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diff --git a/docs/reference/saem.html b/docs/reference/saem.html index b295ab64..7146875f 100644 --- a/docs/reference/saem.html +++ b/docs/reference/saem.html @@ -1,78 +1,65 @@ <!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="This function uses saemix::saemix() as a backend for fitting nonlinear mixed +<!-- 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>Fit nonlinear mixed models with SAEM — saem • mkin</title><script 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fitting nonlinear mixed effects models created from mmkin row objects using the Stochastic Approximation -Expectation Maximisation algorithm (SAEM)."><!-- 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> +Expectation Maximisation algorithm (SAEM)."></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 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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 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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 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fa-github fa-lg"></span></a></li> </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>Fit nonlinear mixed models with SAEM</h1> + + <h1>Fit nonlinear mixed models with SAEM</h1> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/saem.R" class="external-link"><code>R/saem.R</code></a></small> <div class="d-none name"><code>saem.Rd</code></div> </div> @@ -87,7 +74,7 @@ Expectation Maximisation algorithm (SAEM).</p> <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">saem</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> -<span><span class="co"># S3 method for mmkin</span></span> +<span><span class="co"># S3 method for class 'mmkin'</span></span> <span><span class="fu">saem</span><span class="op">(</span></span> <span> <span class="va">object</span>,</span> <span> transformations <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="st">"mkin"</span>, <span class="st">"saemix"</span><span class="op">)</span>,</span> @@ -110,7 +97,7 @@ Expectation Maximisation algorithm (SAEM).</p> <span> <span class="va">...</span></span> <span><span class="op">)</span></span> <span></span> -<span><span class="co"># S3 method for saem.mmkin</span></span> +<span><span class="co"># S3 method for class 'saem.mmkin'</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>, 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>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="fu">saemix_model</span><span class="op">(</span></span> @@ -136,16 +123,18 @@ Expectation Maximisation algorithm (SAEM).</p> <div class="section level2"> <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> - <dl><dt>object</dt> + + +<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt> <dd><p>An <a href="mmkin.html">mmkin</a> row object containing several fits of the same <a href="mkinmod.html">mkinmod</a> model to different datasets</p></dd> -<dt>...</dt> +<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt> <dd><p>Further parameters passed to <a href="https://rdrr.io/pkg/saemix/man/saemixModel.html" class="external-link">saemix::saemixModel</a>.</p></dd> -<dt>transformations</dt> +<dt id="arg-transformations">transformations<a class="anchor" aria-label="anchor" href="#arg-transformations"></a></dt> <dd><p>Per default, all parameter transformations are done in mkin. If this argument is set to 'saemix', parameter transformations are done in 'saemix' for the supported cases, i.e. (as of version 1.1.2) @@ -153,39 +142,39 @@ SFO, FOMC, DFOP and HS without fixing <code>parent_0</code>, and SFO or DFOP wit one SFO metabolite.</p></dd> -<dt>error_model</dt> +<dt id="arg-error-model">error_model<a class="anchor" aria-label="anchor" href="#arg-error-model"></a></dt> <dd><p>Possibility to override the error model used in the mmkin object</p></dd> -<dt>degparms_start</dt> +<dt id="arg-degparms-start">degparms_start<a class="anchor" aria-label="anchor" href="#arg-degparms-start"></a></dt> <dd><p>Parameter values given as a named numeric vector will be used to override the starting values obtained from the 'mmkin' object.</p></dd> -<dt>test_log_parms</dt> +<dt id="arg-test-log-parms">test_log_parms<a class="anchor" aria-label="anchor" href="#arg-test-log-parms"></a></dt> <dd><p>If TRUE, an attempt is made to use more robust starting values for population parameters fitted as log parameters in mkin (like rate constants) by only considering rate constants that pass the t-test when calculating mean degradation parameters using <a href="mean_degparms.html">mean_degparms</a>.</p></dd> -<dt>conf.level</dt> +<dt id="arg-conf-level">conf.level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt> <dd><p>Possibility to adjust the required confidence level for parameter that are tested if requested by 'test_log_parms'.</p></dd> -<dt>solution_type</dt> +<dt id="arg-solution-type">solution_type<a class="anchor" aria-label="anchor" href="#arg-solution-type"></a></dt> <dd><p>Possibility to specify the solution type in case the automatic choice is not desired</p></dd> -<dt>covariance.model</dt> +<dt id="arg-covariance-model">covariance.model<a class="anchor" aria-label="anchor" href="#arg-covariance-model"></a></dt> <dd><p>Will be passed to <code><a href="https://rdrr.io/pkg/saemix/man/saemixModel.html" class="external-link">saemix::saemixModel()</a></code>. Per default, uncorrelated random effects are specified for all degradation parameters.</p></dd> -<dt>omega.init</dt> +<dt id="arg-omega-init">omega.init<a class="anchor" aria-label="anchor" href="#arg-omega-init"></a></dt> <dd><p>Will be passed to <code><a href="https://rdrr.io/pkg/saemix/man/saemixModel.html" class="external-link">saemix::saemixModel()</a></code>. If using mkin transformations and the default covariance model with optionally excluded random effects, the variances of the degradation parameters @@ -195,66 +184,60 @@ mkin transformations or a custom covariance model, the default initialisation of <a href="https://rdrr.io/pkg/saemix/man/saemixModel.html" class="external-link">saemix::saemixModel</a> is used for omega.init.</p></dd> -<dt>covariates</dt> +<dt id="arg-covariates">covariates<a class="anchor" aria-label="anchor" href="#arg-covariates"></a></dt> <dd><p>A data frame with covariate data for use in 'covariate_models', with dataset names as row names.</p></dd> -<dt>covariate_models</dt> +<dt id="arg-covariate-models">covariate_models<a class="anchor" aria-label="anchor" href="#arg-covariate-models"></a></dt> <dd><p>A list containing linear model formulas with one explanatory variable, i.e. of the type 'parameter ~ covariate'. Covariates must be available in the 'covariates' data frame.</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>Character vector of degradation parameters for which there should be no variability over the groups. Only used if the covariance model is not explicitly specified.</p></dd> -<dt>error.init</dt> +<dt id="arg-error-init">error.init<a class="anchor" aria-label="anchor" href="#arg-error-init"></a></dt> <dd><p>Will be passed to <code><a href="https://rdrr.io/pkg/saemix/man/saemixModel.html" class="external-link">saemix::saemixModel()</a></code>.</p></dd> -<dt>nbiter.saemix</dt> +<dt id="arg-nbiter-saemix">nbiter.saemix<a class="anchor" aria-label="anchor" href="#arg-nbiter-saemix"></a></dt> <dd><p>Convenience option to increase the number of iterations</p></dd> -<dt>control</dt> +<dt id="arg-control">control<a class="anchor" aria-label="anchor" href="#arg-control"></a></dt> <dd><p>Passed to <a href="https://rdrr.io/pkg/saemix/man/saemix.html" class="external-link">saemix::saemix</a>.</p></dd> -<dt>verbose</dt> +<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt> <dd><p>Should we print information about created objects of type <a href="https://rdrr.io/pkg/saemix/man/SaemixModel-class.html" class="external-link">saemix::SaemixModel</a> and <a href="https://rdrr.io/pkg/saemix/man/SaemixData-class.html" class="external-link">saemix::SaemixData</a>?</p></dd> -<dt>quiet</dt> +<dt id="arg-quiet">quiet<a class="anchor" aria-label="anchor" href="#arg-quiet"></a></dt> <dd><p>Should we suppress the messages saemix prints at the beginning and the end of the optimisation process?</p></dd> -<dt>x</dt> +<dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt> <dd><p>An saem.mmkin object to print</p></dd> -<dt>digits</dt> +<dt id="arg-digits">digits<a class="anchor" aria-label="anchor" href="#arg-digits"></a></dt> <dd><p>Number of digits to use for printing</p></dd> </dl></div> <div class="section level2"> <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> - - -<p>An S3 object of class 'saem.mmkin', containing the fitted + <p>An S3 object of class 'saem.mmkin', containing the fitted <a href="https://rdrr.io/pkg/saemix/man/SaemixObject-class.html" class="external-link">saemix::SaemixObject</a> as a list component named 'so'. The object also inherits from 'mixed.mmkin'.</p> - - <p>An <a href="https://rdrr.io/pkg/saemix/man/SaemixModel-class.html" class="external-link">saemix::SaemixModel</a> object.</p> - - <p>An <a href="https://rdrr.io/pkg/saemix/man/SaemixData-class.html" class="external-link">saemix::SaemixData</a> object.</p> </div> <div class="section level2"> @@ -320,7 +303,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-in"><span><span class="co"># functions from saemix</span></span></span> <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Loading required package: npde</span> -<span class="r-msg co"><span class="r-pr">#></span> Package saemix, version 3.2</span> +<span class="r-msg co"><span class="r-pr">#></span> Package saemix, version 3.3, March 2024</span> <span class="r-msg co"><span class="r-pr">#></span> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</span> <span class="r-msg co"><span class="r-pr">#></span> </span> <span class="r-msg co"><span class="r-pr">#></span> Attaching package: ‘saemix’</span> @@ -411,11 +394,11 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span> <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_saem_dfop_sfo</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> saemix version used for fitting: 3.2 </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: 4.3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 16 04:17:34 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 16 04:17:34 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.3 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.9 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.4.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Feb 13 14:59:07 2025 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Feb 13 14:59:07 2025 </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 = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -430,7 +413,7 @@ using <a href="mmkin.html">mmkin</a>.</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 3.385 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 3.96 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Constant variance </span> @@ -726,23 +709,23 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-in"><span><span class="co"># }</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 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> 2.1.1.</p> </div> </footer></div> - - + + </body></html> |