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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("mkin") -</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>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, -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&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>(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>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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