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diff --git a/docs/index.html b/docs/index.html index a8d8521d..4ec9fd79 100644 --- a/docs/index.html +++ b/docs/index.html @@ -1,8 +1,20 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Kinetic Evaluation of Chemical Degradation Data • 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]> +<!-- Generated by pkgdown: do not edit by hand --><html> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> +<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>Kinetic Evaluation of Chemical Degradation Data • 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> +<![endif]--> +</head> +<body> <div class="container template-home"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> @@ -15,7 +27,8 @@ <a class="navbar-brand" href="index.html">mkin</a> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"><li> + <ul class="nav navbar-nav"> +<li> <a href="reference/index.html">Functions and data</a> </li> <li class="dropdown"> @@ -24,7 +37,8 @@ <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"><li> + <ul class="dropdown-menu" role="menu"> +<li> <a href="articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -36,25 +50,33 @@ <li> <a href="articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> - </ul></li> + </ul> +</li> <li> <a href="news/index.html">News</a> </li> - </ul><ul class="nav navbar-nav navbar-right"><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 --> + </ul> +</div> +<!--/.nav-collapse --> + </div> +<!--/.container --> +</div> +<!--/.navbar --> </header><div class="row"> <div class="contents col-md-9"> <div id="mkin" class="section level1"> -<div class="page-header"><h1 class="hasAnchor"><a href="#mkin" class="anchor"> </a>mkin</h1></div> +<div class="page-header"><h1 class="hasAnchor"> +<a href="#mkin" class="anchor"> </a>mkin</h1></div> <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> <div id="installation" class="section level2"> @@ -66,7 +88,7 @@ <div id="background" class="section level2"> <h2 class="hasAnchor"> <a href="#background" class="anchor"> </a>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> +<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> </div> <div id="usage" class="section level2"> <h2 class="hasAnchor"> @@ -76,23 +98,25 @@ <div id="documentation" class="section level2"> <h2 class="hasAnchor"> <a href="#documentation" class="anchor"> </a>Documentation</h2> -<p>The HTML documentation is available at <a href="http://jranke.github.io/mkin">github</a> and at <a href="http://kinfit.r-forge.r-project.org/mkin_static/index.html">R-Forge</a>.</p> +<p>The HTML documentation is available at <a href="http://pkgdown.jrwb.de/mkin">jrwb.de</a>, at <a href="http://jranke.github.io/mkin">github</a> and at <a href="http://kinfit.r-forge.r-project.org/mkin_static/index.html">R-Forge</a>.</p> </div> <div id="features" class="section level2"> <h2 class="hasAnchor"> <a href="#features" class="anchor"> </a>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> +<ul> +<li>Highly flexible model specification using <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/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/reference/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/reference/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/articles/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/reference/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>By default, kinetic rate constants and kinetic formation fractions are transformed internally using <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/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 = "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></div> +</ul> +</div> <div id="gui" class="section level2"> <h2 class="hasAnchor"> <a href="#gui" class="anchor"> </a>GUI</h2> @@ -111,29 +135,42 @@ <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="https://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="https://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>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://showcase.tessella.com/products/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> </div> <div id="development" class="section level2"> <h2 class="hasAnchor"> <a href="#development" class="anchor"> </a>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> +<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> </div> </div> </div> <div class="col-md-3" id="sidebar"> - <h2>Links</h2><ul class="list-unstyled"><li>Download from CRAN at <br><a href="https://cran.r-project.org/package=mkin">https://​cran.r-project.org/​package=mkin</a></li> -<li>Browse source code at <br><a href="http://github.com/jranke/mkin">http://​github.com/​jranke/​mkin</a></li> -<li>Report a bug at <br><a href="http://github.com/jranke/mkin/issues">http://​github.com/​jranke/​mkin/​issues</a></li> -</ul><h2>License</h2> + <h2>Links</h2> +<ul class="list-unstyled"> +<li>Download from CRAN at <br><a href="https://cran.r-project.org/package=mkin">https://cran.r-project.org/package=mkin</a> +</li> +<li>Browse source code at <br><a href="http://github.com/jranke/mkin">http://github.com/jranke/mkin</a> +</li> +<li>Report a bug at <br><a href="http://github.com/jranke/mkin/issues">http://github.com/jranke/mkin/issues</a> +</li> +</ul> +<h2>License</h2> <p>GPL</p> -<h2>Developers</h2><ul class="list-unstyled"><li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li> +<h2>Developers</h2> +<ul class="list-unstyled"> +<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li> <li><a href="authors.html">All authors...</a></li> -</ul><html><body><h2>Dev status</h2><ul class="list-unstyled"><li><a href="https://cran.r-project.org/package=mkin"> - <img src="http://www.r-pkg.org/badges/version/mkin"></a></li> -</ul></body></html></div> +</ul> +<html><body> +<h2>Dev status</h2> +<ul class="list-unstyled"> +<li><a href="https://cran.r-project.org/package=mkin"><img src="http://www.r-pkg.org/badges/version/mkin"></a></li> +</ul> +</body></html> +</div> </div> @@ -145,6 +182,8 @@ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> </div> - </footer></div> + </footer> +</div> - </body></html> + </body> +</html> diff --git a/docs/news/index.html b/docs/news/index.html index cbf35a73..2e7f0e34 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -100,16 +100,29 @@ </div> <div class="contents"> + <div id="mkin-0-9-45-1-2016-12-20" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-45-1-2016-12-20" class="anchor"> </a>mkin 0.9.45.1 (2016-12-20)</h1> +<div id="new-features" class="section level2"> +<h2 class="hasAnchor"> +<a href="#new-features" class="anchor"> </a>New features</h2> +<ul> +<li>A <code>twa</code> function, calculating maximum time weighted average concentrations for the parent (SFO, FOMC and DFOP).</li> +</ul> +</div> +</div> <div id="mkin-0-9-45-2016-12-08" class="section level1"> <h1 class="hasAnchor"> <a href="#mkin-0-9-45-2016-12-08" class="anchor"> </a>mkin 0.9.45 (2016-12-08)</h1> <div id="minor-changes" class="section level2"> <h2 class="hasAnchor"> <a href="#minor-changes" class="anchor"> </a>Minor changes</h2> -<ul><li><p><code>plot.mkinfit</code> and <code>plot.mmkin</code>: If the plotting device is <code>tikz</code>, LaTeX markup is being used for the chi2 error in the graphs.</p></li> +<ul> +<li><p><code>plot.mkinfit</code> and <code>plot.mmkin</code>: If the plotting device is <code>tikz</code>, LaTeX markup is being used for the chi2 error in the graphs.</p></li> <li><p>Use <code>pkgdown</code>, the successor of <code>staticdocs</code> for generating static HTML documentation. Include example output and graphs also for <code>dontrun</code> sections.</p></li> <li><p><code>plot.mkinfit</code>: Plotting does not fail any more when the compiled model is not available, e.g. because it was removed from the temporary directory. In this case, the uncompiled model is now used for plotting</p></li> -</ul></div> +</ul> +</div> </div> <div id="mkin-0-9-44-2016-06-29" class="section level1"> <h1 class="hasAnchor"> @@ -117,8 +130,10 @@ <div id="bug-fixes" class="section level2"> <h2 class="hasAnchor"> <a href="#bug-fixes" class="anchor"> </a>Bug fixes</h2> -<ul><li>The test <code>test_FOMC_ill-defined</code> failed on several architectures, so the test is now skipped</li> -</ul></div> +<ul> +<li>The test <code>test_FOMC_ill-defined</code> failed on several architectures, so the test is now skipped</li> +</ul> +</div> </div> <div id="mkin-0-9-43-2016-06-28" class="section level1"> <h1 class="hasAnchor"> @@ -126,31 +141,37 @@ <div id="major-changes" class="section level2"> <h2 class="hasAnchor"> <a href="#major-changes" class="anchor"> </a>Major changes</h2> -<ul><li><p>The title was changed to <code>Kinetic evaluations of chemical degradation data</code></p></li> +<ul> +<li><p>The title was changed to <code>Kinetic evaluations of chemical degradation data</code></p></li> <li><p><code>plot.mkinfit</code>: Add the possibility to show fits (and residual plots if requested) separately for the observed variables</p></li> <li><p><code>plot.mkinfit</code>: Add the possibility to show the chi2 error levels in the plot, similar to the way they are shown in <code>plot.mmkin</code></p></li> <li><p><code>plot_sep</code>: Add this function as a convenience wrapper for plotting observed variables of mkinfit objects separately, with chi2 error values and residual plots.</p></li> <li><p>Vignettes: The main vignette <code>mkin</code> was converted to R markdown and updated. The other vignettes were also updated to show current improved functionality.</p></li> <li><p>The function <code>add_err</code> was added to the package, making it easy to generate simulated data using an error model based on the normal distribution</p></li> -</ul></div> +</ul> +</div> <div id="minor-changes-1" class="section level2"> <h2 class="hasAnchor"> <a href="#minor-changes-1" class="anchor"> </a>Minor changes</h2> -<ul><li><p>Remove an outdated reference to the inline package in the <code>compiled_models</code> vignette</p></li> +<ul> +<li><p>Remove an outdated reference to the inline package in the <code>compiled_models</code> vignette</p></li> <li><p><code>mkinfit</code>: Do not error out in cases where the fit converges, but the Jacobian for the untransformed model cost can not be estimated. Give a warning instead and return NA for the t-test results.</p></li> <li><p><code>summary.mkinfit</code>: Give a warning message when the covariance matrix can not be obtained.</p></li> <li><p>A test has been added to containing a corresponding edge case to check that the warnings are correctly issued and the fit does not terminate.</p></li> <li><p><code>plot.mmkin</code>: Round the chi2 error value to three significant digits, instead of two decimal digits.</p></li> <li><p><code>mkinfit</code>: Return the <code>err</code> values used on weighted fits as a column named <code>err</code>. Also include these inverse weights when the column <code>value</code> in the observed data is used, which is returned as <code>observed</code> in the data component of the mkinfit object.</p></li> -</ul></div> +</ul> +</div> <div id="bug-fixes-1" class="section level2"> <h2 class="hasAnchor"> <a href="#bug-fixes-1" class="anchor"> </a>Bug fixes</h2> -<ul><li><p><code>endpoints</code>: When the name of a substance degrading to a metabolite (e.g. a parent compound) used in the model formulation ended in the letter <code>f</code>, some rate parameters could be listed as formation fractions with mixed up names. These would also appear in the summary.</p></li> +<ul> +<li><p><code>endpoints</code>: When the name of a substance degrading to a metabolite (e.g. a parent compound) used in the model formulation ended in the letter <code>f</code>, some rate parameters could be listed as formation fractions with mixed up names. These would also appear in the summary.</p></li> <li><p><code>mkinfit</code>: Check for all observed variables when checking if the user tried to fix formation fractions when fitting them using ilr transformation.</p></li> <li><p><code>plot.mmkin</code>: Set the plot margins correctly, also in the case of a single fit to be plotted, so the main title is placed in a reasonable way.</p></li> <li><p><code>plot.mkinfit</code>: Correct default values for <code>col_obs</code>, <code>pch_obs</code> and <code>lty_obs</code> for the case that <code>obs_vars</code> is specified.</p></li> -</ul></div> +</ul> +</div> </div> <div id="mkin-0-9-42-2016-03-25" class="section level1"> <h1 class="hasAnchor"> @@ -158,15 +179,19 @@ <div id="major-changes-1" class="section level2"> <h2 class="hasAnchor"> <a href="#major-changes-1" class="anchor"> </a>Major changes</h2> -<ul><li>Add the argument <code>from_max_mean</code> to <code>mkinfit</code>, for fitting only the decline from the maximum observed value for models with a single observed variable</li> -</ul></div> +<ul> +<li>Add the argument <code>from_max_mean</code> to <code>mkinfit</code>, for fitting only the decline from the maximum observed value for models with a single observed variable</li> +</ul> +</div> <div id="minor-changes-2" class="section level2"> <h2 class="hasAnchor"> <a href="#minor-changes-2" class="anchor"> </a>Minor changes</h2> -<ul><li><p>Add plots to <code>compiled_models</code> vignette</p></li> +<ul> +<li><p>Add plots to <code>compiled_models</code> vignette</p></li> <li><p>Give an explanatory error message when mkinmod fails due to a missing definition of a target variable</p></li> <li><p><code><a href="../reference/print.mkinmod.html">print.mkinmod()</a></code>: Improve formatting when printing mkinmod model definitions</p></li> -</ul></div> +</ul> +</div> </div> <div id="mkin-0-9-41-2015-11-09" class="section level1"> <h1 class="hasAnchor"> @@ -174,17 +199,21 @@ <div id="minor-changes-3" class="section level2"> <h2 class="hasAnchor"> <a href="#minor-changes-3" class="anchor"> </a>Minor changes</h2> -<ul><li><p>Add an R6 class <code>mkinds</code> representing datasets with a printing method</p></li> +<ul> +<li><p>Add an R6 class <code>mkinds</code> representing datasets with a printing method</p></li> <li><p>Add a printing method for mkinmod objects</p></li> <li><p>Make it possible to specify arbitrary strings as names for the compounds in <code>mkinmod</code>, and show them in the plot</p></li> <li><p>Use an index.r file to group help topics in static documentation</p></li> -</ul></div> +</ul> +</div> <div id="bug-fixes-2" class="section level2"> <h2 class="hasAnchor"> <a href="#bug-fixes-2" class="anchor"> </a>Bug fixes</h2> -<ul><li> +<ul> +<li> <code><a href="../reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Avoid an error that occurred when printing summaries generated with mkin versions before 0.9-36</li> -</ul></div> +</ul> +</div> </div> <div id="mkin-0-9-40-2015-07-21" class="section level1"> <h1 class="hasAnchor"> @@ -192,15 +221,19 @@ <div id="bug-fixes-3" class="section level2"> <h2 class="hasAnchor"> <a href="#bug-fixes-3" class="anchor"> </a>Bug fixes</h2> -<ul><li> +<ul> +<li> <code><a href="../reference/endpoints.html">endpoints()</a></code>: For DFOP and SFORB models, where <code>optimize()</code> is used, make use of the fact that the DT50 must be between DT50_k1 and DT50_k2 (DFOP) or DT50_b1 and DT50_b2 (SFORB), as <code>optimize()</code> sometimes did not find the minimum. Likewise for finding DT90 values. Also fit on the log scale to make the function more efficient.</li> -</ul></div> +</ul> +</div> <div id="internal-changes" class="section level2"> <h2 class="hasAnchor"> <a href="#internal-changes" class="anchor"> </a>Internal changes</h2> -<ul><li> +<ul> +<li> <code>DESCRIPTION</code>, <code>NAMESPACE</code>, <code>R/*.R</code>: Import (from) stats, graphics and methods packages, and qualify some function calls for non-base packages installed with R to avoid NOTES made by R CMD check –as-cran with upcoming R versions.</li> -</ul></div> +</ul> +</div> </div> <div id="mkin-0-9-39-2015-06-26" class="section level1"> <h1 class="hasAnchor"> @@ -208,15 +241,19 @@ <div id="major-changes-2" class="section level2"> <h2 class="hasAnchor"> <a href="#major-changes-2" class="anchor"> </a>Major changes</h2> -<ul><li><p>New function <code><a href="../reference/mmkin.html">mmkin()</a></code>: This function takes a character vector of model shorthand names, or alternatively a list of mkinmod models, as well as a list of dataset as main arguments. It returns a matrix of mkinfit objects, with a row for each model and a column for each dataset. A subsetting method with single brackets is available. Fitting the models in parallel using the <code>parallel</code> package is supported.</p></li> +<ul> +<li><p>New function <code><a href="../reference/mmkin.html">mmkin()</a></code>: This function takes a character vector of model shorthand names, or alternatively a list of mkinmod models, as well as a list of dataset as main arguments. It returns a matrix of mkinfit objects, with a row for each model and a column for each dataset. A subsetting method with single brackets is available. Fitting the models in parallel using the <code>parallel</code> package is supported.</p></li> <li><p>New function <code><a href="../reference/plot.mmkin.html">plot.mmkin()</a></code>: Plots single-row or single-column <code>mmkin</code> objects including residual plots.</p></li> -</ul></div> +</ul> +</div> <div id="bug-fixes-4" class="section level2"> <h2 class="hasAnchor"> <a href="#bug-fixes-4" class="anchor"> </a>Bug fixes</h2> -<ul><li> +<ul> +<li> <code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Fix the x axis scaling for rate constants and formation fractions that got confused by the introduction of the t-values of transformed parameters.</li> -</ul></div> +</ul> +</div> </div> <div id="mkin-0-9-38-2015-06-24" class="section level1"> <h1 class="hasAnchor"> @@ -224,15 +261,19 @@ <div id="minor-changes-4" class="section level2"> <h2 class="hasAnchor"> <a href="#minor-changes-4" class="anchor"> </a>Minor changes</h2> -<ul><li><p><code>vignettes/compiled_models.html</code>: Show the performance improvement factor actually obtained when building the vignette, as well as mkin version, some system info and the CPU model used for building the vignette.</p></li> +<ul> +<li><p><code>vignettes/compiled_models.html</code>: Show the performance improvement factor actually obtained when building the vignette, as well as mkin version, some system info and the CPU model used for building the vignette.</p></li> <li><p><code>GNUMakefile</code>,<code>vignettes/*</code>: Clean up vignette generation and include table of contents in HTML vignettes.</p></li> -</ul></div> +</ul> +</div> <div id="bug-fixes-5" class="section level2"> <h2 class="hasAnchor"> <a href="#bug-fixes-5" class="anchor"> </a>Bug fixes</h2> -<ul><li> +<ul> +<li> <code><a href="../reference/mkinmod.html">mkinmod()</a></code>: When generating the C code for the derivatives, only declare the time variable when it is needed and remove the ‘-W-no-unused-variable’ compiler flag as the C compiler used in the CRAN checks on Solaris does not know it.</li> -</ul></div> +</ul> +</div> </div> <div id="mkin-0-9-36-2015-06-21" class="section level1"> <h1 class="hasAnchor"> @@ -240,16 +281,20 @@ <div id="major-changes-3" class="section level2"> <h2 class="hasAnchor"> <a href="#major-changes-3" class="anchor"> </a>Major changes</h2> -<ul><li><p><code><a href="../reference/summary.mkinfit.html">summary.mkinfit()</a></code>: A one-sided t-test for significant difference of untransformed parameters from zero is now always shown, based on the assumption of normal distribution for estimators of all untransformed parameters. Use with caution, as this assumption is unrealistic e.g. for rate constants in these nonlinear kinetic models.</p></li> +<ul> +<li><p><code><a href="../reference/summary.mkinfit.html">summary.mkinfit()</a></code>: A one-sided t-test for significant difference of untransformed parameters from zero is now always shown, based on the assumption of normal distribution for estimators of all untransformed parameters. Use with caution, as this assumption is unrealistic e.g. for rate constants in these nonlinear kinetic models.</p></li> <li><p>If a compiler (gcc) is installed, use a version of the differential equation model compiled from C code, which is a huge performance boost for models where only the deSolve method works.</p></li> <li><p><code><a href="../reference/mkinmod.html">mkinmod()</a></code>: Create a list component $cf (of class CFuncList) in the list returned by mkinmod, if a version can be compiled from autogenerated C code (see above).</p></li> <li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: Set the default <code>solution_type</code> to <code>deSolve</code> when a compiled version of the model is present, except when an analytical solution is possible.</p></li> -</ul></div> +</ul> +</div> <div id="minor-changes-5" class="section level2"> <h2 class="hasAnchor"> <a href="#minor-changes-5" class="anchor"> </a>Minor changes</h2> -<ul><li>Added a simple showcase vignette with an evaluation of FOCUS example dataset D</li> -</ul></div> +<ul> +<li>Added a simple showcase vignette with an evaluation of FOCUS example dataset D</li> +</ul> +</div> </div> <div id="mkin-0-9-35-2015-05-15" class="section level1"> <h1 class="hasAnchor"> @@ -257,97 +302,119 @@ <div id="major-changes-4" class="section level2"> <h2 class="hasAnchor"> <a href="#major-changes-4" class="anchor"> </a>Major changes</h2> -<ul><li>Switch from RUnit to testthat for testing</li> -</ul></div> +<ul> +<li>Switch from RUnit to testthat for testing</li> +</ul> +</div> <div id="bug-fixes-6" class="section level2"> <h2 class="hasAnchor"> <a href="#bug-fixes-6" class="anchor"> </a>Bug fixes</h2> -<ul><li><p><code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Avoid warnings that occurred when not all confidence intervals were available in the summary of the fit</p></li> +<ul> +<li><p><code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Avoid warnings that occurred when not all confidence intervals were available in the summary of the fit</p></li> <li><p><code><a href="../reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Fix printing the summary for the case that the number of iterations is not available</p></li> <li><p>NAMESPACE: export S3 methods plot.mkinfit, summary.mkinfit and print.summary.mkinfit to satisfy R CMD check on R-devel</p></li> <li><p><code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Avoid warning in R CMD check about undeclared global variable <code>Lower</code></p></li> -</ul></div> -<div id="new-features" class="section level2"> +</ul> +</div> +<div id="new-features-1" class="section level2"> <h2 class="hasAnchor"> -<a href="#new-features" class="anchor"> </a>New features</h2> -<ul><li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: Report successful termination when quiet = FALSE. This is helpful for more difficult problems fitted with reweight.method = obs, as no progress is often indicated during the reweighting.</p></li> +<a href="#new-features-1" class="anchor"> </a>New features</h2> +<ul> +<li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: Report successful termination when quiet = FALSE. This is helpful for more difficult problems fitted with reweight.method = obs, as no progress is often indicated during the reweighting.</p></li> <li><p>A first test using results established in the expertise written for the German Federal Environmental Agency (UBA) was added.</p></li> <li><p>Add synthetic datasets generated for expertise written for the German Federal Environmental Agency UBA</p></li> <li><p>Add tests based on these datasets</p></li> -</ul></div> +</ul> +</div> </div> <div id="mkin-0-9-34-2014-11-22" class="section level1"> <h1 class="hasAnchor"> <a href="#mkin-0-9-34-2014-11-22" class="anchor"> </a>mkin 0.9-34 (2014-11-22)</h1> -<div id="new-features-1" class="section level2"> +<div id="new-features-2" class="section level2"> <h2 class="hasAnchor"> -<a href="#new-features-1" class="anchor"> </a>New features</h2> -<ul><li><p>Add the convenience function <code><a href="../reference/mkinsub.html">mkinsub()</a></code> for creating the lists used in <code><a href="../reference/mkinmod.html">mkinmod()</a></code></p></li> +<a href="#new-features-2" class="anchor"> </a>New features</h2> +<ul> +<li><p>Add the convenience function <code><a href="../reference/mkinsub.html">mkinsub()</a></code> for creating the lists used in <code><a href="../reference/mkinmod.html">mkinmod()</a></code></p></li> <li><p>Add the possibility to fit indeterminate order rate equation (IORE) models using an analytical solution (parent only) or a numeric solution. Paths from IORE compounds to metabolites are supported when using formation fractions (use_of_ff = ‘max’). Note that the numerical solution (method.ode = ‘deSolve’) of the IORE differential equations sometimes fails due to numerical problems.</p></li> <li><p>Switch to using the Port algorithm (using a model/trust region approach) per default. While needing more iterations than the Levenberg-Marquardt algorithm previously used per default, it is less sensitive to starting parameters.</p></li> -</ul></div> +</ul> +</div> <div id="minor-changes-6" class="section level2"> <h2 class="hasAnchor"> <a href="#minor-changes-6" class="anchor"> </a>Minor changes</h2> -<ul><li><p>The formatting of differential equations in the summary was further improved</p></li> +<ul> +<li><p>The formatting of differential equations in the summary was further improved</p></li> <li><p>Always include 0 on y axis when plotting during the fit</p></li> -</ul></div> +</ul> +</div> </div> <div id="mkin-0-9-33-2014-10-22" class="section level1"> <h1 class="hasAnchor"> <a href="#mkin-0-9-33-2014-10-22" class="anchor"> </a>mkin 0.9-33 (2014-10-22)</h1> -<div id="new-features-2" class="section level2"> +<div id="new-features-3" class="section level2"> <h2 class="hasAnchor"> -<a href="#new-features-2" class="anchor"> </a>New features</h2> -<ul><li><p>The initial value (state.ini) for the observed variable with the highest observed residue is set to 100 in case it has no time zero observation and <code>state.ini = "auto"</code></p></li> +<a href="#new-features-3" class="anchor"> </a>New features</h2> +<ul> +<li><p>The initial value (state.ini) for the observed variable with the highest observed residue is set to 100 in case it has no time zero observation and <code>state.ini = "auto"</code></p></li> <li><p>A basic unit test for <code><a href="../reference/mkinerrmin.html">mkinerrmin()</a></code> was written</p></li> -</ul></div> +</ul> +</div> <div id="bug-fixes-7" class="section level2"> <h2 class="hasAnchor"> <a href="#bug-fixes-7" class="anchor"> </a>Bug fixes</h2> -<ul><li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: The internally fitted parameter for <code>g</code> was named <code>g_ilr</code> even when <code>transform_fractions=FALSE</code></p></li> +<ul> +<li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: The internally fitted parameter for <code>g</code> was named <code>g_ilr</code> even when <code>transform_fractions=FALSE</code></p></li> <li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: The initial value (state.ini) for the parent compound was not set when the parent was not the (only) variable with the highest value in the observed data.</p></li> <li><p><code><a href="../reference/mkinerrmin.html">mkinerrmin()</a></code>: When checking for degrees of freedom for metabolites, check if their time zero value is fixed instead of checking if the observed value is zero. This ensures correct calculation of degrees of freedom also in cases where the metabolite residue at time zero is greater zero.</p></li> <li><p><code><a href="../reference/plot.mkinfit.html">plot.mkinfit()</a></code>: Avoid a warning message about only using the first component of ylim that occurred when ylim was specified explicitly</p></li> -</ul></div> +</ul> +</div> <div id="minor-changes-7" class="section level2"> <h2 class="hasAnchor"> <a href="#minor-changes-7" class="anchor"> </a>Minor changes</h2> -<ul><li><p>The formatting of differential equations in the summary was improved by wrapping overly long lines</p></li> +<ul> +<li><p>The formatting of differential equations in the summary was improved by wrapping overly long lines</p></li> <li><p>The FOCUS_Z vignette was rebuilt with the above improvement and using a width of 70 to avoid output outside of the grey area</p></li> <li><p><code><a href="../reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Avoid a warning that occurred when gmkin showed summaries ofinitial fits without iterations</p></li> <li><p><code><a href="../reference/mkinfit.html">mkinfit()</a></code>: Avoid a warning that occurred when summarising a fit that was performed with maxitmodFit = 0 as done in gmkin for configuring new fits.</p></li> -</ul></div> +</ul> +</div> </div> <div id="mkin-0-9-32-2014-07-24" class="section level1"> <h1 class="hasAnchor"> <a href="#mkin-0-9-32-2014-07-24" class="anchor"> </a>mkin 0.9-32 (2014-07-24)</h1> -<div id="new-features-3" class="section level2"> +<div id="new-features-4" class="section level2"> <h2 class="hasAnchor"> -<a href="#new-features-3" class="anchor"> </a>New features</h2> -<ul><li><p>The number of degrees of freedom is difficult to define in the case of ilr transformation of formation fractions. Now for each source compartment the number of ilr parameters (=number of optimised parameters) is divided by the number of pathways to metabolites (=number of affected data series) which leads to fractional degrees of freedom in some cases.</p></li> +<a href="#new-features-4" class="anchor"> </a>New features</h2> +<ul> +<li><p>The number of degrees of freedom is difficult to define in the case of ilr transformation of formation fractions. Now for each source compartment the number of ilr parameters (=number of optimised parameters) is divided by the number of pathways to metabolites (=number of affected data series) which leads to fractional degrees of freedom in some cases.</p></li> <li><p>The default for the initial value for the first state value is now taken from the mean of the observations at time zero, if available.</p></li> <li><p>The kinetic model can alternatively be specified with a shorthand name for parent only degradation models, e.g. <code>SFO</code>, or <code>DFOP</code>.</p></li> <li><p>Optimisation method, number of model evaluations and time elapsed during optimisation are given in the summary of mkinfit objects.</p></li> <li><p>The maximum number of iterations in the optimisation algorithm can be specified using the argument <code>maxit.modFit</code> to the mkinfit function.</p></li> <li><p>mkinfit gives a warning when the fit does not converge (does not apply to SANN method). This warning is included in the summary.</p></li> -</ul></div> +</ul> +</div> <div id="bug-fixes-8" class="section level2"> <h2 class="hasAnchor"> <a href="#bug-fixes-8" class="anchor"> </a>Bug fixes</h2> -<ul><li><p>Avoid plotting an artifical 0 residual at time zero in <code>mkinresplot</code></p></li> +<ul> +<li><p>Avoid plotting an artifical 0 residual at time zero in <code>mkinresplot</code></p></li> <li><p>In the determination of the degrees of freedom in <code>mkinerrmin</code>, formation fractions were accounted for multiple times in the case of parallel formation of metabolites. See the new feature described above for the solution.</p></li> <li><p><code>transform_rates=FALSE</code> in <code>mkinfit</code> now also works for FOMC and HS models.</p></li> <li><p>Initial values for formation fractions were not set in all cases.</p></li> <li><p>No warning was given when the fit did not converge when a method other than the default Levenberg-Marquardt method <code>Marq</code> was used.</p></li> -</ul></div> +</ul> +</div> <div id="minor-changes-8" class="section level2"> <h2 class="hasAnchor"> <a href="#minor-changes-8" class="anchor"> </a>Minor changes</h2> -<ul><li><p>Vignettes were rebuilt to reflect the changes in the summary method.</p></li> +<ul> +<li><p>Vignettes were rebuilt to reflect the changes in the summary method.</p></li> <li><p>Algorithm <code>Pseudo</code> was excluded because it needs user-defined parameter limits which are not supported.</p></li> <li><p>Algorithm <code>Newton</code> was excluded because of its different way to specify the maximum number of iterations and because it does not appear to provide additional benefits.</p></li> -</ul></div> +</ul> +</div> </div> <div id="mkin-0-9-31-2014-07-14" class="section level1"> <h1 class="hasAnchor"> @@ -355,52 +422,65 @@ <div id="bug-fixes-9" class="section level2"> <h2 class="hasAnchor"> <a href="#bug-fixes-9" class="anchor"> </a>Bug fixes</h2> -<ul><li>The internal renaming of optimised parameters in Version 0.9-30 led to errors in the determination of the degrees of freedom for the chi2 error level calulations in <code><a href="../reference/mkinerrmin.html">mkinerrmin()</a></code> used by the summary function.</li> -</ul></div> +<ul> +<li>The internal renaming of optimised parameters in Version 0.9-30 led to errors in the determination of the degrees of freedom for the chi2 error level calulations in <code><a href="../reference/mkinerrmin.html">mkinerrmin()</a></code> used by the summary function.</li> +</ul> +</div> </div> <div id="mkin-0-9-30-2014-07-11" class="section level1"> <h1 class="hasAnchor"> <a href="#mkin-0-9-30-2014-07-11" class="anchor"> </a>mkin 0.9-30 (2014-07-11)</h1> -<div id="new-features-4" class="section level2"> +<div id="new-features-5" class="section level2"> <h2 class="hasAnchor"> -<a href="#new-features-4" class="anchor"> </a>New features</h2> -<ul><li>It is now possible to use formation fractions in combination with turning off the sink in <code><a href="../reference/mkinmod.html">mkinmod()</a></code>.</li> -</ul></div> +<a href="#new-features-5" class="anchor"> </a>New features</h2> +<ul> +<li>It is now possible to use formation fractions in combination with turning off the sink in <code><a href="../reference/mkinmod.html">mkinmod()</a></code>.</li> +</ul> +</div> <div id="major-changes-5" class="section level2"> <h2 class="hasAnchor"> <a href="#major-changes-5" class="anchor"> </a>Major changes</h2> -<ul><li><p>The original and the transformed parameters now have different names (e.g. <code>k_parent</code> and <code>log_k_parent</code>. They also differ in how many they are when we have formation fractions but no pathway to sink.</p></li> +<ul> +<li><p>The original and the transformed parameters now have different names (e.g. <code>k_parent</code> and <code>log_k_parent</code>. They also differ in how many they are when we have formation fractions but no pathway to sink.</p></li> <li><p>The order of some of the information blocks in <code>print.summary.mkinfit.R()</code> has been ordered in a more logical way.</p></li> -</ul></div> +</ul> +</div> <div id="minor-changes-9" class="section level2"> <h2 class="hasAnchor"> <a href="#minor-changes-9" class="anchor"> </a>Minor changes</h2> -<ul><li><p>The vignette FOCUS_Z has been simplified to use formation fractions with turning off the sink, and slightly amended to use the new versions of DT50 values calculated since mkin 0.9-29.</p></li> +<ul> +<li><p>The vignette FOCUS_Z has been simplified to use formation fractions with turning off the sink, and slightly amended to use the new versions of DT50 values calculated since mkin 0.9-29.</p></li> <li><p>All vignettes have been rebuilt so they reflect all changes.</p></li> <li><p>The ChangeLog was renamed to NEWS.md and the entries were converted to markdown syntax compatible with the <code>tools::news()</code> function built into R.</p></li> <li><p>The test suite was overhauled. Tests of the DFOP and SFORB models with dataset FOCUS_2006_A were removed, as they were too much dependent on the optimisation algorithm and/or starting parameters, because the dataset is SFO (compare kinfit vignette).</p></li> <li><p>Also, the Schaefer complex case can now be fitted using formation fractions, and with the ‘Port’ optimisation method we also fit A2 in the same way as published in the Piacenza paper.</p></li> <li><p>Some more checks were introduced to <code><a href="../reference/mkinfit.html">mkinfit()</a></code>, leading to warnings or stopping execution if unsupported combinations of methods and parameters are requested.</p></li> -</ul></div> +</ul> +</div> </div> <div id="mkin-0-9-29-2014-06-27" class="section level1"> <h1 class="hasAnchor"> <a href="#mkin-0-9-29-2014-06-27" class="anchor"> </a>mkin 0.9-29 (2014-06-27)</h1> -<ul><li><p>R/mkinresplot.R: Make it possible to specify <code>xlim</code></p></li> +<ul> +<li><p>R/mkinresplot.R: Make it possible to specify <code>xlim</code></p></li> <li><p>R/geometric_mean.R, man/geometric_mean.Rd: Add geometric mean function</p></li> <li><p>R/endpoints.R, man/endpoints.Rd: Calculate additional (pseudo)-DT50 values for FOMC, DFOP, HS and SFORB. Avoid calculation of formation fractions from rate constants when they are directly fitted</p></li> -</ul></div> +</ul> +</div> <div id="mkin-0-9-28-2014-05-20" class="section level1"> <h1 class="hasAnchor"> <a href="#mkin-0-9-28-2014-05-20" class="anchor"> </a>mkin 0.9-28 (2014-05-20)</h1> -<ul><li><p>Do not backtransform confidence intervals for formation fractions if more than one compound is formed, as such parameters only define the pathways as a set</p></li> +<ul> +<li><p>Do not backtransform confidence intervals for formation fractions if more than one compound is formed, as such parameters only define the pathways as a set</p></li> <li><p>Add historical remarks and some background to the main package vignette</p></li> <li><p>Correct ‘isotropic’ into ‘isometric’ for the ilr transformation</p></li> -</ul></div> +</ul> +</div> <div id="mkin-0-9-27-2014-05-10" class="section level1"> <h1 class="hasAnchor"> <a href="#mkin-0-9-27-2014-05-10" class="anchor"> </a>mkin 0.9-27 (2014-05-10)</h1> -<ul><li><p>Fork the GUI into a separate package <a href="http://github.com/jranke/gmkin">gmkin</a></p></li> +<ul> +<li><p>Fork the GUI into a separate package <a href="http://github.com/jranke/gmkin">gmkin</a></p></li> <li><p>DESCRIPTION, NAMESPACE, TODO: Adapt and add copyright information</p></li> <li><p>Remove files belonging to the GUI</p></li> <li><p>Possibility to fit without parameter transformations, using bounds as implemented in FME</p></li> @@ -417,18 +497,22 @@ <li><p>Add a starter function for the GUI: <code>gmkin()</code></p></li> <li><p>Change the format of the workspace files of gmkin so they can be distributed and documented in the package</p></li> <li><p>Add gmkin workspace datasets FOCUS_2006_gmkin and FOCUS_2006_Z_gmkin</p></li> -</ul></div> +</ul> +</div> <div id="mkin-0-9-24-2013-11-06" class="section level1"> <h1 class="hasAnchor"> <a href="#mkin-0-9-24-2013-11-06" class="anchor"> </a>mkin 0.9-24 (2013-11-06)</h1> -<ul><li><p>Bugfix re-enabling the fixing of any combination of initial values for state variables</p></li> +<ul> +<li><p>Bugfix re-enabling the fixing of any combination of initial values for state variables</p></li> <li><p>Default values for kinetic rate constants are not all 0.1 any more but are “salted” with a small increment to avoid numeric artefacts with the eigenvalue based solutions</p></li> <li><p>Backtransform fixed ODE parameters for the summary</p></li> -</ul></div> +</ul> +</div> <div id="mkin-0-9-22-2013-10-26" class="section level1"> <h1 class="hasAnchor"> <a href="#mkin-0-9-22-2013-10-26" class="anchor"> </a>mkin 0.9-22 (2013-10-26)</h1> -<ul><li><p>Get rid of the optimisation step in <code>mkinerrmin</code> - this was unnecessary. Thanks to KinGUII for the inspiration - actually this is equation 6-2 in FOCUS kinetics p. 91 that I had overlooked originally</p></li> +<ul> +<li><p>Get rid of the optimisation step in <code>mkinerrmin</code> - this was unnecessary. Thanks to KinGUII for the inspiration - actually this is equation 6-2 in FOCUS kinetics p. 91 that I had overlooked originally</p></li> <li><p>Fix <code>plot.mkinfit</code> as it passed graphical arguments like main to the solver</p></li> <li><p>Do not use <code>plot=TRUE</code> in <code><a href="../reference/mkinfit.html">mkinfit()</a></code> example</p></li> <li><p>The first successful fits in the not so simple GUI</p></li> @@ -439,7 +523,8 @@ <li><p>Correct the output of the data in the case of manual weighting</p></li> <li><p>Implement IRLS assuming different variances for observed variables</p></li> <li><p>Do not use 0 values at time zero for chi2 error level calculations. This is the way it is done in KinGUII and it makes sense. It does impact the chi2 error levels in the output. Generally they seem to be lower for metabolites now, presumably because the mean of the observed values is higher</p></li> -</ul><p>For a detailed list of changes to the mkin source please consult the commit history on <a href="http://github.com/jranke/mkin" class="uri">http://github.com/jranke/mkin</a></p> +</ul> +<p>For a detailed list of changes to the mkin source please consult the commit history on <a href="http://github.com/jranke/mkin" class="uri">http://github.com/jranke/mkin</a></p> </div> </div> </div> @@ -448,6 +533,7 @@ <div id="tocnav"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> + <li><a href="#mkin-0-9-45-1-2016-12-20">0.9.45.1</a></li> <li><a href="#mkin-0-9-45-2016-12-08">0.9.45</a></li> <li><a href="#mkin-0-9-44-2016-06-29">0.9.44</a></li> <li><a href="#mkin-0-9-43-2016-06-28">0.9.43</a></li> 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> |