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Our kinetic models are nonlinear, so we can use various nonlinear -mixed-effects model fitting functions."><!-- 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"> - - - <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"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> - </span> - </div> - - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Reference</a> -</li> -<li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> - Articles - - <span class="caret"></span> - </a> - <ul class="dropdown-menu" role="menu"><li> - <a href="../articles/mkin.html">Introduction to mkin</a> - </li> - <li class="divider"> - <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> - <li> - <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> - </li> - <li> - <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> - </li> - <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> - </li> - <li class="divider"> - <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> - <li> - <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> - </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> - </li> - <li> - <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> - </li> - <li class="divider"> - <li class="dropdown-header">Miscellaneous</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> +mixed-effects model fitting functions."><meta property="og:description" content="The name of the methods expresses that (multiple) hierarchichal +(also known as multilevel) multicompartment kinetic models are +fitted. 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<div class="ref-description"> + <div class="ref-description section level2"> <p>The name of the methods expresses that (<strong>m</strong>ultiple) <strong>h</strong>ierarchichal (also known as multilevel) <strong>m</strong>ulticompartment <strong>kin</strong>etic models are fitted. Our kinetic models are nonlinear, so we can use various nonlinear mixed-effects model fitting functions.</p> </div> - <div id="ref-usage"> - <div class="sourceCode"><pre><code>mhmkin(objects, ...) - -# S3 method for mmkin -mhmkin(objects, ...) - -# S3 method for list -mhmkin( - objects, - backend = "saemix", - algorithm = "saem", - no_random_effect = NULL, - ..., - cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(), - cluster = NULL -) + <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">mhmkin</span><span class="op">(</span><span class="va">objects</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for class 'mmkin'</span></span> +<span><span class="fu">mhmkin</span><span class="op">(</span><span class="va">objects</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for class 'list'</span></span> +<span><span class="fu">mhmkin</span><span class="op">(</span></span> +<span> <span class="va">objects</span>,</span> +<span> backend <span class="op">=</span> <span class="st">"saemix"</span>,</span> +<span> algorithm <span class="op">=</span> <span class="st">"saem"</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> <span class="va">...</span>,</span> +<span> cores <span class="op">=</span> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="fl">1</span> <span class="kw">else</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span>,</span> +<span> cluster <span class="op">=</span> <span class="cn">NULL</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for class 'mhmkin'</span></span> +<span><span class="va">x</span><span class="op">[</span><span class="va">i</span>, <span class="va">j</span>, <span class="va">...</span>, drop <span class="op">=</span> <span class="cn">FALSE</span><span class="op">]</span></span> +<span></span> +<span><span class="co"># S3 method for class 'mhmkin'</span></span> +<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>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> -# S3 method for mhmkin -[(x, i, j, ..., drop = FALSE) + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> -# S3 method for mhmkin -print(x, ...)</code></pre></div> - </div> - <div id="arguments"> - <h2>Arguments</h2> - <dl><dt>objects</dt> +<dl><dt id="arg-objects">objects<a class="anchor" aria-label="anchor" href="#arg-objects"></a></dt> <dd><p>A list of <a href="mmkin.html">mmkin</a> objects containing fits of the same degradation models to the same data, but using different error models. Alternatively, a single <a href="mmkin.html">mmkin</a> object containing fits of several degradation models to the same data</p></dd> -<dt>...</dt> +<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dd><p>Further arguments that will be passed to the nonlinear mixed-effects model fitting function.</p></dd> -<dt>backend</dt> +<dt id="arg-backend">backend<a class="anchor" aria-label="anchor" href="#arg-backend"></a></dt> <dd><p>The backend to be used for fitting. Currently, only saemix is supported</p></dd> -<dt>algorithm</dt> +<dt id="arg-algorithm">algorithm<a class="anchor" aria-label="anchor" href="#arg-algorithm"></a></dt> <dd><p>The algorithm to be used for fitting (currently not used)</p></dd> -<dt>no_random_effect</dt> +<dt id="arg-no-random-effect">no_random_effect<a class="anchor" aria-label="anchor" href="#arg-no-random-effect"></a></dt> <dd><p>Default is NULL and will be passed to <a href="saem.html">saem</a>. If a character vector is supplied, it will be passed to all calls to <a href="saem.html">saem</a>, which will exclude random effects for all matching parameters. Alternatively, @@ -179,7 +134,7 @@ of degradation models in the mmkin object(s), and the number of columns must match the number of error models used in the mmkin object(s).</p></dd> -<dt>cores</dt> +<dt id="arg-cores">cores<a class="anchor" aria-label="anchor" href="#arg-cores"></a></dt> <dd><p>The number of cores to be used for multicore processing. This is only used when the <code>cluster</code> argument is <code>NULL</code>. On Windows machines, cores > 1 is not supported, you need to use the <code>cluster</code> @@ -188,51 +143,47 @@ by <code><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-l is 1.</p></dd> -<dt>cluster</dt> +<dt id="arg-cluster">cluster<a class="anchor" aria-label="anchor" href="#arg-cluster"></a></dt> <dd><p>A cluster as returned by makeCluster to be used for parallel execution.</p></dd> -<dt>x</dt> +<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> <dd><p>An mhmkin object.</p></dd> -<dt>i</dt> +<dt id="arg-i">i<a class="anchor" aria-label="anchor" href="#arg-i"></a></dt> <dd><p>Row index selecting the fits for specific models</p></dd> -<dt>j</dt> +<dt id="arg-j">j<a class="anchor" aria-label="anchor" href="#arg-j"></a></dt> <dd><p>Column index selecting the fits to specific datasets</p></dd> -<dt>drop</dt> +<dt id="arg-drop">drop<a class="anchor" aria-label="anchor" href="#arg-drop"></a></dt> <dd><p>If FALSE, the method always returns an mhmkin object, otherwise either a list of fit objects or a single fit object.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> - - -<p>A two-dimensional <a href="https://rdrr.io/r/base/array.html" class="external-link">array</a> of fit objects and/or try-errors that can + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> + <p>A two-dimensional <a href="https://rdrr.io/r/base/array.html" class="external-link">array</a> of fit objects and/or try-errors that can be indexed using the degradation model names for the first index (row index) and the error model names for the second index (column index), with class attribute 'mhmkin'.</p> - - <p>An object inheriting from <code>mhmkin</code>.</p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p><code>[.mhmkin</code> for subsetting mhmkin objects</p></div> </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</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 class="co"># \dontrun{</span></span></span> <span class="r-in"><span><span class="co"># We start with separate evaluations of all the first six datasets with two</span></span></span> <span class="r-in"><span><span class="co"># degradation models and two error models</span></span></span> @@ -313,27 +264,23 @@ attribute 'mhmkin'.</p> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </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> + </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="copyright"> - <p></p><p>Developed by Johannes Ranke.</p> + <footer><div class="pkgdown-footer-left"> + <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> 2.0.7.</p> +<div class="pkgdown-footer-right"> + <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p> </div> - </footer></div> + </footer></div> + - - </body></html> |