diff options
Diffstat (limited to 'docs/dev/reference/saem.html')
| -rw-r--r-- | docs/dev/reference/saem.html | 668 |
1 files changed, 531 insertions, 137 deletions
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index c132647b..c8a7504f 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -19,7 +19,7 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> </span> </div> @@ -28,7 +28,7 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -43,12 +43,18 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex <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> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> @@ -88,39 +94,51 @@ Expectation Maximisation algorithm (SAEM).</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">saem</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span> - -<span class="co"># S3 method for mmkin</span> -<span class="fu">saem</span><span class="op">(</span> - <span class="va">object</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>, - degparms_start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>, - test_log_parms <span class="op">=</span> <span class="cn">TRUE</span>, - conf.level <span class="op">=</span> <span class="fl">0.6</span>, - solution_type <span class="op">=</span> <span class="st">"auto"</span>, - nbiter.saemix <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">300</span>, <span class="fl">100</span><span class="op">)</span>, - control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>displayProgress <span class="op">=</span> <span class="cn">FALSE</span>, print <span class="op">=</span> <span class="cn">FALSE</span>, nbiter.saemix <span class="op">=</span> <span class="va">nbiter.saemix</span>, - save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - fail_with_errors <span class="op">=</span> <span class="cn">TRUE</span>, - verbose <span class="op">=</span> <span class="cn">FALSE</span>, - quiet <span class="op">=</span> <span class="cn">FALSE</span>, - <span class="va">...</span> -<span class="op">)</span> - -<span class="co"># S3 method for saem.mmkin</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 class="fu">saemix_model</span><span class="op">(</span> - <span class="va">object</span>, - solution_type <span class="op">=</span> <span class="st">"auto"</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>, - degparms_start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>, - test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>, - verbose <span class="op">=</span> <span class="cn">FALSE</span>, - <span class="va">...</span> -<span class="op">)</span> - -<span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <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="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> +<span> degparms_start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>,</span> +<span> test_log_parms <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> conf.level <span class="op">=</span> <span class="fl">0.6</span>,</span> +<span> solution_type <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> covariance.model <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> covariates <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> nbiter.saemix <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">300</span>, <span class="fl">100</span><span class="op">)</span>,</span> +<span> control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>displayProgress <span class="op">=</span> <span class="cn">FALSE</span>, print <span class="op">=</span> <span class="cn">FALSE</span>, nbiter.saemix <span class="op">=</span> <span class="va">nbiter.saemix</span>,</span> +<span> save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> fail_with_errors <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<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="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> +<span> <span class="va">object</span>,</span> +<span> solution_type <span class="op">=</span> <span class="st">"auto"</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> +<span> degparms_start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a></span><span class="op">(</span><span class="op">)</span>,</span> +<span> covariance.model <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> covariates <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> conf.level <span class="op">=</span> <span class="fl">0.6</span>,</span> +<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, covariates <span class="op">=</span> <span class="cn">NULL</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for saem.mmkin</span></span> +<span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">object</span>, ci <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -128,54 +146,115 @@ Expectation Maximisation algorithm (SAEM).</p> <dl><dt>object</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> <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> <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. Currently this is only -supported in cases where the initial concentration of the parent is not fixed, -SFO or DFOP is used for the parent and there is either no metabolite or one.</p></dd> +are done in 'saemix' for the supported cases, i.e. (as of version 1.1.2) +SFO, FOMC, DFOP and HS without fixing <code>parent_0</code>, and SFO or DFOP with +one SFO metabolite.</p></dd> + + <dt>degparms_start</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> <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> <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> <dd><p>Possibility to specify the solution type in case the automatic choice is not desired</p></dd> + + +<dt>covariance.model</dt> +<dd><p>Will be passed to <code><a href="https://rdrr.io/pkg/saemix/man/SaemixModel-class.html" class="external-link">saemix::SaemixModel()</a></code>. Per +default, uncorrelated random effects are specified for all degradation +parameters.</p></dd> + + +<dt>covariates</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> +<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> +<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>nbiter.saemix</dt> <dd><p>Convenience option to increase the number of iterations</p></dd> + + <dt>control</dt> <dd><p>Passed to <a href="https://rdrr.io/pkg/saemix/man/saemix.html" class="external-link">saemix::saemix</a>.</p></dd> + + <dt>fail_with_errors</dt> <dd><p>Should a failure to compute standard errors from the inverse of the Fisher Information Matrix be a failure?</p></dd> + + <dt>verbose</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> <dd><p>Should we suppress the messages saemix prints at the beginning and the end of the optimisation process?</p></dd> + + <dt>x</dt> <dd><p>An saem.mmkin object to print</p></dd> + + <dt>digits</dt> <dd><p>Number of digits to use for printing</p></dd> + + +<dt>ci</dt> +<dd><p>Should a matrix with estimates and confidence interval boundaries +be returned? If FALSE (default), a vector of estimates is returned.</p></dd> + </dl></div> <div id="value"> <h2>Value</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'. -An <a href="https://rdrr.io/pkg/saemix/man/SaemixModel-class.html" class="external-link">saemix::SaemixModel</a> object. -An <a href="https://rdrr.io/pkg/saemix/man/SaemixData-class.html" class="external-link">saemix::SaemixData</a> object.</p> +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 id="details"> <h2>Details</h2> @@ -192,109 +271,424 @@ using <a href="mmkin.html">mmkin</a>.</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span> -<span class="r-in"> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</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="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">)</span></span> -<span class="r-in"><span class="va">f_mmkin_parent_p0_fixed</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">ds</span>,</span> -<span class="r-in"> state.ini <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>parent <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, fixed_initials <span class="op">=</span> <span class="st">"parent"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">f_saem_p0_fixed</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent_p0_fixed</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> -<span class="r-in"></span> -<span class="r-in"><span class="va">f_mmkin_parent</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></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="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">f_saem_sfo</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> -<span class="r-in"><span class="va">f_saem_fomc</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> -<span class="r-in"><span class="va">f_saem_dfop</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span></span> -<span class="r-in"><span class="co"># functions from saemix</span></span> -<span class="r-in"><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> + <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="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span> +<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</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="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_mmkin_parent_p0_fixed</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">ds</span>,</span></span> +<span class="r-in"><span> state.ini <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>parent <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, fixed_initials <span class="op">=</span> <span class="st">"parent"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_saem_p0_fixed</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent_p0_fixed</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">f_mmkin_parent</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></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="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_saem_sfo</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_saem_fomc</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_saem_dfop</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_sfo</span>, <span class="va">f_saem_fomc</span>, <span class="va">f_saem_dfop</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_sfo 5 624.26 622.31 -307.13</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_fomc 7 467.87 465.13 -226.93</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop 9 493.98 490.47 -237.99</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_sfo</span>, <span class="va">f_saem_dfop</span>, test <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> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik Chisq Df Pr(>Chisq) </span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_sfo 5 624.26 622.31 -307.13 </span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop 9 493.98 490.47 -237.99 138.28 4 < 2.2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] "sd(g_qlogis)"</span> +<span class="r-in"><span><span class="va">f_saem_dfop_red</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop</span>, no_random_effect <span class="op">=</span> <span class="st">"g_qlogis"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_dfop</span>, <span class="va">f_saem_dfop_red</span>, test <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> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik Chisq Df Pr(>Chisq)</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_red 8 490.64 487.52 -237.32 </span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop 9 493.98 490.47 -237.99 0 1 1</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_sfo</span>, <span class="va">f_saem_fomc</span>, <span class="va">f_saem_dfop</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_sfo 5 624.26 622.31 -307.13</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_fomc 7 467.87 465.13 -226.93</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop 9 493.98 490.47 -237.99</span> +<span class="r-in"><span><span class="co"># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span></span></span> +<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> </span> -<span class="r-msg co"><span class="r-pr">#></span> Attaching package: ‘npde’</span> -<span class="r-msg co"><span class="r-pr">#></span> The following object is masked from ‘package:nlmixr’:</span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> warfarin</span> -<span class="r-msg co"><span class="r-pr">#></span> Package saemix, version 3.0</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> 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> <span class="r-msg co"><span class="r-pr">#></span> The following objects are masked from ‘package:npde’:</span> <span class="r-msg co"><span class="r-pr">#></span> </span> <span class="r-msg co"><span class="r-pr">#></span> kurtosis, skewness</span> -<span class="r-msg co"><span class="r-pr">#></span> The following object is masked from ‘package:RxODE’:</span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-msg co"><span class="r-pr">#></span> phi</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span><span class="va">f_saem_sfo</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_dfop</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in compare.saemix(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so):</span> object 'f_saem_sfo' not found</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_fomc' not found</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"individual.fit"</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_fomc' not found</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"npde"</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_fomc' not found</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"vpc"</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_fomc' not found</span> -<span class="r-in"></span> -<span class="r-in"><span class="va">f_mmkin_parent_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_mmkin_parent</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> -<span class="r-in"><span class="va">f_saem_fomc_tc</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent_tc</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_fomc_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in compare.saemix(f_saem_fomc$so, f_saem_fomc_tc$so):</span> object 'f_saem_fomc' not found</span> -<span class="r-in"></span> -<span class="r-in"><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="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span> -<span class="r-in"> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span><span class="va">f_saem_sfo</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_saem_dfop</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Likelihoods calculated by importance sampling</span> +<span class="r-out co"><span class="r-pr">#></span> AIC BIC</span> +<span class="r-out co"><span class="r-pr">#></span> 1 624.2598 622.3070</span> +<span class="r-out co"><span class="r-pr">#></span> 2 467.8664 465.1324</span> +<span class="r-out co"><span class="r-pr">#></span> 3 493.9811 490.4660</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="saem-1.png" alt="" width="700" height="433"></span> +<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_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"individual.fit"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="saem-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"npde"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Simulating data using nsim = 1000 simulated datasets</span> +<span class="r-out co"><span class="r-pr">#></span> Computing WRES and npde .</span> +<span class="r-msg co"><span class="r-pr">#></span> Please use npdeSaemix to obtain VPC and npde</span> +<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_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"vpc"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="saem-3.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">f_mmkin_parent_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_mmkin_parent</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_saem_fomc_tc</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin_parent_tc</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_fomc</span>, <span class="va">f_saem_fomc_tc</span>, test <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> Data: 90 observations of 1 variable(s) grouped in 5 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik Chisq Df Pr(>Chisq)</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_fomc 7 467.87 465.13 -226.93 </span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_fomc_tc 8 469.80 466.68 -226.90 0.0645 1 0.7995</span> +<span class="r-in"><span></span></span> +<span class="r-in"><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="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span class="va">fomc_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="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span> -<span class="r-in"> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span><span class="va">fomc_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="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span class="va">dfop_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="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span> -<span class="r-in"> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span><span class="va">dfop_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="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"><span class="co"># The following fit uses analytical solutions for SFO-SFO and DFOP-SFO,</span></span> -<span class="r-in"><span class="co"># and compiled ODEs for FOMC that are much slower</span></span> -<span class="r-in"><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span> -<span class="r-in"> <span class="st">"SFO-SFO"</span> <span class="op">=</span> <span class="va">sfo_sfo</span>, <span class="st">"FOMC-SFO"</span> <span class="op">=</span> <span class="va">fomc_sfo</span>, <span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">dfop_sfo</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="co"># saem fits of SFO-SFO and DFOP-SFO to these data take about five seconds</span></span> -<span class="r-in"><span class="co"># each on this system, as we use analytical solutions written for saemix.</span></span> -<span class="r-in"><span class="co"># When using the analytical solutions written for mkin this took around</span></span> -<span class="r-in"><span class="co"># four minutes</span></span> -<span class="r-in"><span class="va">f_saem_sfo_sfo</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">[</span><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> -<span class="r-in"><span class="va">f_saem_dfop_sfo</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> </span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span> -<span class="r-in"><span class="co"># We can use print, plot and summary methods to check the results</span></span> -<span class="r-in"><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">f_saem_dfop_sfo</span><span class="op">)</span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'print': object 'f_saem_dfop_sfo' not found</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.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 class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_dfop_sfo' not found</span> -<span class="r-in"><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 class="r-err co"><span class="r-pr">#></span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'object' in selecting a method for function 'summary': object 'f_saem_dfop_sfo' not found</span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># The following takes about 6 minutes</span></span> -<span class="r-in"><span class="co">#f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve",</span></span> -<span class="r-in"><span class="co"># control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co">#saemix::compare.saemix(list(</span></span> -<span class="r-in"><span class="co"># f_saem_dfop_sfo$so,</span></span> -<span class="r-in"><span class="co"># f_saem_dfop_sfo_deSolve$so))</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># If the model supports it, we can also use eigenvalue based solutions, which</span></span> -<span class="r-in"><span class="co"># take a similar amount of time</span></span> -<span class="r-in"><span class="co">#f_saem_sfo_sfo_eigen <- saem(f_mmkin["SFO-SFO", ], solution_type = "eigen",</span></span> -<span class="r-in"><span class="co"># control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))</span></span> -<span class="r-in"><span class="co"># }</span></span> +<span class="r-in"><span><span class="co"># The following fit uses analytical solutions for SFO-SFO and DFOP-SFO,</span></span></span> +<span class="r-in"><span><span class="co"># and compiled ODEs for FOMC that are much slower</span></span></span> +<span class="r-in"><span><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> <span class="st">"SFO-SFO"</span> <span class="op">=</span> <span class="va">sfo_sfo</span>, <span class="st">"FOMC-SFO"</span> <span class="op">=</span> <span class="va">fomc_sfo</span>, <span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">dfop_sfo</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># saem fits of SFO-SFO and DFOP-SFO to these data take about five seconds</span></span></span> +<span class="r-in"><span><span class="co"># each on this system, as we use analytical solutions written for saemix.</span></span></span> +<span class="r-in"><span><span class="co"># When using the analytical solutions written for mkin this took around</span></span></span> +<span class="r-in"><span><span class="co"># four minutes</span></span></span> +<span class="r-in"><span><span class="va">f_saem_sfo_sfo</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">[</span><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_saem_dfop_sfo</span> <span class="op"><-</span> <span class="fu">saem</span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># We can use print, plot and summary methods to check the results</span></span></span> +<span class="r-in"><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">f_saem_dfop_sfo</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Kinetic nonlinear mixed-effects model fit by SAEM</span> +<span class="r-out co"><span class="r-pr">#></span> Structural model:</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> +<span class="r-out co"><span class="r-pr">#></span> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span> +<span class="r-out co"><span class="r-pr">#></span> * parent</span> +<span class="r-out co"><span class="r-pr">#></span> d_A1/dt = + f_parent_to_A1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)</span> +<span class="r-out co"><span class="r-pr">#></span> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *</span> +<span class="r-out co"><span class="r-pr">#></span> exp(-k2 * time))) * parent - k_A1 * A1</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Data:</span> +<span class="r-out co"><span class="r-pr">#></span> 170 observations of 2 variable(s) grouped in 5 datasets</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> +<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> +<span class="r-out co"><span class="r-pr">#></span> 842 836.9 -408</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Fitted parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> estimate lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 93.7701 91.1458 96.3945</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_A1 -5.8116 -7.5998 -4.0234</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.9608 -1.3654 -0.5562</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.5841 -3.6876 -1.4805</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.5228 -5.3254 -1.7203</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.1027 -0.8719 0.6665</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 1.8856 1.6676 2.1037</span> +<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.7682 0.7668 4.7695</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_A1 1.7447 0.4047 3.0848</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4525 0.1620 0.7431</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 1.2423 0.4560 2.0285</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 2.0390 0.7601 3.3180</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4439 -0.3069 1.1947</span> +<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: 1.1.2 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Oct 26 09:20:37 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Oct 26 09:20:37 2022 </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> +<span class="r-out co"><span class="r-pr">#></span> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))</span> +<span class="r-out co"><span class="r-pr">#></span> * parent</span> +<span class="r-out co"><span class="r-pr">#></span> d_A1/dt = + f_parent_to_A1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)</span> +<span class="r-out co"><span class="r-pr">#></span> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *</span> +<span class="r-out co"><span class="r-pr">#></span> exp(-k2 * time))) * parent - k_A1 * A1</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Data:</span> +<span class="r-out co"><span class="r-pr">#></span> 170 observations of 2 variable(s) grouped in 5 datasets</span> +<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 8.902 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> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Mean of starting values for individual parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 </span> +<span class="r-out co"><span class="r-pr">#></span> 93.8102 -5.3734 -0.9711 -1.8799 -4.2708 </span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis </span> +<span class="r-out co"><span class="r-pr">#></span> 0.1356 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Fixed degradation parameter values:</span> +<span class="r-out co"><span class="r-pr">#></span> None</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Results:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> +<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> +<span class="r-out co"><span class="r-pr">#></span> 842 836.9 -408</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Optimised parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 93.7701 91.1458 96.3945</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_A1 -5.8116 -7.5998 -4.0234</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.9608 -1.3654 -0.5562</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.5841 -3.6876 -1.4805</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.5228 -5.3254 -1.7203</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.1027 -0.8719 0.6665</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 1.8856 1.6676 2.1037</span> +<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.7682 0.7668 4.7695</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_A1 1.7447 0.4047 3.0848</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4525 0.1620 0.7431</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 1.2423 0.4560 2.0285</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 2.0390 0.7601 3.3180</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4439 -0.3069 1.1947</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Correlation: </span> +<span class="r-out co"><span class="r-pr">#></span> parnt_0 lg_k_A1 f_prnt_ log_k1 log_k2 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_A1 -0.0160 </span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.0263 0.0612 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 0.0100 -0.0014 -0.0033 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 0.0131 0.0050 -0.0011 0.0071 </span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.0419 -0.0199 0.0026 -0.0765 -0.0707</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Random effects:</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.7682 0.7668 4.7695</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_A1 1.7447 0.4047 3.0848</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4525 0.1620 0.7431</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 1.2423 0.4560 2.0285</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 2.0390 0.7601 3.3180</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4439 -0.3069 1.1947</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Variance model:</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 1.886 1.668 2.104</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 93.770115 9.115e+01 96.39447</span> +<span class="r-out co"><span class="r-pr">#></span> k_A1 0.002993 5.005e-04 0.01789</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_A1 0.276720 2.034e-01 0.36443</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.075467 2.503e-02 0.22753</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.029516 4.867e-03 0.17902</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.474353 2.949e-01 0.66073</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Resulting formation fractions:</span> +<span class="r-out co"><span class="r-pr">#></span> ff</span> +<span class="r-out co"><span class="r-pr">#></span> parent_A1 0.2767</span> +<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7233</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> +<span class="r-out co"><span class="r-pr">#></span> parent 14.56 58.26 17.54 9.185 23.48</span> +<span class="r-out co"><span class="r-pr">#></span> A1 231.62 769.41 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Data:</span> +<span class="r-out co"><span class="r-pr">#></span> ds name time observed predicted residual std standardized</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 0 97.2 95.78623 1.41377 1.886 0.749758</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 0 96.4 95.78623 0.61377 1.886 0.325498</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 3 71.1 71.34666 -0.24666 1.886 -0.130812</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 3 69.2 71.34666 -2.14666 1.886 -1.138429</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 6 58.1 56.49768 1.60232 1.886 0.849749</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 6 56.6 56.49768 0.10232 1.886 0.054262</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 10 44.4 44.53511 -0.13511 1.886 -0.071650</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 10 43.4 44.53511 -1.13511 1.886 -0.601974</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 20 33.3 29.77451 3.52549 1.886 1.869656</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 20 29.2 29.77451 -0.57451 1.886 -0.304675</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 34 17.6 19.32540 -1.72540 1.886 -0.915023</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 34 18.0 19.32540 -1.32540 1.886 -0.702894</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 55 10.5 10.42781 0.07219 1.886 0.038282</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 55 9.3 10.42781 -1.12781 1.886 -0.598107</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 90 4.5 3.74190 0.75810 1.886 0.402037</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 90 4.7 3.74190 0.95810 1.886 0.508102</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 112 3.0 1.96485 1.03515 1.886 0.548966</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 112 3.4 1.96485 1.43515 1.886 0.761096</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 132 2.3 1.09395 1.20605 1.886 0.639596</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 parent 132 2.7 1.09395 1.60605 1.886 0.851726</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 3 4.3 4.72702 -0.42702 1.886 -0.226458</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 3 4.6 4.72702 -0.12702 1.886 -0.067361</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 6 7.0 7.51314 -0.51314 1.886 -0.272128</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 6 7.2 7.51314 -0.31314 1.886 -0.166063</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 10 8.2 9.63719 -1.43719 1.886 -0.762179</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 10 8.0 9.63719 -1.63719 1.886 -0.868244</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 20 11.0 11.84931 -0.84931 1.886 -0.450409</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 20 13.7 11.84931 1.85069 1.886 0.981468</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 34 11.5 12.82336 -1.32336 1.886 -0.701808</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 34 12.7 12.82336 -0.12336 1.886 -0.065418</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 55 14.9 12.89456 2.00544 1.886 1.063533</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 55 14.5 12.89456 1.60544 1.886 0.851403</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 90 12.1 11.55919 0.54081 1.886 0.286806</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 90 12.3 11.55919 0.74081 1.886 0.392871</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 112 9.9 10.42334 -0.52334 1.886 -0.277539</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 112 10.2 10.42334 -0.22334 1.886 -0.118442</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 132 8.8 9.37987 -0.57987 1.886 -0.307519</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 6 A1 132 7.8 9.37987 -1.57987 1.886 -0.837844</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 0 93.6 90.95702 2.64298 1.886 1.401639</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 0 92.3 90.95702 1.34298 1.886 0.712217</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 3 87.0 84.77506 2.22494 1.886 1.179942</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 3 82.2 84.77506 -2.57506 1.886 -1.365616</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 7 74.0 77.60962 -3.60962 1.886 -1.914268</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 7 73.9 77.60962 -3.70962 1.886 -1.967301</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 14 64.2 67.50646 -3.30646 1.886 -1.753499</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 14 69.5 67.50646 1.99354 1.886 1.057221</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 30 54.0 52.48909 1.51091 1.886 0.801271</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 30 54.6 52.48909 2.11091 1.886 1.119465</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 60 41.1 39.54372 1.55628 1.886 0.825335</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 60 38.4 39.54372 -1.14372 1.886 -0.606542</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 90 32.5 33.87968 -1.37968 1.886 -0.731676</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 90 35.5 33.87968 1.62032 1.886 0.859298</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 120 28.1 30.41071 -2.31071 1.886 -1.225427</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 120 29.0 30.41071 -1.41071 1.886 -0.748135</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 180 26.5 25.36386 1.13614 1.886 0.602524</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 parent 180 27.6 25.36386 2.23614 1.886 1.185881</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 3 3.9 2.74863 1.15137 1.886 0.610600</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 3 3.1 2.74863 0.35137 1.886 0.186341</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 7 6.9 5.92686 0.97314 1.886 0.516081</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 7 6.6 5.92686 0.67314 1.886 0.356983</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 14 10.4 10.38800 0.01200 1.886 0.006362</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 14 8.3 10.38800 -2.08800 1.886 -1.107320</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 30 14.4 16.93529 -2.53529 1.886 -1.344524</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 30 13.7 16.93529 -3.23529 1.886 -1.715751</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 60 22.1 22.33044 -0.23044 1.886 -0.122209</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 60 22.3 22.33044 -0.03044 1.886 -0.016144</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 90 27.5 24.42300 3.07700 1.886 1.631809</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 90 25.4 24.42300 0.97700 1.886 0.518127</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 120 28.0 25.51140 2.48860 1.886 1.319768</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 120 26.6 25.51140 1.08860 1.886 0.577313</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 180 25.8 26.80282 -1.00282 1.886 -0.531818</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 7 A1 180 25.3 26.80282 -1.50282 1.886 -0.796981</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 0 91.9 91.08733 0.81267 1.886 0.430980</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 0 90.8 91.08733 -0.28733 1.886 -0.152377</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 1 64.9 67.55332 -2.65332 1.886 -1.407123</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 1 66.2 67.55332 -1.35332 1.886 -0.717701</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 3 43.5 41.65811 1.84189 1.886 0.976800</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 3 44.1 41.65811 2.44189 1.886 1.294994</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 8 18.3 19.65773 -1.35773 1.886 -0.720038</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 8 18.1 19.65773 -1.55773 1.886 -0.826103</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 14 10.2 10.65118 -0.45118 1.886 -0.239269</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 14 10.8 10.65118 0.14882 1.886 0.078925</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 27 4.9 3.11694 1.78306 1.886 0.945601</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 27 3.3 3.11694 0.18306 1.886 0.097082</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 48 1.6 0.43165 1.16835 1.886 0.619603</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 48 1.5 0.43165 1.06835 1.886 0.566570</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 70 1.1 0.05441 1.04559 1.886 0.554503</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 parent 70 0.9 0.05441 0.84559 1.886 0.448438</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 1 9.6 7.66431 1.93569 1.886 1.026546</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 1 7.7 7.66431 0.03569 1.886 0.018930</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 3 15.0 15.57948 -0.57948 1.886 -0.307311</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 3 15.1 15.57948 -0.47948 1.886 -0.254279</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 8 21.2 20.38988 0.81012 1.886 0.429625</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 8 21.1 20.38988 0.71012 1.886 0.376593</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 14 19.7 20.16439 -0.46439 1.886 -0.246276</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 14 18.9 20.16439 -1.26439 1.886 -0.670535</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 27 17.5 16.40918 1.09082 1.886 0.578489</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 27 15.9 16.40918 -0.50918 1.886 -0.270030</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 48 9.5 10.12011 -0.62011 1.886 -0.328861</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 48 9.8 10.12011 -0.32011 1.886 -0.169764</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 70 6.2 5.79080 0.40920 1.886 0.217011</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 8 A1 70 6.1 5.79080 0.30920 1.886 0.163979</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 0 99.8 97.38786 2.41214 1.886 1.279218</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 0 98.3 97.38786 0.91214 1.886 0.483731</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 1 77.1 79.25431 -2.15431 1.886 -1.142481</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 1 77.2 79.25431 -2.05431 1.886 -1.089449</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 3 59.0 55.69866 3.30134 1.886 1.750781</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 3 58.1 55.69866 2.40134 1.886 1.273489</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 8 27.4 31.64893 -4.24893 1.886 -2.253314</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 8 29.2 31.64893 -2.44893 1.886 -1.298729</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 14 19.1 22.57316 -3.47316 1.886 -1.841901</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 14 29.6 22.57316 7.02684 1.886 3.726507</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 27 10.1 14.11345 -4.01345 1.886 -2.128430</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 27 18.2 14.11345 4.08655 1.886 2.167199</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 48 4.5 6.95586 -2.45586 1.886 -1.302400</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 48 9.1 6.95586 2.14414 1.886 1.137093</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 70 2.3 3.31753 -1.01753 1.886 -0.539619</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 70 2.9 3.31753 -0.41753 1.886 -0.221424</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 91 2.0 1.63642 0.36358 1.886 0.192816</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 91 1.8 1.63642 0.16358 1.886 0.086751</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 120 2.0 0.61667 1.38333 1.886 0.733614</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 parent 120 2.2 0.61667 1.58333 1.886 0.839679</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 1 4.2 3.67247 0.52753 1.886 0.279763</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 1 3.9 3.67247 0.22753 1.886 0.120666</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 3 7.4 8.36240 -0.96240 1.886 -0.510385</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 3 7.9 8.36240 -0.46240 1.886 -0.245223</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 8 14.5 12.80590 1.69410 1.886 0.898422</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 8 13.7 12.80590 0.89410 1.886 0.474162</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 14 14.2 13.99625 0.20375 1.886 0.108053</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 14 12.2 13.99625 -1.79625 1.886 -0.952596</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 27 13.7 14.22730 -0.52730 1.886 -0.279641</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 27 13.2 14.22730 -1.02730 1.886 -0.544803</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 48 13.6 13.33713 0.26287 1.886 0.139406</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 48 15.4 13.33713 2.06287 1.886 1.093991</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 70 10.4 11.84008 -1.44008 1.886 -0.763708</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 70 11.6 11.84008 -0.24008 1.886 -0.127318</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 91 10.0 10.30732 -0.30732 1.886 -0.162980</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 91 9.5 10.30732 -0.80732 1.886 -0.428142</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 120 9.1 8.33981 0.76019 1.886 0.403149</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 9 A1 120 9.0 8.33981 0.66019 1.886 0.350117</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 0 96.1 93.70349 2.39651 1.886 1.270926</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 0 94.3 93.70349 0.59651 1.886 0.316342</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 8 73.9 77.86253 -3.96253 1.886 -2.101429</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 8 73.9 77.86253 -3.96253 1.886 -2.101429</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 14 69.4 70.18665 -0.78665 1.886 -0.417182</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 14 73.1 70.18665 2.91335 1.886 1.545019</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 21 65.6 64.03245 1.56755 1.886 0.831308</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 21 65.3 64.03245 1.26755 1.886 0.672210</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 41 55.9 54.71491 1.18509 1.886 0.628480</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 41 54.4 54.71491 -0.31491 1.886 -0.167007</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 63 47.0 49.63436 -2.63436 1.886 -1.397065</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 63 49.3 49.63436 -0.33436 1.886 -0.177319</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 91 44.7 45.08853 -0.38853 1.886 -0.206049</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 91 46.7 45.08853 1.61147 1.886 0.854600</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 120 42.1 41.07653 1.02347 1.886 0.542772</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 parent 120 41.3 41.07653 0.22347 1.886 0.118513</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 8 3.3 4.08295 -0.78295 1.886 -0.415218</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 8 3.4 4.08295 -0.68295 1.886 -0.362186</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 14 3.9 6.04367 -2.14367 1.886 -1.136841</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 14 2.9 6.04367 -3.14367 1.886 -1.667165</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 21 6.4 7.59693 -1.19693 1.886 -0.634761</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 21 7.2 7.59693 -0.39693 1.886 -0.210502</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 41 9.1 9.86436 -0.76436 1.886 -0.405361</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 41 8.5 9.86436 -1.36436 1.886 -0.723555</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 63 11.7 10.99397 0.70603 1.886 0.374425</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 63 12.0 10.99397 1.00603 1.886 0.533522</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 91 13.3 11.91274 1.38726 1.886 0.735696</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 91 13.2 11.91274 1.28726 1.886 0.682663</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 120 14.3 12.66519 1.63481 1.886 0.866981</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 120 12.1 12.66519 -0.56519 1.886 -0.299733</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The following takes about 6 minutes</span></span></span> +<span class="r-in"><span><span class="co">#f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve",</span></span></span> +<span class="r-in"><span><span class="co"># control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co">#saemix::compare.saemix(list(</span></span></span> +<span class="r-in"><span><span class="co"># f_saem_dfop_sfo$so,</span></span></span> +<span class="r-in"><span><span class="co"># f_saem_dfop_sfo_deSolve$so))</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># If the model supports it, we can also use eigenvalue based solutions, which</span></span></span> +<span class="r-in"><span><span class="co"># take a similar amount of time</span></span></span> +<span class="r-in"><span><span class="co">#f_saem_sfo_sfo_eigen <- saem(f_mmkin["SFO-SFO", ], solution_type = "eigen",</span></span></span> +<span class="r-in"><span><span class="co"># control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))</span></span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -309,7 +703,7 @@ using <a href="mmkin.html">mmkin</a>.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <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> |