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diff --git a/inst/web/index.html b/inst/web/index.html new file mode 100644 index 00000000..a08af34f --- /dev/null +++ b/inst/web/index.html @@ -0,0 +1,452 @@ +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<title>Index. mkin 0.9-41</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 0.9-41</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.rstudio.com/web/packages/mkin/index.html"><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("mkin") +</code></pre> + +<p>If looking for the latest features, you can install directly from +<a href="http://github.com/jranke/mkin">github</a>, e.g. using the <code>devtools</code> package. +Using <code>quick = TRUE</code> skips docs, multiple-architecture builds, demos, and +vignettes, to make installation as fast and painless as possible.</p> + +<pre><code class="r">require(devtools) +install_github("jranke/mkin", quick = TRUE) +</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 +'Credits and historical remarks' 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>Model optimisation with +<a href="http://kinfit.r-forge.r-project.org/mkin_static/mkinfit.html"><code>mkinfit</code></a> +internally using the <code>modFit</code> function from the <code>FME</code> package, +but using the Port routine <code>nlminb</code> per default.</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 RenĂ© 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 = "obs"</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, +either IORE kinetics (often producing failures of the integration algorithm) +or SFORB kinetics (working nicely) can be used for the metabolite, adding one +respectively two parameters to the system.</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>, +<a href="http://cran.r-project.org/package=minpack.lm">minpack.lm</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> was +<a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&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&root=kinfit&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… 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><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 specifc 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> + </div> + + <div class="span3 offset1"> + <h2>Vignettes</h2> + <ul> + <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/FOCUS_Z.pdf">Example evaluation of FOCUS dataset Z</a></li> + <li><a href="vignettes/mkin.pdf">Routines for fitting kinetic models with one or more state variables to chemical degradation data</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</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>RenĂ© 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>. 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