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Optionally (default is FALSE), the data are listed in full."><!-- 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 data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - 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</li> - <li> - <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> - </li> - <li> - <a href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> - </li> - <li> - <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> - </li> - <li> - <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> - </li> - <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> - </li> - <li class="divider"> - <li class="dropdown-header">Performance</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/web_only/benchmarks.html">Benchmark timings for mkin</a> - 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</ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> + </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> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Summary method for class "nlme.mmkin"</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/summary.nlme.mmkin.R" class="external-link"><code>R/summary.nlme.mmkin.R</code></a></small> - <div class="hidden name"><code>summary.nlme.mmkin.Rd</code></div> + </ul></div> + + + </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>Summary method for class "nlme.mmkin"</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/summary.nlme.mmkin.R" class="external-link"><code>R/summary.nlme.mmkin.R</code></a></small> + <div class="d-none name"><code>summary.nlme.mmkin.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Lists model equations, initial parameter values, optimised parameters for fixed effects (population), random effects (deviations from the population mean) and residual error model, as well as the resulting @@ -120,7 +89,8 @@ endpoints such as formation fractions and DT50 values. Optionally (default is FALSE), the data are listed in full.</p> </div> - <div id="ref-usage"> + <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="co"># S3 method for nlme.mmkin</span></span> <span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span></span> <span> <span class="va">object</span>,</span> @@ -135,8 +105,8 @@ endpoints such as formation fractions and DT50 values. Optionally <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">verbose</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>an object of class <a href="nlme.mmkin.html">nlme.mmkin</a></p></dd> @@ -172,8 +142,8 @@ distribution</p></dd> <dd><p>Number of digits to use for printing</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The summary function returns a list based on the <a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a> object @@ -212,14 +182,14 @@ model.</p></dd> </dl><p>The print method is called for its side effect, i.e. printing the summary.</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke for the mkin specific parts José Pinheiro and Douglas Bates for the components inherited from nlme</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Generate five datasets following SFO kinetics</span></span></span> <span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> @@ -256,9 +226,9 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.163 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.6 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:39:53 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:39:53 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 16 04:19:41 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 16 04:19:41 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> @@ -268,7 +238,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.451 s using 4 iterations</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.182 s using 4 iterations</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -412,26 +382,22 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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