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diff --git a/docs/news/index.html b/docs/news/index.html index 13b82597..4776f207 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -83,7 +83,11 @@ <div class="section level2"> <h2 class="page-header" data-toc-text="1.1.1" id="mkin-111">mkin 1.1.1<a class="anchor" aria-label="anchor" href="#mkin-111"></a></h2> -<ul><li>‘dimethenamid_2018’: Update example code to use saemix</li> +<ul><li><p>‘dimethenamid_2018’: Update example code to use saemix</p></li> +<li><p>‘CAKE_export’: Check for validity of the map argument, updates</p></li> +<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> </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 3e26de5b..b94f7f0e 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: 2022-03-16T13:42Z +last_built: 2022-04-09T15:50Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index 44297d1b..f16a9e6c 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -96,11 +96,11 @@ specified as well.</p> filename <span class="op">=</span> <span class="st">"CAKE_export.csf"</span>, path <span class="op">=</span> <span class="st">"."</span>, overwrite <span class="op">=</span> <span class="cn">FALSE</span>, - study <span class="op">=</span> <span class="st">"Codlemone aerobic soil degradation"</span>, + study <span class="op">=</span> <span class="st">"Degradinol aerobic soil degradation"</span>, description <span class="op">=</span> <span class="st">""</span>, time_unit <span class="op">=</span> <span class="st">"days"</span>, res_unit <span class="op">=</span> <span class="st">"% AR"</span>, - comment <span class="op">=</span> <span class="st">"Created using mkin::CAKE_export"</span>, + comment <span class="op">=</span> <span class="st">""</span>, date <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.Date</a></span><span class="op">(</span><span class="op">)</span>, optimiser <span class="op">=</span> <span class="st">"IRLS"</span> <span class="op">)</span></code></pre></div> diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png Binary files differindex 26efcdd2..fa5f3834 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 065f21f6..3caf465f 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 50a52a1c..88ebd2d4 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 0f3d8214..7e87d63d 100644 --- a/docs/reference/Rplot004.png +++ b/docs/reference/Rplot004.png diff --git a/docs/reference/dimethenamid_2018-1.png b/docs/reference/dimethenamid_2018-1.png Binary files differindex be59fc90..4300b0c0 100644 --- a/docs/reference/dimethenamid_2018-1.png +++ b/docs/reference/dimethenamid_2018-1.png diff --git a/docs/reference/dimethenamid_2018-2.png b/docs/reference/dimethenamid_2018-2.png Binary files differindex 0bbb14d8..36db063c 100644 --- a/docs/reference/dimethenamid_2018-2.png +++ b/docs/reference/dimethenamid_2018-2.png diff --git a/docs/reference/dimethenamid_2018-3.png b/docs/reference/dimethenamid_2018-3.png Binary files differindex 71087e85..efb89bdb 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 85e954ac..d2ed8647 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -186,20 +186,25 @@ specific pieces of information in the comments.</p> <span class="r-in"><span class="co"># between these variants</span></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="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span class="r-plt img"><img src="dimethenamid_2018-2.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="co"># Therefore we use nonlinear mixed-effects models</span></span> +<span class="r-in"><span class="co"># We can also specify a default value for the failing</span></span> +<span class="r-in"><span class="co"># log parameters, to mimic FOCUS guidance</span></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="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span class="r-in"> default_log_parms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">1000</span><span class="op">)</span></span> +<span class="r-plt img"><img src="dimethenamid_2018-3.png" alt="" width="700" height="433"></span> +<span class="r-in"><span class="co"># As these attempts are not satisfying, we use nonlinear mixed-effects models</span></span> <span class="r-in"><span class="co"># f_dmta_nlme_tc <- nlme(dmta_sfo_sfo3p_tc)</span></span> <span class="r-in"><span class="co"># nlme reaches maxIter = 50 without convergence</span></span> <span class="r-in"><span class="va">f_dmta_saem_tc</span> <span class="op"><-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span></span> <span class="r-in"><span class="co"># I am commenting out the convergence plot as rendering them</span></span> -<span class="r-in"><span class="co"># with pkgdown fails (at least without further tweaks to the </span></span> +<span class="r-in"><span class="co"># with pkgdown fails (at least without further tweaks to the</span></span> <span class="r-in"><span class="co"># graphics device used)</span></span> <span class="r-in"><span class="co">#saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")</span></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_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: Wed Mar 16 14:32:04 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Mar 16 14:32:04 2022 </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> </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> @@ -212,7 +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 927.963 s</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> 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> @@ -300,8 +305,7 @@ specific pieces of information in the comments.</p> <span class="r-in"><span class="co"># covariance.model = diag(c(0, rep(1, 7))))</span></span> <span class="r-in"><span class="co"># saemix::plot(f_dmta_saem_tc_2$so, plot.type = "convergence")</span></span> <span class="r-in"><span class="co"># This does not perform better judged by AIC and BIC</span></span> -<span class="r-in"><span class="fu">saemix</span><span class="fu">::</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_dmta_saem_tc</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_dmta_saem_tc_2</span><span class="op">$</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 saemix::compare.saemix(f_dmta_saem_tc$so, f_dmta_saem_tc_2$so):</span> object 'f_dmta_saem_tc_2' not found</span> +<span class="r-in"><span class="co"># saemix::compare.saemix(f_dmta_saem_tc$so, f_dmta_saem_tc_2$so)</span></span> <span class="r-in"><span class="co"># }</span></span> </code></pre></div> </div> diff --git a/docs/reference/mean_degparms.html b/docs/reference/mean_degparms.html index aaeb44ea..efe91b6f 100644 --- a/docs/reference/mean_degparms.html +++ b/docs/reference/mean_degparms.html @@ -87,7 +87,13 @@ </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mean_degparms</span><span class="op">(</span><span class="va">object</span>, random <span class="op">=</span> <span class="cn">FALSE</span>, test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>, conf.level <span class="op">=</span> <span class="fl">0.6</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mean_degparms</span><span class="op">(</span> + <span class="va">object</span>, + random <span class="op">=</span> <span class="cn">FALSE</span>, + test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>, + conf.level <span class="op">=</span> <span class="fl">0.6</span>, + default_log_parms <span class="op">=</span> <span class="cn">NA</span> +<span class="op">)</span></code></pre></div> </div> <div id="arguments"> @@ -103,6 +109,10 @@ rate constants) pass the t-test for significant difference from zero.</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>default_log_parms</dt> +<dd><p>If set to a numeric value, this is used +as a default value for the tested log parameters that failed the +t-test.</p></dd> </dl></div> <div id="value"> <h2>Value</h2> diff --git a/docs/reference/plot.mixed.mmkin-2.png b/docs/reference/plot.mixed.mmkin-2.png Binary files differindex 67c9b8ab..8678c166 100644 --- a/docs/reference/plot.mixed.mmkin-2.png +++ b/docs/reference/plot.mixed.mmkin-2.png diff --git a/docs/reference/plot.mixed.mmkin-3.png b/docs/reference/plot.mixed.mmkin-3.png Binary files differindex 0840c7da..9bd01852 100644 --- a/docs/reference/plot.mixed.mmkin-3.png +++ b/docs/reference/plot.mixed.mmkin-3.png diff --git a/docs/reference/plot.mixed.mmkin-4.png b/docs/reference/plot.mixed.mmkin-4.png Binary files differindex a78087bb..d2fa1ae1 100644 --- a/docs/reference/plot.mixed.mmkin-4.png +++ b/docs/reference/plot.mixed.mmkin-4.png diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html index b405b84a..52971427 100644 --- a/docs/reference/plot.mixed.mmkin.html +++ b/docs/reference/plot.mixed.mmkin.html @@ -99,6 +99,7 @@ pred_over <span class="op">=</span> <span class="cn">NULL</span>, test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>, conf.level <span class="op">=</span> <span class="fl">0.6</span>, + default_log_parms <span class="op">=</span> <span class="cn">NA</span>, ymax <span class="op">=</span> <span class="st">"auto"</span>, maxabs <span class="op">=</span> <span class="st">"auto"</span>, ncol.legend <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op"><=</span> <span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">+</span> <span class="fl">1</span>, <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op"><=</span> <span class="fl">8</span>, <span class="fl">3</span>, <span class="fl">4</span><span class="op">)</span><span class="op">)</span>, @@ -143,6 +144,9 @@ from <a href="mkinpredict.html">mkinpredict</a> with a compatible <a href="mkinm <dt>conf.level</dt> <dd><p>Passed to <a href="mean_degparms.html">mean_degparms</a> in the case of an <a href="mixed.html">mixed.mmkin</a> object</p></dd> +<dt>default_log_parms</dt> +<dd><p>Passed to <a href="mean_degparms.html">mean_degparms</a> in the case of an +<a href="mixed.html">mixed.mmkin</a> object</p></dd> <dt>ymax</dt> <dd><p>Vector of maximum y axis values</p></dd> <dt>maxabs</dt> |
