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Diffstat (limited to 'docs/reference')
89 files changed, 1219 insertions, 1356 deletions
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+ <meta http-equiv="refresh" content="0;URL=https://pkgdown.jrwb.de/mkin/reference/multistart.html" /> + <meta name="robots" content="noindex"> + <link rel="canonical" href="https://pkgdown.jrwb.de/mkin/reference/multistart.html"> + </head> +</html> + diff --git a/docs/reference/check_failed.html b/docs/reference/check_failed.html new file mode 100644 index 00000000..516e4967 --- /dev/null +++ b/docs/reference/check_failed.html @@ -0,0 +1,100 @@ +<!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>Check if fit within an mhmkin object failed — check_failed • 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, 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</ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + + <h1>Check if fit within an mhmkin object failed</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mhmkin.R" class="external-link"><code>R/mhmkin.R</code></a></small> + <div class="d-none name"><code>check_failed.Rd</code></div> + </div> + + <div class="ref-description section level2"> + <p>Check if fit within an mhmkin object failed</p> + </div> + + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">check_failed</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div> + </div> + + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> + + +<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> +<dd><p>The object to be checked</p></dd> + +</dl></div> + + </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"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> +</div> + + </footer></div> + + + + + + </body></html> + diff --git a/docs/reference/ds_dfop.html b/docs/reference/ds_dfop.html new file mode 100644 index 00000000..6b8c7d09 --- /dev/null +++ b/docs/reference/ds_dfop.html @@ -0,0 +1,8 @@ +<html> + <head> + <meta http-equiv="refresh" content="0;URL=https://pkgdown.jrwb.de/mkin/reference/ds_mixed.html" /> + <meta name="robots" content="noindex"> + <link rel="canonical" 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index 00000000..f6530f49 --- /dev/null +++ b/docs/reference/f_time_norm_focus.mkindsg.html @@ -0,0 +1,8 @@ +<html> + <head> + <meta http-equiv="refresh" content="0;URL=https://pkgdown.jrwb.de/mkin/reference/f_time_norm_focus.html" /> + <meta name="robots" content="noindex"> + <link rel="canonical" href="https://pkgdown.jrwb.de/mkin/reference/f_time_norm_focus.html"> + </head> +</html> + diff --git a/docs/reference/f_time_norm_focus.numeric.html b/docs/reference/f_time_norm_focus.numeric.html new file mode 100644 index 00000000..f6530f49 --- /dev/null +++ b/docs/reference/f_time_norm_focus.numeric.html @@ -0,0 +1,8 @@ +<html> + <head> + <meta http-equiv="refresh" content="0;URL=https://pkgdown.jrwb.de/mkin/reference/f_time_norm_focus.html" /> + <meta name="robots" content="noindex"> + <link rel="canonical" href="https://pkgdown.jrwb.de/mkin/reference/f_time_norm_focus.html"> + </head> +</html> + diff --git a/docs/reference/hierarchical_kinetics.html b/docs/reference/hierarchical_kinetics.html index 5cc24e79..b44a6c99 100644 --- a/docs/reference/hierarchical_kinetics.html +++ b/docs/reference/hierarchical_kinetics.html @@ -1,88 +1,75 @@ <!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"><meta name="description" content='R markdown format for setting up hierarchical kinetics based on a template +<!-- 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>Hierarchical kinetics template — hierarchical_kinetics • mkin</title><script 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+ </div> </nav><div class="container template-reference-topic"> <div class="row"> <main id="main" class="col-md-9"><div class="page-header"> - <img src="" class="logo" alt=""><h1>Hierarchical kinetics template</h1> + + <h1>Hierarchical kinetics template</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/hierarchical_kinetics.R" class="external-link"><code>R/hierarchical_kinetics.R</code></a></small> <div class="d-none name"><code>hierarchical_kinetics.Rd</code></div> </div> @@ -105,22 +92,24 @@ includes them.</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>...</dt> + + +<dl><dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dd><p>Arguments to <code><a href="https://pkgs.rstudio.com/rmarkdown/reference/pdf_document.html" class="external-link">rmarkdown::pdf_document</a></code></p></dd> -<dt>keep_tex</dt> -<dd><p>Keep the intermediate tex file used in the conversion to PDF</p></dd> +<dt id="arg-keep-tex">keep_tex<a class="anchor" aria-label="anchor" href="#arg-keep-tex"></a></dt> +<dd><p>Keep the intermediate tex file used in the conversion to PDF. +Note that this argument does not control whether to keep the auxiliary +files (e.g., <code class="file">.aux</code>) generated by LaTeX when compiling <code class="file">.tex</code> to +<code class="file">.pdf</code>. To keep these files, you may set <code>options(tinytex.clean = +FALSE)</code>.</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>R Markdown output format to pass to + <p>R Markdown output format to pass to <code><a href="https://pkgs.rstudio.com/rmarkdown/reference/render.html" class="external-link">render</a></code></p> - - </div> <div class="section level2"> <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> @@ -147,23 +136,23 @@ and then to run 'tinytex::tlmgr_install(c("float", "listing"))'.</p> <span class="r-in"><span></span></span> </code></pre></div> </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"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by 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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"> - <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a> - <div class="dropdown-menu" aria-labelledby="dropdown-articles"> - <a class="dropdown-item" href="../articles/mkin.html">Introduction to mkin</a> - <div class="dropdown-divider"></div> - <h6 class="dropdown-header" data-toc-skip>Example evaluations with (generalised) nonlinear least squares</h6> - <a class="dropdown-item" href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> - <a class="dropdown-item" href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> - <a class="dropdown-item" href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> - <div class="dropdown-divider"></div> - <h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6> - <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> - <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> - <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> - <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> - <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> - <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a> - <div class="dropdown-divider"></div> - <h6 class="dropdown-header" data-toc-skip>Performance</h6> - <a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> - <a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> - <a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> - <div class="dropdown-divider"></div> - <h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6> - <a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> - <a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> - </div> -</li> -<li class="nav-item"> - <a class="nav-link" href="../news/index.html">News</a> -</li> - </ul><form class="form-inline my-2 my-lg-0" role="search"> - <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> - - <ul class="navbar-nav"><li class="nav-item"> - <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> - <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"> - <p></p><p>Developed by Johannes Ranke.</p> + <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown-footer-right"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p> </div> </footer></div> - - + + </body></html> diff --git a/docs/reference/intervals.html b/docs/reference/intervals.html new file mode 100644 index 00000000..ef2e29e9 --- /dev/null +++ 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class='op'>=</span> <span class='cn'>NULL</span>, sink <span class='op'>=</span> <span class='cn'>TRUE</span>, full_name <span class='op'>=</span> <span class='cn'>NA</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>submodel</th> - <td><p>Character vector of length one to specify the submodel type. -See <code><a href='mkinmod.html'>mkinmod</a></code> for the list of allowed submodel names.</p></td> - </tr> - <tr> - <th>to</th> - <td><p>Vector of the names of the state variable to which a -transformation shall be included in the model.</p></td> - </tr> - <tr> - <th>sink</th> - <td><p>Should a pathway to sink be included in the model in addition to -the pathways to other state variables?</p></td> - </tr> - <tr> - <th>full_name</th> - <td><p>An optional name to be used e.g. for plotting fits -performed with the model. You can use non-ASCII characters here, but then -your R code will not be portable, <em>i.e.</em> may produce unintended plot -results on other operating systems or system configurations.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>A list for use with <code><a href='mkinmod.html'>mkinmod</a></code>.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - - <p>Johannes Ranke</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='co'># One parent compound, one metabolite, both single first order.</span> -<span class='va'>SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> -<span class='co'># The same model using mkinsub</span> -<span class='va'>SFO_SFO.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> -<span class='co'># \dontrun{</span> - <span class='co'># Now supplying full names</span> - <span class='va'>SFO_SFO.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, full_name <span class='op'>=</span> <span class='st'>"Test compound"</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'>mkinsub</span><span class='op'>(</span><span class='st'>"SFO"</span>, full_name <span class='op'>=</span> <span class='st'>"Metabolite M1"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='co'># }</span> -</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> -</div> - - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> -</div> - - </footer> - </div> - - - - - </body> </html> - diff --git a/docs/reference/multistart.saem.mmkin.html b/docs/reference/multistart.saem.mmkin.html new file mode 100644 index 00000000..9700ef05 --- /dev/null +++ b/docs/reference/multistart.saem.mmkin.html @@ -0,0 +1,8 @@ +<html> + <head> + <meta http-equiv="refresh" content="0;URL=https://pkgdown.jrwb.de/mkin/reference/multistart.html" /> + <meta 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href='mkinds.html'>mkinds</a></code> object.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Not used.</p></td> - </tr> - </table> - - - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> -</div> - - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> -</div> - - </footer> - </div> - - - - - </body> </html> - diff --git a/docs/reference/print.mkindsg.html b/docs/reference/print.mkindsg.html new file mode 100644 index 00000000..02429abf --- /dev/null +++ b/docs/reference/print.mkindsg.html @@ -0,0 +1,8 @@ +<html> + <head> + <meta http-equiv="refresh" content="0;URL=https://pkgdown.jrwb.de/mkin/reference/mkindsg.html" /> + <meta name="robots" content="noindex"> + <link rel="canonical" 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href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> - </li> - <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> - </li> - <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> - </li> - <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> - </li> - <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</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="fab fa fab 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>Print mkinmod objects</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinmod.R'><code>R/mkinmod.R</code></a></small> - <div class="hidden name"><code>print.mkinmod.Rd</code></div> - </div> - - <div class="ref-description"> - <p>Print mkinmod objects in a way that the user finds his way to get to its -components.</p> - </div> - - <pre class="usage"><span class='co'># S3 method for mkinmod</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>An <code><a href='mkinmod.html'>mkinmod</a></code> object.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Not used.</p></td> - </tr> - </table> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> - <span class='no'>m_synth_SFO_lin</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>), - <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>), - <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> - <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>m_synth_SFO_lin</span>)</div><div class='output co'>#> <mkinmod> model generated with -#> Use of formation fractions $use_of_ff: max -#> Specification $spec: -#> $parent -#> $type: SFO; $to: M1; $sink: TRUE -#> $M1 -#> $type: SFO; $to: M2; $sink: TRUE -#> $M2 -#> $type: SFO; $sink: TRUE -#> Coefficient matrix $coefmat available -#> Compiled model $cf available -#> Differential equations: -#> d_parent/dt = - k_parent * parent -#> d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1 -#> d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2</div><div class='input'> -</div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> -</div> - - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> -</div> - - </footer> - </div> - - - - - </body> </html> - diff --git a/docs/reference/print.mmkin.html b/docs/reference/print.mmkin.html index 0c094bfc..a15ee4df 100644 --- a/docs/reference/print.mmkin.html +++ b/docs/reference/print.mmkin.html @@ -1,194 +1,8 @@ -<!-- Generated by pkgdown: do not edit by hand --> -<!DOCTYPE html> -<html lang="en"> +<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>Print method for mmkin objects — print.mmkin • mkin</title> - - -<!-- jquery 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href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>An <a href='mmkin.html'>mmkin</a> object.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Not used.</p></td> - </tr> - </table> - - - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> -</div> - - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> -</div> - - </footer> - </div> - - - - - </body> </html> - diff --git a/docs/reference/print.multistart.html b/docs/reference/print.multistart.html new file mode 100644 index 00000000..9700ef05 --- /dev/null +++ b/docs/reference/print.multistart.html @@ -0,0 +1,8 @@ +<html> + <head> + <meta http-equiv="refresh" 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clearpage <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> - </div> - - <div id="arguments"> - <h2>Arguments</h2> - <dl><dt>object</dt> -<dd><p>The object for which the summary is to be listed</p></dd> - - -<dt>caption</dt> -<dd><p>An optional caption</p></dd> - - -<dt>label</dt> -<dd><p>An optional label</p></dd> - - -<dt>clearpage</dt> -<dd><p>Should a new page be started after the listing?</p></dd> - -</dl></div> - - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> - - - <footer><div class="copyright"> - <p></p><p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> -</div> - - </footer></div> - - - - - - - </body></html> +<html> + <head> + <meta http-equiv="refresh" 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