <code><a href="endpoints.html">endpoints</a></code><br />Function to calculate endpoints for further use from kinetic models fitted with mkinfit
-</li>
-
- <li>
- <code><a href="mkinerrmin.html">mkinerrmin</a></code><br />Calculate the minimum error to assume in order to pass the variance test
-</li>
-
- </ul>
- <h3>Work with mmkin objects</h3>
- <p>Functions working with aggregated results</p>
-
-
- <ul class="index">
-
- <li>
- <code><a href="Extract.mmkin.html">[.mmkin</a></code><br />Subsetting method for mmkin objects</li>
-
- <li>
- <code><a href="plot.mmkin.html">plot.mmkin</a></code><br /> Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object
-</li>
-
- </ul>
- <h3>Datasets and known results</h3>
-
-
- <ul class="index">
-
- <li>
- <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_datasets</a></code>(FOCUS_2006_A, FOCUS_2006_B, FOCUS_2006_C, FOCUS_2006_D, FOCUS_2006_E, FOCUS_2006_F)<br />Datasets A to F from the FOCUS Kinetics report from 2006
-</li>
-
- <li>
- <code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code><br />Results of fitting the SFO model to Datasets A to F of FOCUS (2006)
-</li>
-
- <li>
- <code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">FOCUS_2006_FOMC_ref_A_to_F</a></code><br />Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)
-</li>
-
- <li>
- <code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code><br />Results of fitting the HS model to Datasets A to F of FOCUS (2006)
-</li>
-
- <li>
- <code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code><br />Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)
-</li>
-
- <li>
- <code><a href="mccall81_245T.html">mccall81_245T</a></code><br /> Datasets on aerobic soil metabolism of 2,4,5-T in six soils
-</li>
-
- <li>
- <code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code>(schaefer07_complex_results)<br /> Metabolism data set used for checking the software quality of KinGUI
-</li>
-
- <li>
- <code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code><br /> Synthetic datasets for one parent compound with two metabolites
-</li>
-
- </ul>
- <h3>Helper functions</h3>
-
-
- <ul class="index">
-
- <li>
- <code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code><br /> Convert a dataframe with observations over time into long format
-</li>
-
- <li>
- <code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code><br /> Convert a dataframe from long to wide format
-</li>
-
- <li>
- <code><a href="mkinsub.html">mkinsub</a></code><br /> Function to set up a kinetic submodel for one state variable
-</li>
-
- <li>
- <code><a href="mkinds.html">mkinds</a></code><br />A dataset class for mkin</li>
-
- <li>
- <code><a href="print.mkinds.html">print.mkinds</a></code><br /> Print mkinds objects
-</li>
-
- <li>
- <code><a href="print.mkinmod.html">print.mkinmod</a></code><br /> Print mkinmod objects
-</li>
-
- <li>
- <code><a href="mkinpredict.html">mkinpredict</a></code><br /> Produce predictions from a kinetic model using specific parameters
-</li>
-
- <li>
- <code><a href="transform_odeparms.html">transform_odeparms</a></code>(backtransform_odeparms)<br /> Functions to transform and backtransform kinetic parameters for fitting
-</li>
-
- <li>
- <code><a href="ilr.html">ilr</a></code>(invilr)<br /> Function to perform isometric log-ratio transformation
-</li>
-
- <li>
- <code><a href="geometric_mean.html">geometric_mean</a></code><br /> Calculate the geometric mean </li>
-
- </ul>
- <h3>Analytical solutions</h3>
- <p>Parent only model solutions</p>
-
-
- <ul class="index">
-
- <li>
- <code><a href="SFO.solution.html">SFO.solution</a></code><br /> Single First-Order kinetics </li>
-
- <li>
- <code><a href="FOMC.solution.html">FOMC.solution</a></code><br /> First-Order Multi-Compartment kinetics </li>
-
- <li>
- <code><a href="DFOP.solution.html">DFOP.solution</a></code><br />Double First-Order in Parallel kinetics
-</li>
-
- <li>
- <code><a href="SFORB.solution.html">SFORB.solution</a></code><br /> Single First-Order Reversible Binding kinetics </li>
-
- <li>
- <code><a href="HS.solution.html">HS.solution</a></code><br /> Hockey-Stick kinetics </li>
-
- <li>
- <code><a href="IORE.solution.html">IORE.solution</a></code><br /> Indeterminate order rate equation kinetics </li>
-
- </ul>
- <h3>Deprecated functions</h3>
- <p>Functions that have been superseeded</p>
-
-
- <ul class="index">
-
- <li>
- <code><a href="mkinplot.html">mkinplot</a></code><br /> Plot the observed data and the fitted model of an mkinfit object
-</li>
-
- </ul>
- <h3>Other</h3>
-
-
- <ul class="index">
-
- <li>
- <code><a href="add_err.html">add_err</a></code><br /> Add normally distributed errors to simulated kinetic degradation data
-</li>
-
- </ul>
- </div>
-
- <div class="span3 offset1">
- <h2>Vignettes</h2>
- <ul>
- <li><a href="vignettes/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li>
- <li><a href="vignettes/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></li>
- <li><a href="vignettes/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li>
- <li><a href="vignettes/mkin.html">mkin - Kinetic evaluation of chemical degradation data</a></li>
- <li><a href="vignettes/FOCUS_Z.pdf">Example evaluation of FOCUS dataset Z</a></li>
- </ul>
-
- <h2>Dependencies</h2>
- <ul>
- <li><strong>Depends</strong>: minpack.lm, rootSolve, inline, parallel</li>
- <li><strong>Imports</strong>: stats, graphics, methods, FME, deSolve, R6</li>
- <li><strong>Suggests</strong>: knitr, testthat, microbenchmark, ggplot2</li>
-
- </ul>
- <h2>Authors</h2>
- <ul>
- <li><a href="mailto:jranke@uni-bremen.de">Johannes Ranke</a> [aut, cre, cph]</li>
- <li>Katrin Lindenberger [ctb]</li>
- <li>René Lehmann [ctb]</li>
- <li>Eurofins Regulatory AG [cph]</li>
- </ul>
-
- </div>
-</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="http://twitter.github.com/bootstrap">bootstrap</a>.</p>
- </footer>
- </div>
- </body>
-</html> \ No newline at end of file

Contact - Imprint