diff options
20 files changed, 33 insertions, 29 deletions
diff --git a/docs/articles/web_only/dimethenamid_2018.html b/docs/articles/web_only/dimethenamid_2018.html index 09aa5150..32653b5d 100644 --- a/docs/articles/web_only/dimethenamid_2018.html +++ b/docs/articles/web_only/dimethenamid_2018.html @@ -105,7 +105,7 @@ <h1 data-toc-skip>Example evaluations of the dimethenamid data from 2018</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 7 March 2022, built on 16 Mar 2022</h4> + <h4 data-toc-skip class="date">Last change 7 March 2022, built on 30 Jun 2022</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/dimethenamid_2018.rmd" class="external-link"><code>vignettes/web_only/dimethenamid_2018.rmd</code></a></small> <div class="hidden name"><code>dimethenamid_2018.rmd</code></div> @@ -155,20 +155,20 @@ error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <p>The plot of the individual SFO fits shown below suggests that at least in some datasets the degradation slows down towards later time points, and that the scatter of the residuals error is smaller for smaller values (panel to the right):</p> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_sfo_const-1.png" width="700"></p> <p>Using biexponential decline (DFOP) results in a slightly more random scatter of the residuals:</p> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_const-1.png" width="700"></p> <p>The population curve (bold line) in the above plot results from taking the mean of the individual transformed parameters, i.e. of log k1 and log k2, as well as of the logit of the g parameter of the DFOP model). Here, this procedure does not result in parameters that represent the degradation well, because in some datasets the fitted value for k2 is extremely close to zero, leading to a log k2 value that dominates the average. This is alleviated if only rate constants that pass the t-test for significant difference from zero (on the untransformed scale) are considered in the averaging:</p> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_const_test-1.png" width="700"></p> <p>While this is visually much more satisfactory, such an average procedure could introduce a bias, as not all results from the individual fits enter the population curve with the same weight. This is where nonlinear mixed-effects models can help out by treating all datasets with equally by fitting a parameter distribution model together with the degradation model and the error model (see below).</p> <p>The remaining trend of the residuals to be higher for higher predicted residues is reduced by using the two-component error model:</p> <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><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="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_tc_test-1.png" width="700"></p> <p>However, note that in the case of using this error model, the fits to the Flaach and BBA 2.3 datasets appear to be ill-defined, indicated by the fact that they did not converge:</p> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> @@ -222,7 +222,7 @@ f_parent_nlme_dfop_tc 3 10 671.91 702.34 -325.96 2 vs 3 134.69 <.0001 <p>While the SFO variants converge fast, the additional parameters introduced by this lead to convergence warnings for the DFOP model. The model comparison clearly show that adding correlations between random effects does not improve the fits.</p> <p>The selected model (DFOP with two-component error) fitted to the data assuming no correlations between random effects is shown below.</p> <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_nlme_dfop_tc</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><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_parent_nlme_dfop_tc</span><span class="op">)</span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/plot_parent_nlme-1.png" width="700"></p> </div> <div class="section level4"> @@ -369,7 +369,7 @@ DFOP tc more iterations 665.88 663.80</code></pre> <div class="section level3"> <h3 id="comparison">Comparison<a class="anchor" aria-label="anchor" href="#comparison"></a> </h3> -<p>The following table gives the AIC values obtained with both backend packages using the same control parameters (800 iterations burn-in, 300 iterations second phase, 15 chains). Note that</p> +<p>The following table gives the AIC values obtained with both backend packages using the same control parameters (800 iterations burn-in, 300 iterations second phase, 15 chains).</p> <div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">AIC_all</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span> check.names <span class="op">=</span> <span class="cn">FALSE</span>, diff --git a/docs/index.html b/docs/index.html index 4491b50f..0cd8de66 100644 --- a/docs/index.html +++ b/docs/index.html @@ -151,7 +151,7 @@ <li>The usual one-sided t-test for significant difference from zero is nevertheless shown based on estimators for the untransformed parameters.</li> <li>Summary and plotting functions. The <code>summary</code> of an <code>mkinfit</code> object is in fact a full report that should give enough information to be able to approximately reproduce the fit with other tools.</li> <li>The chi-squared error level as defined in the FOCUS kinetics guidance (see below) is calculated for each observed variable.</li> -<li>The ‘variance by variable’ error model which is often fitted using Iteratively Reweighted Least Squares (IRLS) should now be specified as <code>error_model = "obs"</code>.</li> +<li>The ‘variance by variable’ error model which is often fitted using Iteratively Reweighted Least Squares (IRLS) can be specified as <code>error_model = "obs"</code>.</li> </ul> </div> <div class="section level3"> diff --git a/docs/news/index.html b/docs/news/index.html index 4776f207..8c72e5ab 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -88,6 +88,7 @@ <li><p>‘saem()’: Slightly improve speed in the case that no analytical solution for saemix is implemented, activate a test of the respective code</p></li> <li><p>‘mean_degparms’: New argument ‘default_log_parms’ that makes it possible to supply a surrogate value (default) for log parameters that fail the t-test</p></li> <li><p>‘plot.mixed.mmkin’: Pass the frame argument also to residual plots, take the ‘default_log_parms’ argument for ‘mean_degparms’ used for constructing approximate population curves, plot population curve last to avoid that it is covered by data</p></li> +<li><p>‘plot.mkinfit’: Respect argument ‘maxabs’ for residual plots, and make it possible to give ylim as a list, for row layouts</p></li> </ul></div> <div class="section level2"> <h2 class="page-header" data-toc-text="1.1.0" id="mkin-110-2022-03-14">mkin 1.1.0 (2022-03-14)<a class="anchor" aria-label="anchor" href="#mkin-110-2022-03-14"></a></h2> diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index b94f7f0e..59dce612 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -11,7 +11,7 @@ articles: benchmarks: web_only/benchmarks.html compiled_models: web_only/compiled_models.html dimethenamid_2018: web_only/dimethenamid_2018.html -last_built: 2022-04-09T15:50Z +last_built: 2022-06-30T07:49Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png Binary files differindex fa5f3834..17a35806 100644 --- a/docs/reference/Rplot001.png +++ b/docs/reference/Rplot001.png diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png Binary files differindex 3caf465f..f06a860e 100644 --- a/docs/reference/Rplot002.png +++ b/docs/reference/Rplot002.png diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png Binary files differindex 88ebd2d4..f8bf10bb 100644 --- a/docs/reference/Rplot003.png +++ b/docs/reference/Rplot003.png diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png Binary files differindex 7e87d63d..12d337a4 100644 --- a/docs/reference/Rplot004.png +++ b/docs/reference/Rplot004.png diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png Binary files differindex 76f25647..cb419daa 100644 --- a/docs/reference/Rplot005.png +++ b/docs/reference/Rplot005.png diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html index 2516edff..1c70a094 100644 --- a/docs/reference/create_deg_func.html +++ b/docs/reference/create_deg_func.html @@ -120,8 +120,8 @@ <span class="r-in"> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.394 1.000 0.393 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.678 1.721 0.677 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.401 1.00 0.401 0.000 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 1.211 3.02 1.210 0.002 0</span> <span class="r-out co"><span class="r-pr">#></span> sys.child</span> <span class="r-out co"><span class="r-pr">#></span> 1 0</span> <span class="r-out co"><span class="r-pr">#></span> 2 0</span> @@ -134,8 +134,8 @@ <span class="r-in"> deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> <span class="r-in"> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.829 1.000 0.829 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 1.559 1.881 1.559 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.84 1.000 0.839 0.001 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 3.19 3.798 3.188 0.001 0</span> <span class="r-out co"><span class="r-pr">#></span> sys.child</span> <span class="r-out co"><span class="r-pr">#></span> 1 0</span> <span class="r-out co"><span class="r-pr">#></span> 2 0</span> diff --git a/docs/reference/dimethenamid_2018-3.png b/docs/reference/dimethenamid_2018-3.png Binary files differindex efb89bdb..7c876208 100644 --- a/docs/reference/dimethenamid_2018-3.png +++ b/docs/reference/dimethenamid_2018-3.png diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html index d2ed8647..e913fa27 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -202,9 +202,9 @@ specific pieces of information in the comments.</p> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_dmta_saem_tc</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.0 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sat Apr 9 18:03:34 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sat Apr 9 18:03:34 2022 </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: Thu Jun 30 10:21:01 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Jun 30 10:21:01 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_DMTA/dt = - k_DMTA * DMTA</span> @@ -217,7 +217,7 @@ specific pieces of information in the comments.</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 deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 787.836 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 1845.619 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 9 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: Two-component variance function </span> diff --git a/docs/reference/nlme.mmkin-1.png b/docs/reference/nlme.mmkin-1.png Binary files differindex d93b0950..45e4eebe 100644 --- a/docs/reference/nlme.mmkin-1.png +++ b/docs/reference/nlme.mmkin-1.png diff --git a/docs/reference/nlme.mmkin-2.png b/docs/reference/nlme.mmkin-2.png Binary files differindex 5afccfbb..b9a68e92 100644 --- a/docs/reference/nlme.mmkin-2.png +++ b/docs/reference/nlme.mmkin-2.png diff --git a/docs/reference/nlme.mmkin-3.png b/docs/reference/nlme.mmkin-3.png Binary files differindex bf3aac6c..2a724bed 100644 --- a/docs/reference/nlme.mmkin-3.png +++ b/docs/reference/nlme.mmkin-3.png diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 4c2ff570..b74d1e7b 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -155,7 +155,8 @@ variables in the model.</p></dd> <dt>xlim</dt> <dd><p>Plot range in x direction.</p></dd> <dt>ylim</dt> -<dd><p>Plot range in y direction.</p></dd> +<dd><p>Plot range in y direction. If given as a list, plot ranges +for the different plot rows can be given for row layout.</p></dd> <dt>col_obs</dt> <dd><p>Colors used for plotting the observed data and the corresponding model prediction lines.</p></dd> @@ -237,7 +238,9 @@ latex is being used for the formatting of the chi2 error level, if <span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, full <span class="op">=</span> <span class="st">"Metabolite M1"</span> <span class="op">)</span><span class="op">)</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">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> <span class="r-plt img"><img src="plot.mkinfit-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span class="fu">plot_res</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> diff --git a/docs/reference/saem-4.png b/docs/reference/saem-4.png Binary files differindex 5f65ba2e..bb775c25 100644 --- a/docs/reference/saem-4.png +++ b/docs/reference/saem-4.png diff --git a/docs/reference/saem.html b/docs/reference/saem.html index cc597665..f9e6565f 100644 --- a/docs/reference/saem.html +++ b/docs/reference/saem.html @@ -303,9 +303,9 @@ using <a href="mmkin.html">mmkin</a>.</p> <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-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.0 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:15:26 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:15:26 2022 </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: Thu Jun 30 10:23:53 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Jun 30 10:23:53 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> @@ -320,7 +320,7 @@ 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 8.741 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 8.85 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> diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html index 3f98bec7..4879269e 100644 --- a/docs/reference/summary.nlme.mmkin.html +++ b/docs/reference/summary.nlme.mmkin.html @@ -96,7 +96,7 @@ endpoints such as formation fractions and DT50 values. Optionally <div id="ref-usage"> <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for nlme.mmkin</span> -<span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</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">object</span>, data <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, @@ -201,12 +201,12 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-wrn co"><span class="r-pr">#></span> iteration limit reached without convergence (10)</span> <span class="r-in"><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span 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_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.155 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 14 08:58:29 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 14 08:58:29 2022 </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: Thu Jun 30 10:23:57 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Jun 30 10:23:57 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 = - k_parent * parent</span> @@ -216,7 +216,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.527 s using 4 iterations</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.538 s using 4 iterations</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/vignettes/web_only/dimethenamid_2018.rmd b/vignettes/web_only/dimethenamid_2018.rmd index f34ca3ae..41681d45 100644 --- a/vignettes/web_only/dimethenamid_2018.rmd +++ b/vignettes/web_only/dimethenamid_2018.rmd @@ -362,7 +362,7 @@ print(AIC_parent_saemix_methods_defaults) The following table gives the AIC values obtained with both backend packages using the same control parameters (800 iterations burn-in, 300 iterations -second phase, 15 chains). Note that +second phase, 15 chains). ```{r AIC_all, cache = FALSE} AIC_all <- data.frame( |
