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diff --git a/docs/reference/index.html b/docs/reference/index.html index d4a1b253..63e1e634 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,662 +1,735 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><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, shrink-to-fit=no"><title>Function reference • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function reference"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></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> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><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, shrink-to-fit=no"><title>Package index • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Package index"></head><body> <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - - <nav class="navbar fixed-top navbar-default navbar-expand-lg bg-light"><div class="container"> - + + <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="default" aria-label="Site navigation"><div class="container"> + <a class="navbar-brand me-2" href="../index.html">mkin</a> - <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.6</small> + <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.9</small> + - <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> <span class="navbar-toggler-icon"></span> </button> <div id="navbar" class="collapse navbar-collapse ms-3"> - <ul class="navbar-nav me-auto"><li class="active nav-item"> - <a class="nav-link" href="../reference/index.html">Reference</a> -</li> + <ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li> <li class="nav-item dropdown"> - 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<span class="fab fa fab fa-github fa-lg"></span> - - </a> -</li> + <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button> + <ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/mkin.html">Introduction to mkin</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with (generalised) nonlinear least squares</h6></li> + <li><a class="dropdown-item" href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></li> + <li><a class="dropdown-item" href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li> + <li><a class="dropdown-item" href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6></li> + <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li> + <li><a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li> + <li><a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li> + <li><a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li> + <li><a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Performance</h6></li> + <li><a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li> + <li><a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a></li> + <li><a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a></li> + <li><hr class="dropdown-divider"></li> + <li><h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6></li> + <li><a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a></li> + <li><a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a></li> + </ul></li> +<li class="nav-item"><a class="nav-link" href="../coverage/coverage.html">Test coverage</a></li> +<li class="nav-item"><a class="nav-link" href="../news/index.html">News</a></li> + </ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search"> + <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li> +<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li> </ul></div> - + </div> </nav><div class="container template-reference-index"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Function reference</h1> + + <h1>Package index</h1> </div> <div class="section level2"> <h2 id="main-functions">Main functions<a class="anchor" aria-label="anchor" href="#main-functions"></a></h2> - - <p class="section-desc"></p><p>Essential functionality</p> - - </div><div id="" class="section level2"> - - - + <div class="section-desc"><p>Essential functionality</p></div> + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="mkinmod.html">mkinmod()</a></code> <code><a href="mkinmod.html">print(<i><mkinmod></i>)</a></code> <code><a href="mkinmod.html">mkinsub()</a></code> + + <code><a href="mkinmod.html">mkinmod()</a></code> <code><a href="mkinmod.html">print(<i><mkinmod></i>)</a></code> <code><a href="mkinmod.html">mkinsub()</a></code> + </dt> <dd>Function to set up a kinetic model with one or more state variables</dd> </dl><dl><dt> - - <code><a href="mkinfit.html">mkinfit()</a></code> + + <code><a href="mkinfit.html">mkinfit()</a></code> + </dt> <dd>Fit a kinetic model to data with one or more state variables</dd> </dl><dl><dt> - - <code><a href="mmkin.html">mmkin()</a></code> <code><a href="mmkin.html">print(<i><mmkin></i>)</a></code> + + <code><a href="mmkin.html">mmkin()</a></code> <code><a href="mmkin.html">print(<i><mmkin></i>)</a></code> + </dt> - <dd>Fit one or more kinetic models with one or more state variables to one or -more datasets</dd> + <dd>Fit one or more kinetic models with one or more state variables to one or more datasets</dd> </dl><dl><dt> - - <code><a href="mhmkin.html">mhmkin()</a></code> <code><a href="mhmkin.html">`[`(<i><mhmkin></i>)</a></code> <code><a href="mhmkin.html">print(<i><mhmkin></i>)</a></code> + + <code><a href="mhmkin.html">mhmkin()</a></code> <code><a href="mhmkin.html">`[`(<i><mhmkin></i>)</a></code> <code><a href="mhmkin.html">print(<i><mhmkin></i>)</a></code> + </dt> - <dd>Fit nonlinear mixed-effects models built from one or more kinetic -degradation models and one or more error models</dd> + <dd>Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models</dd> </dl></div><div class="section level2"> <h2 id="generics">Generics<a class="anchor" aria-label="anchor" href="#generics"></a></h2> - - <p class="section-desc"></p><p>Generic functions introduced by the package</p> - - </div><div id="" class="section level2"> - - - + <div class="section-desc"><p>Generic functions introduced by the package</p></div> + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="parms.html">parms()</a></code> + + <code><a href="parms.html">parms()</a></code> + </dt> <dd>Extract model parameters</dd> </dl><dl><dt> - - <code><a href="status.html">status()</a></code> <code><a href="status.html">print(<i><status.mmkin></i>)</a></code> <code><a href="status.html">print(<i><status.mhmkin></i>)</a></code> + + <code><a href="status.html">status()</a></code> <code><a href="status.html">print(<i><status.mmkin></i>)</a></code> <code><a href="status.html">print(<i><status.mhmkin></i>)</a></code> + </dt> <dd>Method to get status information for fit array objects</dd> </dl><dl><dt> - - <code><a href="illparms.html">illparms()</a></code> <code><a href="illparms.html">print(<i><illparms.mkinfit></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.mmkin></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.saem.mmkin></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.mhmkin></i>)</a></code> + + <code><a href="illparms.html">illparms()</a></code> <code><a href="illparms.html">print(<i><illparms.mkinfit></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.mmkin></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.saem.mmkin></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.mhmkin></i>)</a></code> + </dt> <dd>Method to get the names of ill-defined parameters</dd> </dl><dl><dt> - - <code><a href="endpoints.html">endpoints()</a></code> + + <code><a href="endpoints.html">endpoints()</a></code> + </dt> - <dd>Function to calculate endpoints for further use from kinetic models fitted -with mkinfit</dd> + <dd>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</dd> </dl><dl><dt> - - <code><a href="aw.html">aw()</a></code> + + <code><a href="aw.html">aw()</a></code> + </dt> <dd>Calculate Akaike weights for model averaging</dd> </dl></div><div class="section level2"> <h2 id="show-results">Show results<a class="anchor" aria-label="anchor" href="#show-results"></a></h2> - - <p class="section-desc"></p><p>Functions working with mkinfit objects</p> - - </div><div id="" class="section level2"> - - - + <div class="section-desc"><p>Functions working with mkinfit objects</p></div> + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="plot.mkinfit.html">plot(<i><mkinfit></i>)</a></code> <code><a href="plot.mkinfit.html">plot_sep()</a></code> <code><a href="plot.mkinfit.html">plot_res()</a></code> <code><a href="plot.mkinfit.html">plot_err()</a></code> + + <code><a href="plot.mkinfit.html">plot(<i><mkinfit></i>)</a></code> <code><a href="plot.mkinfit.html">plot_sep()</a></code> <code><a href="plot.mkinfit.html">plot_res()</a></code> <code><a href="plot.mkinfit.html">plot_err()</a></code> + </dt> <dd>Plot the observed data and the fitted model of an mkinfit object</dd> </dl><dl><dt> - - <code><a href="summary.mkinfit.html">summary(<i><mkinfit></i>)</a></code> <code><a href="summary.mkinfit.html">print(<i><summary.mkinfit></i>)</a></code> + + <code><a href="summary.mkinfit.html">summary(<i><mkinfit></i>)</a></code> <code><a href="summary.mkinfit.html">print(<i><summary.mkinfit></i>)</a></code> + </dt> <dd>Summary method for class "mkinfit"</dd> </dl><dl><dt> - - <code><a href="confint.mkinfit.html">confint(<i><mkinfit></i>)</a></code> + + <code><a href="confint.mkinfit.html">confint(<i><mkinfit></i>)</a></code> + </dt> <dd>Confidence intervals for parameters of mkinfit objects</dd> </dl><dl><dt> - - <code><a href="update.mkinfit.html">update(<i><mkinfit></i>)</a></code> + + <code><a href="update.mkinfit.html">update(<i><mkinfit></i>)</a></code> + </dt> <dd>Update an mkinfit model with different arguments</dd> </dl><dl><dt> - - <code><a href="lrtest.mkinfit.html">lrtest(<i><mkinfit></i>)</a></code> <code><a href="lrtest.mkinfit.html">lrtest(<i><mmkin></i>)</a></code> + + <code><a href="lrtest.mkinfit.html">lrtest(<i><mkinfit></i>)</a></code> <code><a href="lrtest.mkinfit.html">lrtest(<i><mmkin></i>)</a></code> + </dt> <dd>Likelihood ratio test for mkinfit models</dd> </dl><dl><dt> - - <code><a href="loftest.html">loftest()</a></code> + + <code><a href="loftest.html">loftest()</a></code> + </dt> <dd>Lack-of-fit test for models fitted to data with replicates</dd> </dl><dl><dt> - - <code><a href="mkinerrmin.html">mkinerrmin()</a></code> + + <code><a href="mkinerrmin.html">mkinerrmin()</a></code> + </dt> <dd>Calculate the minimum error to assume in order to pass the variance test</dd> </dl><dl><dt> - - <code><a href="CAKE_export.html">CAKE_export()</a></code> + + <code><a href="CAKE_export.html">CAKE_export()</a></code> + </dt> <dd>Export a list of datasets format to a CAKE study file</dd> </dl></div><div class="section level2"> <h2 id="work-with-mmkin-objects">Work with mmkin objects<a class="anchor" aria-label="anchor" href="#work-with-mmkin-objects"></a></h2> - - <p class="section-desc"></p><p>Functions working with aggregated results</p> - - </div><div id="" class="section level2"> - - - + <div class="section-desc"><p>Functions working with aggregated results</p></div> + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="Extract.mmkin.html">`[`(<i><mmkin></i>)</a></code> + + <code><a href="Extract.mmkin.html">`[`(<i><mmkin></i>)</a></code> + </dt> <dd>Subsetting method for mmkin objects</dd> </dl><dl><dt> - - <code><a href="plot.mmkin.html">plot(<i><mmkin></i>)</a></code> + + <code><a href="plot.mmkin.html">plot(<i><mmkin></i>)</a></code> + </dt> - <dd>Plot model fits (observed and fitted) and the residuals for a row or column -of an mmkin object</dd> + <dd>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</dd> </dl><dl><dt> - - <code><a href="AIC.mmkin.html">AIC(<i><mmkin></i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i><mmkin></i>)</a></code> + + <code><a href="AIC.mmkin.html">AIC(<i><mmkin></i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i><mmkin></i>)</a></code> + </dt> <dd>Calculate the AIC for a column of an mmkin object</dd> </dl><dl><dt> - - <code><a href="summary.mmkin.html">summary(<i><mmkin></i>)</a></code> <code><a href="summary.mmkin.html">print(<i><summary.mmkin></i>)</a></code> + + <code><a href="summary.mmkin.html">summary(<i><mmkin></i>)</a></code> <code><a href="summary.mmkin.html">print(<i><summary.mmkin></i>)</a></code> + </dt> <dd>Summary method for class "mmkin"</dd> </dl></div><div class="section level2"> <h2 id="mixed-models">Mixed models<a class="anchor" aria-label="anchor" href="#mixed-models"></a></h2> - - <p class="section-desc"></p><p>Create and work with nonlinear hierarchical models</p> - - </div><div id="" class="section level2"> - - - + <div class="section-desc"><p>Create and work with nonlinear hierarchical models</p></div> + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="hierarchical_kinetics.html">hierarchical_kinetics()</a></code> + + <code><a href="hierarchical_kinetics.html">hierarchical_kinetics()</a></code> + </dt> <dd>Hierarchical kinetics template</dd> </dl><dl><dt> - - <code><a href="read_spreadsheet.html">read_spreadsheet()</a></code> + + <code><a href="read_spreadsheet.html">read_spreadsheet()</a></code> + </dt> <dd>Read datasets and relevant meta information from a spreadsheet file</dd> </dl><dl><dt> - - <code><a href="nlme.mmkin.html">nlme(<i><mmkin></i>)</a></code> <code><a href="nlme.mmkin.html">print(<i><nlme.mmkin></i>)</a></code> <code><a href="nlme.mmkin.html">update(<i><nlme.mmkin></i>)</a></code> + + <code><a href="nlme.mmkin.html">nlme(<i><mmkin></i>)</a></code> <code><a href="nlme.mmkin.html">print(<i><nlme.mmkin></i>)</a></code> <code><a href="nlme.mmkin.html">update(<i><nlme.mmkin></i>)</a></code> + </dt> <dd>Create an nlme model for an mmkin row object</dd> </dl><dl><dt> - - <code><a href="saem.html">saem()</a></code> <code><a href="saem.html">print(<i><saem.mmkin></i>)</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> + + <code><a href="saem.html">saem()</a></code> <code><a href="saem.html">print(<i><saem.mmkin></i>)</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> + </dt> <dd>Fit nonlinear mixed models with SAEM</dd> </dl><dl><dt> - - <code><a href="mhmkin.html">mhmkin()</a></code> <code><a href="mhmkin.html">`[`(<i><mhmkin></i>)</a></code> <code><a href="mhmkin.html">print(<i><mhmkin></i>)</a></code> + + <code><a href="mhmkin.html">mhmkin()</a></code> <code><a href="mhmkin.html">`[`(<i><mhmkin></i>)</a></code> <code><a href="mhmkin.html">print(<i><mhmkin></i>)</a></code> + </dt> - <dd>Fit nonlinear mixed-effects models built from one or more kinetic -degradation models and one or more error models</dd> + <dd>Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models</dd> </dl><dl><dt> - - <code><a href="plot.mixed.mmkin.html">plot(<i><mixed.mmkin></i>)</a></code> + + <code><a href="plot.mixed.mmkin.html">plot(<i><mixed.mmkin></i>)</a></code> + </dt> <dd>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</dd> </dl><dl><dt> - - <code><a href="summary.nlme.mmkin.html">summary(<i><nlme.mmkin></i>)</a></code> <code><a href="summary.nlme.mmkin.html">print(<i><summary.nlme.mmkin></i>)</a></code> + + <code><a href="summary.nlme.mmkin.html">summary(<i><nlme.mmkin></i>)</a></code> <code><a href="summary.nlme.mmkin.html">print(<i><summary.nlme.mmkin></i>)</a></code> + </dt> <dd>Summary method for class "nlme.mmkin"</dd> </dl><dl><dt> - - <code><a href="summary.saem.mmkin.html">summary(<i><saem.mmkin></i>)</a></code> <code><a href="summary.saem.mmkin.html">print(<i><summary.saem.mmkin></i>)</a></code> + + <code><a href="summary.saem.mmkin.html">summary(<i><saem.mmkin></i>)</a></code> <code><a href="summary.saem.mmkin.html">print(<i><summary.saem.mmkin></i>)</a></code> + </dt> <dd>Summary method for class "saem.mmkin"</dd> </dl><dl><dt> - - <code><a href="anova.saem.mmkin.html">anova(<i><saem.mmkin></i>)</a></code> + + <code><a href="anova.saem.mmkin.html">anova(<i><saem.mmkin></i>)</a></code> + </dt> <dd>Anova method for saem.mmkin objects</dd> </dl><dl><dt> - - <code><a href="logLik.saem.mmkin.html">logLik(<i><saem.mmkin></i>)</a></code> + + <code><a href="logLik.saem.mmkin.html">logLik(<i><saem.mmkin></i>)</a></code> + </dt> <dd>logLik method for saem.mmkin objects</dd> </dl><dl><dt> - - <code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">nlme_data()</a></code> + + <code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">nlme_data()</a></code> + </dt> <dd>Helper functions to create nlme models from mmkin row objects</dd> </dl><dl><dt> - - <code><a href="get_deg_func.html">get_deg_func()</a></code> + + <code><a href="get_deg_func.html">get_deg_func()</a></code> + </dt> <dd>Retrieve a degradation function from the mmkin namespace</dd> </dl><dl><dt> - - <code><a href="mixed.html">mixed()</a></code> <code><a href="mixed.html">print(<i><mixed.mmkin></i>)</a></code> + + <code><a href="mixed.html">mixed()</a></code> <code><a href="mixed.html">print(<i><mixed.mmkin></i>)</a></code> + </dt> <dd>Create a mixed effects model from an mmkin row object</dd> </dl><dl><dt> - - <code><a href="reexports.html">reexports</a></code> <code><a href="reexports.html">intervals</a></code> <code><a href="reexports.html">lrtest</a></code> <code><a href="reexports.html">nlme</a></code> + + <code><a href="reexports.html">reexports</a></code> <code><a href="reexports.html">intervals</a></code> <code><a href="reexports.html">lrtest</a></code> <code><a href="reexports.html">nlme</a></code> + </dt> <dd>Objects exported from other packages</dd> </dl><dl><dt> - - <code><a href="intervals.saem.mmkin.html">intervals(<i><saem.mmkin></i>)</a></code> + + <code><a href="intervals.saem.mmkin.html">intervals(<i><saem.mmkin></i>)</a></code> + </dt> <dd>Confidence intervals for parameters in saem.mmkin objects</dd> </dl><dl><dt> - - <code><a href="multistart.html">multistart()</a></code> <code><a href="multistart.html">print(<i><multistart></i>)</a></code> <code><a href="multistart.html">best()</a></code> <code><a href="multistart.html">which.best()</a></code> + + <code><a href="multistart.html">multistart()</a></code> <code><a href="multistart.html">print(<i><multistart></i>)</a></code> <code><a href="multistart.html">best()</a></code> <code><a href="multistart.html">which.best()</a></code> + </dt> <dd>Perform a hierarchical model fit with multiple starting values</dd> </dl><dl><dt> - - <code><a href="llhist.html">llhist()</a></code> + + <code><a href="llhist.html">llhist()</a></code> + </dt> <dd>Plot the distribution of log likelihoods from multistart objects</dd> </dl><dl><dt> - - <code><a href="parplot.html">parplot()</a></code> + + <code><a href="parplot.html">parplot()</a></code> + </dt> <dd>Plot parameter variability of multistart objects</dd> + </dl><dl><dt> + + <code><a href="check_failed.html">check_failed()</a></code> + + </dt> + <dd>Check if fit within an mhmkin object failed</dd> </dl></div><div class="section level2"> <h2 id="datasets-and-known-results">Datasets and known results<a class="anchor" aria-label="anchor" href="#datasets-and-known-results"></a></h2> - - - - </div><div id="" class="section level2"> - - - + + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="ds_mixed.html">ds_mixed</a></code> <code><a href="ds_mixed.html">ds_sfo</a></code> <code><a href="ds_mixed.html">ds_fomc</a></code> <code><a href="ds_mixed.html">ds_dfop</a></code> <code><a href="ds_mixed.html">ds_hs</a></code> <code><a href="ds_mixed.html">ds_dfop_sfo</a></code> + + <code><a href="ds_mixed.html">ds_mixed</a></code> <code><a href="ds_mixed.html">ds_sfo</a></code> <code><a href="ds_mixed.html">ds_fomc</a></code> <code><a href="ds_mixed.html">ds_dfop</a></code> <code><a href="ds_mixed.html">ds_hs</a></code> <code><a href="ds_mixed.html">ds_dfop_sfo</a></code> + </dt> <dd>Synthetic data for hierarchical kinetic degradation models</dd> </dl><dl><dt> - - <code><a href="D24_2014.html">D24_2014</a></code> + + <code><a href="D24_2014.html">D24_2014</a></code> + </dt> <dd>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014</dd> </dl><dl><dt> - - <code><a href="dimethenamid_2018.html">dimethenamid_2018</a></code> + + <code><a href="dimethenamid_2018.html">dimethenamid_2018</a></code> + </dt> <dd>Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018</dd> </dl><dl><dt> - - <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_A</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_B</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_C</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_D</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_E</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_F</a></code> + + <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_A</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_B</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_C</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_D</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_E</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_F</a></code> + </dt> <dd>Datasets A to F from the FOCUS Kinetics report from 2006</dd> </dl><dl><dt> - - <code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code> + + <code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code> + </dt> <dd>Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</dd> </dl><dl><dt> - - <code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">FOCUS_2006_FOMC_ref_A_to_F</a></code> + + <code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">FOCUS_2006_FOMC_ref_A_to_F</a></code> + </dt> <dd>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</dd> </dl><dl><dt> - - <code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code> + + <code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code> + </dt> <dd>Results of fitting the HS model to Datasets A to F of FOCUS (2006)</dd> </dl><dl><dt> - - <code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code> + + <code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code> + </dt> <dd>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</dd> </dl><dl><dt> - - <code><a href="NAFTA_SOP_2015.html">NAFTA_SOP_Appendix_B</a></code> <code><a href="NAFTA_SOP_2015.html">NAFTA_SOP_Appendix_D</a></code> + + <code><a href="NAFTA_SOP_2015.html">NAFTA_SOP_Appendix_B</a></code> <code><a href="NAFTA_SOP_2015.html">NAFTA_SOP_Appendix_D</a></code> + </dt> <dd>Example datasets from the NAFTA SOP published 2015</dd> </dl><dl><dt> - - <code><a href="NAFTA_SOP_Attachment.html">NAFTA_SOP_Attachment</a></code> + + <code><a href="NAFTA_SOP_Attachment.html">NAFTA_SOP_Attachment</a></code> + </dt> <dd>Example datasets from Attachment 1 to the NAFTA SOP published 2015</dd> </dl><dl><dt> - - <code><a href="mccall81_245T.html">mccall81_245T</a></code> + + <code><a href="mccall81_245T.html">mccall81_245T</a></code> + </dt> <dd>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</dd> </dl><dl><dt> - - <code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code> + + <code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code> + </dt> <dd>Metabolism data set used for checking the software quality of KinGUI</dd> </dl><dl><dt> - - <code><a href="synthetic_data_for_UBA_2014.html">synthetic_data_for_UBA_2014</a></code> + + <code><a href="synthetic_data_for_UBA_2014.html">synthetic_data_for_UBA_2014</a></code> + </dt> <dd>Synthetic datasets for one parent compound with two metabolites</dd> </dl><dl><dt> - - <code><a href="experimental_data_for_UBA.html">experimental_data_for_UBA_2019</a></code> + + <code><a href="experimental_data_for_UBA.html">experimental_data_for_UBA_2019</a></code> + </dt> <dd>Experimental datasets used for development and testing of error models</dd> </dl><dl><dt> - - <code><a href="test_data_from_UBA_2014.html">test_data_from_UBA_2014</a></code> + + <code><a href="test_data_from_UBA_2014.html">test_data_from_UBA_2014</a></code> + </dt> <dd>Three experimental datasets from two water sediment systems and one soil</dd> </dl><dl><dt> - - <code><a href="focus_soil_moisture.html">focus_soil_moisture</a></code> + + <code><a href="focus_soil_moisture.html">focus_soil_moisture</a></code> + </dt> <dd>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar</dd> </dl><dl><dt> - - <code><a href="mkinds.html">print(<i><mkinds></i>)</a></code> + + <code><a href="mkinds.html">print(<i><mkinds></i>)</a></code> + </dt> <dd>A dataset class for mkin</dd> </dl><dl><dt> - - <code><a href="mkindsg.html">print(<i><mkindsg></i>)</a></code> + + <code><a href="mkindsg.html">print(<i><mkindsg></i>)</a></code> + </dt> <dd>A class for dataset groups for mkin</dd> </dl></div><div class="section level2"> <h2 id="nafta-guidance">NAFTA guidance<a class="anchor" aria-label="anchor" href="#nafta-guidance"></a></h2> - - - - </div><div id="" class="section level2"> - - - + + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="nafta.html">nafta()</a></code> <code><a href="nafta.html">print(<i><nafta></i>)</a></code> + + <code><a href="nafta.html">nafta()</a></code> <code><a href="nafta.html">print(<i><nafta></i>)</a></code> + </dt> <dd>Evaluate parent kinetics using the NAFTA guidance</dd> </dl><dl><dt> - - <code><a href="plot.nafta.html">plot(<i><nafta></i>)</a></code> + + <code><a href="plot.nafta.html">plot(<i><nafta></i>)</a></code> + </dt> <dd>Plot the results of the three models used in the NAFTA scheme.</dd> </dl></div><div class="section level2"> <h2 id="utility-functions">Utility functions<a class="anchor" aria-label="anchor" href="#utility-functions"></a></h2> - - - - </div><div id="" class="section level2"> - - - + + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="summary_listing.html">summary_listing()</a></code> <code><a href="summary_listing.html">tex_listing()</a></code> <code><a href="summary_listing.html">html_listing()</a></code> + + <code><a href="summary_listing.html">summary_listing()</a></code> <code><a href="summary_listing.html">tex_listing()</a></code> <code><a href="summary_listing.html">html_listing()</a></code> + </dt> <dd>Display the output of a summary function according to the output format</dd> </dl><dl><dt> - - <code><a href="f_time_norm_focus.html">f_time_norm_focus()</a></code> + + <code><a href="f_time_norm_focus.html">f_time_norm_focus()</a></code> + </dt> <dd>Normalisation factors for aerobic soil degradation according to FOCUS guidance</dd> </dl><dl><dt> - - <code><a href="set_nd_nq.html">set_nd_nq()</a></code> <code><a href="set_nd_nq.html">set_nd_nq_focus()</a></code> + + <code><a href="set_nd_nq.html">set_nd_nq()</a></code> <code><a href="set_nd_nq.html">set_nd_nq_focus()</a></code> + </dt> <dd>Set non-detects and unquantified values in residue series without replicates</dd> </dl><dl><dt> - - <code><a href="max_twa_parent.html">max_twa_parent()</a></code> <code><a href="max_twa_parent.html">max_twa_sfo()</a></code> <code><a href="max_twa_parent.html">max_twa_fomc()</a></code> <code><a href="max_twa_parent.html">max_twa_dfop()</a></code> <code><a href="max_twa_parent.html">max_twa_hs()</a></code> + + <code><a href="max_twa_parent.html">max_twa_parent()</a></code> <code><a href="max_twa_parent.html">max_twa_sfo()</a></code> <code><a href="max_twa_parent.html">max_twa_fomc()</a></code> <code><a href="max_twa_parent.html">max_twa_dfop()</a></code> <code><a href="max_twa_parent.html">max_twa_hs()</a></code> + </dt> - <dd>Function to calculate maximum time weighted average concentrations from -kinetic models fitted with mkinfit</dd> + <dd>Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit</dd> </dl><dl><dt> - - <code><a href="mkin_wide_to_long.html">mkin_wide_to_long()</a></code> + + <code><a href="mkin_wide_to_long.html">mkin_wide_to_long()</a></code> + </dt> <dd>Convert a dataframe with observations over time into long format</dd> </dl><dl><dt> - - <code><a href="mkin_long_to_wide.html">mkin_long_to_wide()</a></code> + + <code><a href="mkin_long_to_wide.html">mkin_long_to_wide()</a></code> + </dt> <dd>Convert a dataframe from long to wide format</dd> </dl></div><div class="section level2"> <h2 id="helper-functions-mainly-used-internally">Helper functions mainly used internally<a class="anchor" aria-label="anchor" href="#helper-functions-mainly-used-internally"></a></h2> - - - - </div><div id="" class="section level2"> - - - + + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="mkinpredict.html">mkinpredict()</a></code> + + <code><a href="mkinpredict.html">mkinpredict()</a></code> + </dt> <dd>Produce predictions from a kinetic model using specific parameters</dd> </dl><dl><dt> - - <code><a href="transform_odeparms.html">transform_odeparms()</a></code> <code><a href="transform_odeparms.html">backtransform_odeparms()</a></code> + + <code><a href="transform_odeparms.html">transform_odeparms()</a></code> <code><a href="transform_odeparms.html">backtransform_odeparms()</a></code> + </dt> <dd>Functions to transform and backtransform kinetic parameters for fitting</dd> </dl><dl><dt> - - <code><a href="ilr.html">ilr()</a></code> <code><a href="ilr.html">invilr()</a></code> + + <code><a href="ilr.html">ilr()</a></code> <code><a href="ilr.html">invilr()</a></code> + </dt> <dd>Function to perform isometric log-ratio transformation</dd> </dl><dl><dt> - - <code><a href="logLik.mkinfit.html">logLik(<i><mkinfit></i>)</a></code> + + <code><a href="logLik.mkinfit.html">logLik(<i><mkinfit></i>)</a></code> + </dt> <dd>Calculated the log-likelihood of a fitted mkinfit object</dd> </dl><dl><dt> - - <code><a href="residuals.mkinfit.html">residuals(<i><mkinfit></i>)</a></code> + + <code><a href="residuals.mkinfit.html">residuals(<i><mkinfit></i>)</a></code> + </dt> <dd>Extract residuals from an mkinfit model</dd> </dl><dl><dt> - - <code><a href="nobs.mkinfit.html">nobs(<i><mkinfit></i>)</a></code> + + <code><a href="nobs.mkinfit.html">nobs(<i><mkinfit></i>)</a></code> + </dt> <dd>Number of observations on which an mkinfit object was fitted</dd> </dl><dl><dt> - - <code><a href="mkinresplot.html">mkinresplot()</a></code> + + <code><a href="mkinresplot.html">mkinresplot()</a></code> + </dt> <dd>Function to plot residuals stored in an mkin object</dd> </dl><dl><dt> - - <code><a href="mkinparplot.html">mkinparplot()</a></code> + + <code><a href="mkinparplot.html">mkinparplot()</a></code> + </dt> <dd>Function to plot the confidence intervals obtained using mkinfit</dd> </dl><dl><dt> - - <code><a href="mkinerrplot.html">mkinerrplot()</a></code> + + <code><a href="mkinerrplot.html">mkinerrplot()</a></code> + </dt> <dd>Function to plot squared residuals and the error model for an mkin object</dd> </dl><dl><dt> - - <code><a href="mean_degparms.html">mean_degparms()</a></code> + + <code><a href="mean_degparms.html">mean_degparms()</a></code> + </dt> <dd>Calculate mean degradation parameters for an mmkin row object</dd> </dl><dl><dt> - - <code><a href="create_deg_func.html">create_deg_func()</a></code> + + <code><a href="create_deg_func.html">create_deg_func()</a></code> + </dt> <dd>Create degradation functions for known analytical solutions</dd> </dl></div><div class="section level2"> <h2 id="analytical-solutions">Analytical solutions<a class="anchor" aria-label="anchor" href="#analytical-solutions"></a></h2> - - <p class="section-desc"></p><p>Parent only model solutions</p> - - </div><div id="" class="section level2"> - - - + <div class="section-desc"><p>Parent only model solutions</p></div> + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="SFO.solution.html">SFO.solution()</a></code> + + <code><a href="SFO.solution.html">SFO.solution()</a></code> + </dt> <dd>Single First-Order kinetics</dd> </dl><dl><dt> - - <code><a href="FOMC.solution.html">FOMC.solution()</a></code> + + <code><a href="FOMC.solution.html">FOMC.solution()</a></code> + </dt> <dd>First-Order Multi-Compartment kinetics</dd> </dl><dl><dt> - - <code><a href="DFOP.solution.html">DFOP.solution()</a></code> + + <code><a href="DFOP.solution.html">DFOP.solution()</a></code> + </dt> <dd>Double First-Order in Parallel kinetics</dd> </dl><dl><dt> - - <code><a href="SFORB.solution.html">SFORB.solution()</a></code> + + <code><a href="SFORB.solution.html">SFORB.solution()</a></code> + </dt> <dd>Single First-Order Reversible Binding kinetics</dd> </dl><dl><dt> - - <code><a href="HS.solution.html">HS.solution()</a></code> + + <code><a href="HS.solution.html">HS.solution()</a></code> + </dt> <dd>Hockey-Stick kinetics</dd> </dl><dl><dt> - - <code><a href="IORE.solution.html">IORE.solution()</a></code> + + <code><a href="IORE.solution.html">IORE.solution()</a></code> + </dt> <dd>Indeterminate order rate equation kinetics</dd> </dl><dl><dt> - - <code><a href="logistic.solution.html">logistic.solution()</a></code> + + <code><a href="logistic.solution.html">logistic.solution()</a></code> + </dt> <dd>Logistic kinetics</dd> </dl></div><div class="section level2"> <h2 id="generate-synthetic-datasets">Generate synthetic datasets<a class="anchor" aria-label="anchor" href="#generate-synthetic-datasets"></a></h2> - - - - </div><div id="" class="section level2"> - - - + + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="add_err.html">add_err()</a></code> + + <code><a href="add_err.html">add_err()</a></code> + </dt> <dd>Add normally distributed errors to simulated kinetic degradation data</dd> </dl><dl><dt> - - <code><a href="sigma_twocomp.html">sigma_twocomp()</a></code> + + <code><a href="sigma_twocomp.html">sigma_twocomp()</a></code> + </dt> <dd>Two-component error model</dd> </dl></div><div class="section level2"> <h2 id="deprecated-functions">Deprecated functions<a class="anchor" aria-label="anchor" href="#deprecated-functions"></a></h2> - - <p class="section-desc"></p><p>Functions that have been superseded</p> - - </div><div id="" class="section level2"> - - - + <div class="section-desc"><p>Functions that have been superseded</p></div> + + + </div><div class="section level2"> + + + <dl><dt> - - <code><a href="mkinplot.html">mkinplot()</a></code> + + <code><a href="mkinplot.html">mkinplot()</a></code> + </dt> <dd>Plot the observed data and the fitted model of an mkinfit object</dd> </dl></div> - </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2> </nav></aside></div> <footer><div class="pkgdown-footer-left"> - 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