diff options
Diffstat (limited to 'docs/articles/web_only')
26 files changed, 1734 insertions, 1036 deletions
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 0dafb98a..ea20ecd9 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -62,19 +62,25 @@ <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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <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> <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -105,7 +111,7 @@ <h1 data-toc-skip>Example evaluation of FOCUS dataset Z</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 16 January 2018 (rebuilt 2022-05-18)</h4> + <h4 data-toc-skip class="date">Last change 16 January 2018 (rebuilt 2022-11-17)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/FOCUS_Z.rmd" class="external-link"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small> <div class="hidden name"><code>FOCUS_Z.rmd</code></div> @@ -120,88 +126,88 @@ </h2> <p>The following code defines the example dataset from Appendix 7 to the FOCUS kinetics report <span class="citation">(FOCUS Work Group on Degradation Kinetics 2014, 354)</span>.</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> -<span class="va">LOD</span> <span class="op">=</span> <span class="fl">0.5</span> -<span class="va">FOCUS_2006_Z</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> - t <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">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">4</span>, <span class="fl">7</span>, <span class="fl">10</span>, <span class="fl">14</span>, <span class="fl">21</span>, - <span class="fl">42</span>, <span class="fl">61</span>, <span class="fl">96</span>, <span class="fl">124</span><span class="op">)</span>, - Z0 <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">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>, - <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span><span class="op">)</span>, - Z1 <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">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="fl">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>, - <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>, - Z2 <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">0</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>, - <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>, - Z3 <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">0</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>, - <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span><span class="op">)</span><span class="op">)</span> - -<span class="va">FOCUS_2006_Z_mkin</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">FOCUS_2006_Z</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><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"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span><span class="va">LOD</span> <span class="op">=</span> <span class="fl">0.5</span></span> +<span><span class="va">FOCUS_2006_Z</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></span> +<span> t <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">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">4</span>, <span class="fl">7</span>, <span class="fl">10</span>, <span class="fl">14</span>, <span class="fl">21</span>,</span> +<span> <span class="fl">42</span>, <span class="fl">61</span>, <span class="fl">96</span>, <span class="fl">124</span><span class="op">)</span>,</span> +<span> Z0 <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">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>,</span> +<span> <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span><span class="op">)</span>,</span> +<span> Z1 <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">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="fl">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>,</span> +<span> <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>,</span> +<span> Z2 <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">0</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>,</span> +<span> <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>,</span> +<span> Z3 <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">0</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>,</span> +<span> <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span><span class="op">)</span><span class="op">)</span></span> +<span></span> +<span><span class="va">FOCUS_2006_Z_mkin</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">FOCUS_2006_Z</span><span class="op">)</span></span></code></pre></div> </div> <div class="section level2"> <h2 id="parent-and-one-metabolite">Parent and one metabolite<a class="anchor" aria-label="anchor" href="#parent-and-one-metabolite"></a> </h2> <p>The next step is to set up the models used for the kinetic analysis. As the simultaneous fit of parent and the first metabolite is usually straightforward, Step 1 (SFO for parent only) is skipped here. We start with the model 2a, with formation and decline of metabolite Z1 and the pathway from parent directly to sink included (default in mkin).</p> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.2a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> +<code class="sourceCode R"><span><span class="va">Z.2a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.2a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span> -<span class="co">## value of zero were removed from the data</span></code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.2a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">m.Z.2a</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div> -<pre><code><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span> -<span class="co">## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642</span> -<span class="co">## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600</span> -<span class="co">## k_Z1 0.48212 0.063265 7.6207 2.8154e-08 0.40341 0.5762</span> -<span class="co">## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000</span> -<span class="co">## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.2a</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> +<pre><code><span><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span></span> +<span><span class="co">## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642</span></span> +<span><span class="co">## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600</span></span> +<span><span class="co">## k_Z1 0.48212 0.063265 7.6207 2.8154e-08 0.40341 0.5762</span></span> +<span><span class="co">## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000</span></span> +<span><span class="co">## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</span></span></code></pre> <p>As obvious from the parameter summary (the component of the summary), the kinetic rate constant from parent compound Z to sink is very small and the t-test for this parameter suggests that it is not significantly different from zero. This suggests, in agreement with the analysis in the FOCUS kinetics report, to simplify the model by removing the pathway to sink.</p> <p>A similar result can be obtained when formation fractions are used in the model formulation:</p> <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.2a.ff</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, - use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> +<code class="sourceCode R"><span><span class="va">Z.2a.ff</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> +<span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.2a.ff</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a.ff</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span> -<span class="co">## value of zero were removed from the data</span></code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.2a.ff</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a.ff</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png" width="700"></p> <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">m.Z.2a.ff</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div> -<pre><code><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span> -<span class="co">## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642</span> -<span class="co">## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600</span> -<span class="co">## k_Z1 0.48212 0.063265 7.6207 2.8154e-08 0.40341 0.5762</span> -<span class="co">## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000</span> -<span class="co">## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> +<pre><code><span><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span></span> +<span><span class="co">## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642</span></span> +<span><span class="co">## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600</span></span> +<span><span class="co">## k_Z1 0.48212 0.063265 7.6207 2.8154e-08 0.40341 0.5762</span></span> +<span><span class="co">## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000</span></span> +<span><span class="co">## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</span></span></code></pre> <p>Here, the ilr transformed formation fraction fitted in the model takes a very large value, and the backtransformed formation fraction from parent Z to Z1 is practically unity. Here, the covariance matrix used for the calculation of confidence intervals is not returned as the model is overparameterised.</p> <p>A simplified model is obtained by removing the pathway to the sink. </p> <p>In the following, we use the parameterisation with formation fractions in order to be able to compare with the results in the FOCUS guidance, and as it makes it easier to use parameters obtained in a previous fit when adding a further metabolite.</p> <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> +<code class="sourceCode R"><span><span class="va">Z.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span> -<span class="co">## value of zero were removed from the data</span></code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> <div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.3</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.3</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png" width="700"></p> <div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">m.Z.3</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div> -<pre><code><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span> -<span class="co">## Z0_0 97.01488 2.597342 37.352 2.0106e-24 91.67597 102.3538</span> -<span class="co">## k_Z0 2.23601 0.146904 15.221 9.1477e-15 1.95354 2.5593</span> -<span class="co">## k_Z1 0.48212 0.041727 11.554 4.8268e-12 0.40355 0.5760</span> -<span class="co">## sigma 4.80411 0.620208 7.746 1.6110e-08 3.52925 6.0790</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.3</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> +<pre><code><span><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span></span> +<span><span class="co">## Z0_0 97.01488 2.597342 37.352 2.0106e-24 91.67597 102.3538</span></span> +<span><span class="co">## k_Z0 2.23601 0.146904 15.221 9.1477e-15 1.95354 2.5593</span></span> +<span><span class="co">## k_Z1 0.48212 0.041727 11.554 4.8268e-12 0.40355 0.5760</span></span> +<span><span class="co">## sigma 4.80411 0.620208 7.746 1.6110e-08 3.52925 6.0790</span></span></code></pre> <p>As there is only one transformation product for Z0 and no pathway to sink, the formation fraction is internally fixed to unity.</p> </div> <div class="section level2"> @@ -209,56 +215,58 @@ </h2> <p>As suggested in the FOCUS report, the pathway to sink was removed for metabolite Z1 as well in the next step. While this step appears questionable on the basis of the above results, it is followed here for the purpose of comparison. Also, in the FOCUS report, it is assumed that there is additional empirical evidence that Z1 quickly and exclusively hydrolyses to Z2.</p> <div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> +<code class="sourceCode R"><span><span class="va">Z.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span> -<span class="co">## value of zero were removed from the data</span></code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> <div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.5</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.5</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png" width="700"></p> <p>Finally, metabolite Z3 is added to the model. We use the optimised differential equation parameter values from the previous fit in order to accelerate the optimization.</p> <div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.FOCUS</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>, - Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, - use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> +<code class="sourceCode R"><span><span class="va">Z.FOCUS</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,</span> +<span> Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> +<span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb30"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.FOCUS</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.FOCUS</span>, <span class="va">FOCUS_2006_Z_mkin</span>, - parms.ini <span class="op">=</span> <span class="va">m.Z.5</span><span class="op">$</span><span class="va">bparms.ode</span>, - quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, :</span> -<span class="co">## Observations with value of zero were removed from the data</span></code></pre> -<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p> +<code class="sourceCode R"><span><span class="va">m.Z.FOCUS</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.FOCUS</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span> +<span> parms.ini <span class="op">=</span> <span class="va">m.Z.5</span><span class="op">$</span><span class="va">bparms.ode</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, :</span></span> +<span><span class="co">## Observations with value of zero were removed from the data</span></span></code></pre> +<pre><code><span><span class="co">## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation did not converge:</span></span> +<span><span class="co">## false convergence (8)</span></span></code></pre> <div class="sourceCode" id="cb33"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div> -<pre><code><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span> -<span class="co">## Z0_0 96.838397 1.994270 48.5583 4.0284e-42 92.826435 100.850359</span> -<span class="co">## k_Z0 2.215406 0.118459 18.7018 1.0416e-23 1.989466 2.467005</span> -<span class="co">## k_Z1 0.478300 0.028257 16.9267 6.2409e-22 0.424702 0.538662</span> -<span class="co">## k_Z2 0.451616 0.042137 10.7178 1.6305e-14 0.374328 0.544863</span> -<span class="co">## k_Z3 0.058693 0.015245 3.8499 1.7803e-04 0.034805 0.098976</span> -<span class="co">## f_Z2_to_Z3 0.471509 0.058352 8.0804 9.6622e-11 0.357739 0.588317</span> -<span class="co">## sigma 3.984431 0.383402 10.3923 4.5575e-14 3.213126 4.755736</span></code></pre> -<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## $ff</span> -<span class="co">## Z2_Z3 Z2_sink </span> -<span class="co">## 0.47151 0.52849 </span> -<span class="co">## </span> -<span class="co">## $distimes</span> -<span class="co">## DT50 DT90</span> -<span class="co">## Z0 0.31288 1.0394</span> -<span class="co">## Z1 1.44919 4.8141</span> -<span class="co">## Z2 1.53481 5.0985</span> -<span class="co">## Z3 11.80971 39.2310</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></span></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p> +<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> +<pre><code><span><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span></span> +<span><span class="co">## Z0_0 96.838822 1.994274 48.5584 4.0280e-42 92.826981 100.850664</span></span> +<span><span class="co">## k_Z0 2.215393 0.118458 18.7019 1.0413e-23 1.989456 2.466989</span></span> +<span><span class="co">## k_Z1 0.478305 0.028258 16.9266 6.2418e-22 0.424708 0.538666</span></span> +<span><span class="co">## k_Z2 0.451627 0.042139 10.7176 1.6314e-14 0.374339 0.544872</span></span> +<span><span class="co">## k_Z3 0.058692 0.015245 3.8499 1.7803e-04 0.034808 0.098965</span></span> +<span><span class="co">## f_Z2_to_Z3 0.471502 0.058351 8.0805 9.6608e-11 0.357769 0.588274</span></span> +<span><span class="co">## sigma 3.984431 0.383402 10.3923 4.5575e-14 3.213126 4.755736</span></span></code></pre> +<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## $ff</span></span> +<span><span class="co">## Z2_Z3 Z2_sink </span></span> +<span><span class="co">## 0.4715 0.5285 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $distimes</span></span> +<span><span class="co">## DT50 DT90</span></span> +<span><span class="co">## Z0 0.31288 1.0394</span></span> +<span><span class="co">## Z1 1.44917 4.8141</span></span> +<span><span class="co">## Z2 1.53478 5.0984</span></span> +<span><span class="co">## Z3 11.80986 39.2315</span></span></code></pre> <p>This fit corresponds to the final result chosen in Appendix 7 of the FOCUS report. Confidence intervals returned by mkin are based on internally transformed parameters, however.</p> </div> <div class="section level2"> @@ -266,107 +274,105 @@ </h2> <p>As the FOCUS report states, there is a certain tailing of the time course of metabolite Z3. Also, the time course of the parent compound is not fitted very well using the SFO model, as residues at a certain low level remain.</p> <p>Therefore, an additional model is offered here, using the single first-order reversible binding (SFORB) model for metabolite Z3. As expected, the <span class="math inline">\(\chi^2\)</span> error level is lower for metabolite Z3 using this model and the graphical fit for Z3 is improved. However, the covariance matrix is not returned.</p> -<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.mkin.1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>, - Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> -<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.mkin.1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.1</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span> -<span class="co">## value of zero were removed from the data</span></code></pre> -<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span><span class="op">)</span></code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p> +<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">Z.mkin.1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,</span> +<span> Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> +<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.1</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> <div class="sourceCode" id="cb42"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">m.Z.mkin.1</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">cov.unscaled</span></code></pre></div> -<pre><code><span class="co">## NULL</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span><span class="op">)</span></span></code></pre></div> +<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p> +<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">cov.unscaled</span></span></code></pre></div> +<pre><code><span><span class="co">## NULL</span></span></code></pre> <p>Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.</p> -<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.mkin.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> -<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.mkin.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span> -<span class="co">## value of zero were removed from the data</span></code></pre> -<pre><code><span class="co">## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Optimisation did not converge:</span> -<span class="co">## false convergence (8)</span></code></pre> +<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">Z.mkin.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> +<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> <div class="sourceCode" id="cb49"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.3</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.3</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png" width="700"></p> <p>This results in a much better representation of the behaviour of the parent compound Z0.</p> <p>Finally, Z3 is added as well. These models appear overparameterised (no covariance matrix returned) if the sink for Z1 is left in the models.</p> <div class="sourceCode" id="cb50"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.mkin.4</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>, - Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> +<code class="sourceCode R"><span><span class="va">Z.mkin.4</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,</span> +<span> Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb52"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.mkin.4</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.4</span>, <span class="va">FOCUS_2006_Z_mkin</span>, - parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.3</span><span class="op">$</span><span class="va">bparms.ode</span>, - quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini =</span> -<span class="co">## m.Z.mkin.3$bparms.ode, : Observations with value of zero were removed from the</span> -<span class="co">## data</span></code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.4</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.4</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span> +<span> parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.3</span><span class="op">$</span><span class="va">bparms.ode</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini =</span></span> +<span><span class="co">## m.Z.mkin.3$bparms.ode, : Observations with value of zero were removed from the</span></span> +<span><span class="co">## data</span></span></code></pre> <div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.4</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.4</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png" width="700"></p> <p>The error level of the fit, but especially of metabolite Z3, can be improved if the SFORB model is chosen for this metabolite, as this model is capable of representing the tailing of the metabolite decline phase.</p> <div class="sourceCode" id="cb55"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.mkin.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>, - Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> +<code class="sourceCode R"><span><span class="va">Z.mkin.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,</span> +<span> Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb57"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.mkin.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, - parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.4</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">]</span>, - quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini =</span> -<span class="co">## m.Z.mkin.4$bparms.ode[1:4], : Observations with value of zero were removed from</span> -<span class="co">## the data</span></code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span> +<span> parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.4</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">]</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini =</span></span> +<span><span class="co">## m.Z.mkin.4$bparms.ode[1:4], : Observations with value of zero were removed from</span></span> +<span><span class="co">## the data</span></span></code></pre> <div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png" width="700"></p> <p>The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized is excessively small, it seems reasonable to fix it to zero.</p> <div class="sourceCode" id="cb60"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.mkin.5a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, - parms.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><span class="va">m.Z.mkin.5</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span><span class="op">]</span>, - k_Z3_bound_free <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, - fixed_parms <span class="op">=</span> <span class="st">"k_Z3_bound_free"</span>, - quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini =</span> -<span class="co">## c(m.Z.mkin.5$bparms.ode[1:7], : Observations with value of zero were removed</span> -<span class="co">## from the data</span></code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.5a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span> +<span> parms.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><span class="va">m.Z.mkin.5</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span><span class="op">]</span>,</span> +<span> k_Z3_bound_free <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span> +<span> fixed_parms <span class="op">=</span> <span class="st">"k_Z3_bound_free"</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini =</span></span> +<span><span class="co">## c(m.Z.mkin.5$bparms.ode[1:7], : Observations with value of zero were removed</span></span> +<span><span class="co">## from the data</span></span></code></pre> <div class="sourceCode" id="cb62"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png" width="700"></p> <p>As expected, the residual plots for Z0 and Z3 are more random than in the case of the all SFO model for which they were shown above. In conclusion, the model is proposed as the best-fit model for the dataset from Appendix 7 of the FOCUS report.</p> <p>A graphical representation of the confidence intervals can finally be obtained.</p> <div class="sourceCode" id="cb63"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png" width="700"></p> <p>The endpoints obtained with this model are</p> <div class="sourceCode" id="cb64"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## $ff</span> -<span class="co">## Z0_free Z2_Z3 Z2_sink Z3_free </span> -<span class="co">## 1.00000 0.53656 0.46344 1.00000 </span> -<span class="co">## </span> -<span class="co">## $SFORB</span> -<span class="co">## Z0_b1 Z0_b2 Z3_b1 Z3_b2 </span> -<span class="co">## 2.4471376 0.0075126 0.0800073 0.0000000 </span> -<span class="co">## </span> -<span class="co">## $distimes</span> -<span class="co">## DT50 DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2</span> -<span class="co">## Z0 0.3043 1.1848 0.35666 0.28325 92.264 NA NA</span> -<span class="co">## Z1 1.5148 5.0320 NA NA NA NA NA</span> -<span class="co">## Z2 1.6414 5.4526 NA NA NA NA NA</span> -<span class="co">## Z3 NA NA NA NA NA 8.6636 Inf</span></code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## $ff</span></span> +<span><span class="co">## Z0_free Z2_Z3 Z2_sink Z3_free </span></span> +<span><span class="co">## 1.00000 0.53656 0.46344 1.00000 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $SFORB</span></span> +<span><span class="co">## Z0_b1 Z0_b2 Z0_g Z3_b1 Z3_b2 Z3_g </span></span> +<span><span class="co">## 2.4471322 0.0075125 0.9519862 0.0800069 0.0000000 0.9347820 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $distimes</span></span> +<span><span class="co">## DT50 DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2</span></span> +<span><span class="co">## Z0 0.3043 1.1848 0.35666 0.28325 92.266 NA NA</span></span> +<span><span class="co">## Z1 1.5148 5.0320 NA NA NA NA NA</span></span> +<span><span class="co">## Z2 1.6414 5.4526 NA NA NA NA NA</span></span> +<span><span class="co">## Z3 NA NA NA NA NA 8.6636 Inf</span></span></code></pre> <p>It is clear the degradation rate of Z3 towards the end of the experiment is very low as DT50_Z3_b2 (the second Eigenvalue of the system of two differential equations representing the SFORB system for Z3, corresponding to the slower rate constant of the DFOP model) is reported to be infinity. However, this appears to be a feature of the data.</p> </div> <div class="section level2"> @@ -398,7 +404,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer> diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png Binary files differindex 229bae82..bc6efaf7 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png Binary files differindex e13ad9aa..55c1b645 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png Binary files differindex ae160414..8e63cd04 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png Binary files differindex 23e270d1..3902e059 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png Binary files differindex 77965455..d95cac25 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png Binary files differindex 250d0df5..cb333a1c 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png Binary files differindex 5a01c03e..db807f14 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index df1e06db..b8ec5059 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -62,19 +62,25 @@ <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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <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> <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -105,7 +111,7 @@ <h1 data-toc-skip>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">26 February 2019 (rebuilt 2022-05-18)</h4> + <h4 data-toc-skip class="date">26 February 2019 (rebuilt 2022-11-17)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/NAFTA_examples.rmd" class="external-link"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small> <div class="hidden name"><code>NAFTA_examples.rmd</code></div> @@ -128,205 +134,205 @@ <h3 id="example-on-page-5-upper-panel">Example on page 5, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-5-upper-panel"></a> </h3> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p5a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> +<code class="sourceCode R"><span><span class="va">p5a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<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">p5a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><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">p5a</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5a-1.png" width="700"></p> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">p5a</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 465.21753 56.27506 32.06401 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 64.4304</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 95.8401 4.67e-21 92.245 99.4357</span> -<span class="co">## k_parent 0.0102 3.92e-12 0.009 0.0117</span> -<span class="co">## sigma 4.8230 3.81e-06 3.214 6.4318</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 1.01e+02 NA 9.91e+01 1.02e+02</span> -<span class="co">## k__iore_parent 1.54e-05 NA 4.08e-06 5.84e-05</span> -<span class="co">## N_parent 2.57e+00 NA 2.25e+00 2.89e+00</span> -<span class="co">## sigma 1.68e+00 NA 1.12e+00 2.24e+00</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.99e+01 1.41e-26 98.8116 101.0810</span> -<span class="co">## k1 2.67e-02 5.05e-06 0.0243 0.0295</span> -<span class="co">## k2 2.95e-12 5.00e-01 0.0000 Inf</span> -<span class="co">## g 6.47e-01 3.67e-06 0.6248 0.6677</span> -<span class="co">## sigma 1.27e+00 8.91e-06 0.8395 1.6929</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 67.7 2.25e+02 6.77e+01</span> -<span class="co">## IORE 58.2 1.07e+03 3.22e+02</span> -<span class="co">## DFOP 55.5 4.28e+11 2.35e+11</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 321.51</span></code></pre> +<code class="sourceCode R"><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">p5a</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 465.21753 56.27506 32.06401 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 64.4304</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 95.8401 4.67e-21 92.245 99.4357</span></span> +<span><span class="co">## k_parent 0.0102 3.92e-12 0.009 0.0117</span></span> +<span><span class="co">## sigma 4.8230 3.81e-06 3.214 6.4318</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.01e+02 NA 9.91e+01 1.02e+02</span></span> +<span><span class="co">## k__iore_parent 1.54e-05 NA 4.08e-06 5.84e-05</span></span> +<span><span class="co">## N_parent 2.57e+00 NA 2.25e+00 2.89e+00</span></span> +<span><span class="co">## sigma 1.68e+00 NA 1.12e+00 2.24e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.99e+01 1.41e-26 98.8116 101.0810</span></span> +<span><span class="co">## k1 2.67e-02 5.05e-06 0.0243 0.0295</span></span> +<span><span class="co">## k2 2.26e-12 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 6.47e-01 3.67e-06 0.6248 0.6677</span></span> +<span><span class="co">## sigma 1.27e+00 8.91e-06 0.8395 1.6929</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 67.7 2.25e+02 6.77e+01</span></span> +<span><span class="co">## IORE 58.2 1.07e+03 3.22e+02</span></span> +<span><span class="co">## DFOP 55.5 5.59e+11 3.07e+11</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 321.51</span></span></code></pre> </div> <div class="section level3"> <h3 id="example-on-page-5-lower-panel">Example on page 5, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-5-lower-panel"></a> </h3> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p5b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> +<code class="sourceCode R"><span><span class="va">p5b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> -<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">p5b</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><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">p5b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5b-1.png" width="700"></p> <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">p5b</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 94.81123 10.10936 7.55871 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 11.77879</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 96.497 2.32e-24 94.85271 98.14155</span> -<span class="co">## k_parent 0.008 3.42e-14 0.00737 0.00869</span> -<span class="co">## sigma 2.295 1.22e-05 1.47976 3.11036</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.85e+01 1.17e-28 9.79e+01 9.92e+01</span> -<span class="co">## k__iore_parent 1.53e-04 6.50e-03 7.21e-05 3.26e-04</span> -<span class="co">## N_parent 1.94e+00 5.88e-13 1.76e+00 2.12e+00</span> -<span class="co">## sigma 7.49e-01 1.63e-05 4.82e-01 1.02e+00</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.84e+01 1.24e-27 97.8078 98.9187</span> -<span class="co">## k1 1.55e-02 4.10e-04 0.0143 0.0167</span> -<span class="co">## k2 9.41e-12 5.00e-01 0.0000 Inf</span> -<span class="co">## g 6.89e-01 2.92e-03 0.6626 0.7142</span> -<span class="co">## sigma 6.48e-01 2.38e-05 0.4147 0.8813</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 86.6 2.88e+02 8.66e+01</span> -<span class="co">## IORE 85.5 7.17e+02 2.16e+02</span> -<span class="co">## DFOP 83.6 1.21e+11 7.36e+10</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 215.87</span></code></pre> +<code class="sourceCode R"><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">p5b</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 94.81123 10.10936 7.55871 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 11.77879</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.497 2.32e-24 94.85271 98.14155</span></span> +<span><span class="co">## k_parent 0.008 3.42e-14 0.00737 0.00869</span></span> +<span><span class="co">## sigma 2.295 1.22e-05 1.47976 3.11036</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.85e+01 1.17e-28 9.79e+01 9.92e+01</span></span> +<span><span class="co">## k__iore_parent 1.53e-04 6.50e-03 7.21e-05 3.26e-04</span></span> +<span><span class="co">## N_parent 1.94e+00 5.88e-13 1.76e+00 2.12e+00</span></span> +<span><span class="co">## sigma 7.49e-01 1.63e-05 4.82e-01 1.02e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.84e+01 1.24e-27 97.8078 98.9187</span></span> +<span><span class="co">## k1 1.55e-02 4.10e-04 0.0143 0.0167</span></span> +<span><span class="co">## k2 8.63e-12 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 6.89e-01 2.92e-03 0.6626 0.7142</span></span> +<span><span class="co">## sigma 6.48e-01 2.38e-05 0.4147 0.8813</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 86.6 2.88e+02 8.66e+01</span></span> +<span><span class="co">## IORE 85.5 7.17e+02 2.16e+02</span></span> +<span><span class="co">## DFOP 83.6 1.32e+11 8.04e+10</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 215.87</span></span></code></pre> </div> <div class="section level3"> <h3 id="example-on-page-6">Example on page 6<a class="anchor" aria-label="anchor" href="#example-on-page-6"></a> </h3> <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p6</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p6"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> +<code class="sourceCode R"><span><span class="va">p6</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p6"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> -<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">p6</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><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">p6</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p6-1.png" width="700"></p> <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">p6</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 188.45361 51.00699 42.46931 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 58.39888</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 94.7759 7.29e-24 92.3478 97.2039</span> -<span class="co">## k_parent 0.0179 8.02e-16 0.0166 0.0194</span> -<span class="co">## sigma 3.0696 3.81e-06 2.0456 4.0936</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 97.12446 2.63e-26 95.62461 98.62431</span> -<span class="co">## k__iore_parent 0.00252 1.95e-03 0.00134 0.00472</span> -<span class="co">## N_parent 1.49587 4.07e-13 1.33896 1.65279</span> -<span class="co">## sigma 1.59698 5.05e-06 1.06169 2.13227</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.66e+01 1.57e-25 95.3476 97.8979</span> -<span class="co">## k1 2.55e-02 7.33e-06 0.0233 0.0278</span> -<span class="co">## k2 4.40e-11 5.00e-01 0.0000 Inf</span> -<span class="co">## g 8.61e-01 7.55e-06 0.8314 0.8867</span> -<span class="co">## sigma 1.46e+00 6.93e-06 0.9661 1.9483</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 38.6 1.28e+02 3.86e+01</span> -<span class="co">## IORE 34.0 1.77e+02 5.32e+01</span> -<span class="co">## DFOP 34.1 7.43e+09 1.58e+10</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 53.17</span></code></pre> +<code class="sourceCode R"><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">p6</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 188.45361 51.00699 42.46931 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 58.39888</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 94.7759 7.29e-24 92.3478 97.2039</span></span> +<span><span class="co">## k_parent 0.0179 8.02e-16 0.0166 0.0194</span></span> +<span><span class="co">## sigma 3.0696 3.81e-06 2.0456 4.0936</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.12446 2.63e-26 95.62461 98.62431</span></span> +<span><span class="co">## k__iore_parent 0.00252 1.95e-03 0.00134 0.00472</span></span> +<span><span class="co">## N_parent 1.49587 4.07e-13 1.33896 1.65279</span></span> +<span><span class="co">## sigma 1.59698 5.05e-06 1.06169 2.13227</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.66e+01 1.57e-25 95.3476 97.8979</span></span> +<span><span class="co">## k1 2.55e-02 7.33e-06 0.0233 0.0278</span></span> +<span><span class="co">## k2 3.22e-11 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 8.61e-01 7.55e-06 0.8314 0.8867</span></span> +<span><span class="co">## sigma 1.46e+00 6.93e-06 0.9661 1.9483</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 38.6 1.28e+02 3.86e+01</span></span> +<span><span class="co">## IORE 34.0 1.77e+02 5.32e+01</span></span> +<span><span class="co">## DFOP 34.1 1.01e+10 2.15e+10</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 53.17</span></span></code></pre> </div> <div class="section level3"> <h3 id="example-on-page-7">Example on page 7<a class="anchor" aria-label="anchor" href="#example-on-page-7"></a> </h3> <div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p7</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p7"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> +<code class="sourceCode R"><span><span class="va">p7</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p7"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> -<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">p7</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><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">p7</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p7-1.png" width="700"></p> <div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">p7</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 3661.661 3195.030 3174.145 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 3334.194</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 96.41796 4.80e-53 93.32245 99.51347</span> -<span class="co">## k_parent 0.00735 7.64e-21 0.00641 0.00843</span> -<span class="co">## sigma 7.94557 1.83e-15 6.46713 9.42401</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.92e+01 NA 9.55e+01 1.03e+02</span> -<span class="co">## k__iore_parent 1.60e-05 NA 1.45e-07 1.77e-03</span> -<span class="co">## N_parent 2.45e+00 NA 1.35e+00 3.54e+00</span> -<span class="co">## sigma 7.42e+00 NA 6.04e+00 8.80e+00</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.89e+01 9.44e-49 95.4640 102.2573</span> -<span class="co">## k1 1.81e-02 1.75e-01 0.0116 0.0281</span> -<span class="co">## k2 2.81e-10 5.00e-01 0.0000 Inf</span> -<span class="co">## g 6.06e-01 2.19e-01 0.4826 0.7178</span> -<span class="co">## sigma 7.40e+00 2.97e-15 6.0201 8.7754</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 94.3 3.13e+02 9.43e+01</span> -<span class="co">## IORE 96.7 1.51e+03 4.55e+02</span> -<span class="co">## DFOP 96.4 4.87e+09 2.46e+09</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 454.55</span></code></pre> +<code class="sourceCode R"><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">p7</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 3661.661 3195.030 3174.145 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 3334.194</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.41796 4.80e-53 93.32245 99.51347</span></span> +<span><span class="co">## k_parent 0.00735 7.64e-21 0.00641 0.00843</span></span> +<span><span class="co">## sigma 7.94557 1.83e-15 6.46713 9.42401</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.92e+01 NA 9.55e+01 1.03e+02</span></span> +<span><span class="co">## k__iore_parent 1.60e-05 NA 1.45e-07 1.77e-03</span></span> +<span><span class="co">## N_parent 2.45e+00 NA 1.35e+00 3.54e+00</span></span> +<span><span class="co">## sigma 7.42e+00 NA 6.04e+00 8.80e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.89e+01 9.44e-49 95.4640 102.2573</span></span> +<span><span class="co">## k1 1.81e-02 1.75e-01 0.0116 0.0281</span></span> +<span><span class="co">## k2 3.63e-10 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 6.06e-01 2.19e-01 0.4826 0.7178</span></span> +<span><span class="co">## sigma 7.40e+00 2.97e-15 6.0201 8.7754</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 94.3 3.13e+02 9.43e+01</span></span> +<span><span class="co">## IORE 96.7 1.51e+03 4.55e+02</span></span> +<span><span class="co">## DFOP 96.4 3.77e+09 1.91e+09</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 454.55</span></span></code></pre> </div> </div> <div class="section level2"> @@ -337,52 +343,52 @@ </h3> <p>For this dataset, the IORE fit does not converge when the default starting values used by mkin for the IORE model are used. Therefore, a lower value for the rate constant is used here.</p> <div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p8</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p8"</span><span class="op">]</span><span class="op">]</span>, parms.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>k__iore_parent <span class="op">=</span> <span class="fl">1e-3</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> +<code class="sourceCode R"><span><span class="va">p8</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p8"</span><span class="op">]</span><span class="op">]</span>, parms.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>k__iore_parent <span class="op">=</span> <span class="fl">1e-3</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> -<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">p8</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><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">p8</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p> <div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">p8</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 1996.9408 444.9237 547.5616 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 477.4924</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 88.16549 6.53e-29 83.37344 92.95754</span> -<span class="co">## k_parent 0.00803 1.67e-13 0.00674 0.00957</span> -<span class="co">## sigma 7.44786 4.17e-10 5.66209 9.23363</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.77e+01 7.03e-35 9.44e+01 1.01e+02</span> -<span class="co">## k__iore_parent 6.14e-05 3.20e-02 2.12e-05 1.78e-04</span> -<span class="co">## N_parent 2.27e+00 4.23e-18 2.00e+00 2.54e+00</span> -<span class="co">## sigma 3.52e+00 5.36e-10 2.67e+00 4.36e+00</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 95.70619 8.99e-32 91.87941 99.53298</span> -<span class="co">## k1 0.02500 5.25e-04 0.01422 0.04394</span> -<span class="co">## k2 0.00273 6.84e-03 0.00125 0.00597</span> -<span class="co">## g 0.58835 2.84e-06 0.36595 0.77970</span> -<span class="co">## sigma 3.90001 6.94e-10 2.96260 4.83741</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 86.3 287 86.3</span> -<span class="co">## IORE 53.4 668 201.0</span> -<span class="co">## DFOP 55.6 517 253.0</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 201.03</span></code></pre> +<code class="sourceCode R"><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">p8</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 1996.9408 444.9237 547.5616 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 477.4924</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 88.16549 6.53e-29 83.37344 92.95754</span></span> +<span><span class="co">## k_parent 0.00803 1.67e-13 0.00674 0.00957</span></span> +<span><span class="co">## sigma 7.44786 4.17e-10 5.66209 9.23363</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.77e+01 7.03e-35 9.44e+01 1.01e+02</span></span> +<span><span class="co">## k__iore_parent 6.14e-05 3.20e-02 2.12e-05 1.78e-04</span></span> +<span><span class="co">## N_parent 2.27e+00 4.23e-18 2.00e+00 2.54e+00</span></span> +<span><span class="co">## sigma 3.52e+00 5.36e-10 2.67e+00 4.36e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 95.70619 8.99e-32 91.87941 99.53298</span></span> +<span><span class="co">## k1 0.02500 5.25e-04 0.01422 0.04394</span></span> +<span><span class="co">## k2 0.00273 6.84e-03 0.00125 0.00597</span></span> +<span><span class="co">## g 0.58835 2.84e-06 0.36595 0.77970</span></span> +<span><span class="co">## sigma 3.90001 6.94e-10 2.96260 4.83741</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 86.3 287 86.3</span></span> +<span><span class="co">## IORE 53.4 668 201.0</span></span> +<span><span class="co">## DFOP 55.6 517 253.0</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 201.03</span></span></code></pre> </div> </div> <div class="section level2"> @@ -392,160 +398,165 @@ <h3 id="example-on-page-9-upper-panel">Example on page 9, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-9-upper-panel"></a> </h3> <div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p9a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> +<code class="sourceCode R"><span><span class="va">p9a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> -<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">p9a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><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">p9a</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p> <div class="sourceCode" id="cb35"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">p9a</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 839.35238 88.57064 9.93363 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 105.5678</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 88.1933 3.06e-12 79.9447 96.4419</span> -<span class="co">## k_parent 0.0409 2.07e-07 0.0324 0.0516</span> -<span class="co">## sigma 7.2429 3.92e-05 4.4768 10.0090</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.89e+01 1.12e-16 9.54e+01 1.02e+02</span> -<span class="co">## k__iore_parent 1.93e-05 1.13e-01 3.49e-06 1.06e-04</span> -<span class="co">## N_parent 2.91e+00 1.45e-09 2.50e+00 3.32e+00</span> -<span class="co">## sigma 2.35e+00 5.31e-05 1.45e+00 3.26e+00</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.85e+01 2.54e-20 97.390 99.672</span> -<span class="co">## k1 1.38e-01 3.52e-05 0.131 0.146</span> -<span class="co">## k2 9.02e-13 5.00e-01 0.000 Inf</span> -<span class="co">## g 6.52e-01 8.13e-06 0.642 0.661</span> -<span class="co">## sigma 7.88e-01 6.13e-02 0.481 1.095</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 16.9 5.63e+01 1.69e+01</span> -<span class="co">## IORE 11.6 3.37e+02 1.01e+02</span> -<span class="co">## DFOP 10.5 1.38e+12 7.68e+11</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 101.43</span></code></pre> +<code class="sourceCode R"><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">p9a</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 839.35238 88.57064 9.93363 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 105.5678</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 88.1933 3.06e-12 79.9447 96.4419</span></span> +<span><span class="co">## k_parent 0.0409 2.07e-07 0.0324 0.0516</span></span> +<span><span class="co">## sigma 7.2429 3.92e-05 4.4768 10.0090</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.89e+01 1.12e-16 9.54e+01 1.02e+02</span></span> +<span><span class="co">## k__iore_parent 1.93e-05 1.13e-01 3.49e-06 1.06e-04</span></span> +<span><span class="co">## N_parent 2.91e+00 1.45e-09 2.50e+00 3.32e+00</span></span> +<span><span class="co">## sigma 2.35e+00 5.31e-05 1.45e+00 3.26e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.85e+01 2.54e-20 97.390 99.672</span></span> +<span><span class="co">## k1 1.38e-01 3.52e-05 0.131 0.146</span></span> +<span><span class="co">## k2 9.02e-13 5.00e-01 0.000 Inf</span></span> +<span><span class="co">## g 6.52e-01 8.13e-06 0.642 0.661</span></span> +<span><span class="co">## sigma 7.88e-01 6.13e-02 0.481 1.095</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 16.9 5.63e+01 1.69e+01</span></span> +<span><span class="co">## IORE 11.6 3.37e+02 1.01e+02</span></span> +<span><span class="co">## DFOP 10.5 1.38e+12 7.69e+11</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 101.43</span></span></code></pre> <p>In this example, the residuals of the SFO indicate a lack of fit of this model, so even if it was an abiotic experiment, the data do not suggest a simple exponential decline.</p> </div> <div class="section level3"> <h3 id="example-on-page-9-lower-panel">Example on page 9, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-9-lower-panel"></a> </h3> <div class="sourceCode" id="cb37"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p9b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r"> -<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">p9b</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="va">p9b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p9b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">p9b</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 35.64867 23.22334 35.64867 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 28.54188</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 94.7123 2.15e-19 93.178 96.2464</span> -<span class="co">## k_parent 0.0389 4.47e-14 0.037 0.0408</span> -<span class="co">## sigma 1.5957 1.28e-04 0.932 2.2595</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 93.863 2.32e-18 92.4565 95.269</span> -<span class="co">## k__iore_parent 0.127 1.85e-02 0.0504 0.321</span> -<span class="co">## N_parent 0.711 1.88e-05 0.4843 0.937</span> -<span class="co">## sigma 1.288 1.76e-04 0.7456 1.830</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 94.7123 1.61e-16 93.1355 96.2891</span> -<span class="co">## k1 0.0389 1.08e-04 0.0266 0.0569</span> -<span class="co">## k2 0.0389 2.24e-04 0.0255 0.0592</span> -<span class="co">## g 0.5256 5.00e-01 0.0000 1.0000</span> -<span class="co">## sigma 1.5957 2.50e-04 0.9135 2.2779</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 17.8 59.2 17.8</span> -<span class="co">## IORE 18.4 49.2 14.8</span> -<span class="co">## DFOP 17.8 59.2 17.8</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 14.8</span></code></pre> +<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p9b</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 35.64867 23.22334 35.64867 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 28.54188</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 94.7123 2.15e-19 93.178 96.2464</span></span> +<span><span class="co">## k_parent 0.0389 4.47e-14 0.037 0.0408</span></span> +<span><span class="co">## sigma 1.5957 1.28e-04 0.932 2.2595</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 93.863 2.32e-18 92.4565 95.269</span></span> +<span><span class="co">## k__iore_parent 0.127 1.85e-02 0.0504 0.321</span></span> +<span><span class="co">## N_parent 0.711 1.88e-05 0.4843 0.937</span></span> +<span><span class="co">## sigma 1.288 1.76e-04 0.7456 1.830</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 94.7123 1.61e-16 93.1355 96.2891</span></span> +<span><span class="co">## k1 0.0389 1.08e-04 0.0266 0.0569</span></span> +<span><span class="co">## k2 0.0389 2.23e-04 0.0255 0.0592</span></span> +<span><span class="co">## g 0.5256 NaN NA NA</span></span> +<span><span class="co">## sigma 1.5957 2.50e-04 0.9135 2.2779</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 17.8 59.2 17.8</span></span> +<span><span class="co">## IORE 18.4 49.2 14.8</span></span> +<span><span class="co">## DFOP 17.8 59.2 17.8</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 14.8</span></span></code></pre> <p>Here, mkin gives a longer slow DT50 for the DFOP model (17.8 days) than PestDF (13.5 days). Presumably, this is related to the fact that PestDF gives a negative value for the proportion of the fast degradation which should be between 0 and 1, inclusive. This parameter is called f in PestDF and g in mkin. In mkin, it is restricted to the interval from 0 to 1.</p> </div> <div class="section level3"> <h3 id="example-on-page-10">Example on page 10<a class="anchor" aria-label="anchor" href="#example-on-page-10"></a> </h3> -<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p10</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p10"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> -<span class="co">## doubtful</span></code></pre> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb49"><pre class="downlit sourceCode r"> -<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">p10</span><span class="op">)</span></code></pre></div> +<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">p10</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p10"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p10</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">p10</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 899.4089 336.4348 899.4089 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 413.4841</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 101.7315 6.42e-11 91.9259 111.5371</span> -<span class="co">## k_parent 0.0495 1.70e-07 0.0404 0.0607</span> -<span class="co">## sigma 8.0152 1.28e-04 4.6813 11.3491</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 96.86 3.32e-12 90.848 102.863</span> -<span class="co">## k__iore_parent 2.96 7.91e-02 0.687 12.761</span> -<span class="co">## N_parent 0.00 5.00e-01 -0.372 0.372</span> -<span class="co">## sigma 4.90 1.77e-04 2.837 6.968</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 101.7315 1.41e-09 91.6534 111.8097</span> -<span class="co">## k1 0.0495 6.32e-03 0.0241 0.1018</span> -<span class="co">## k2 0.0495 2.41e-03 0.0272 0.0901</span> -<span class="co">## g 0.4487 5.00e-01 NA NA</span> -<span class="co">## sigma 8.0152 2.50e-04 4.5886 11.4418</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 14.0 46.5 14.00</span> -<span class="co">## IORE 16.4 29.4 8.86</span> -<span class="co">## DFOP 14.0 46.5 14.00</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 8.86</span></code></pre> +<div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p10</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 899.4089 336.4348 899.4089 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 413.4841</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 101.7315 6.42e-11 91.9259 111.5371</span></span> +<span><span class="co">## k_parent 0.0495 1.70e-07 0.0404 0.0607</span></span> +<span><span class="co">## sigma 8.0152 1.28e-04 4.6813 11.3491</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.86 3.32e-12 90.848 102.863</span></span> +<span><span class="co">## k__iore_parent 2.96 7.91e-02 0.687 12.761</span></span> +<span><span class="co">## N_parent 0.00 5.00e-01 -0.372 0.372</span></span> +<span><span class="co">## sigma 4.90 1.77e-04 2.837 6.968</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 101.7315 1.41e-09 91.6534 111.8097</span></span> +<span><span class="co">## k1 0.0495 6.58e-03 0.0303 0.0809</span></span> +<span><span class="co">## k2 0.0495 2.60e-03 0.0410 0.0598</span></span> +<span><span class="co">## g 0.4487 5.00e-01 NA NA</span></span> +<span><span class="co">## sigma 8.0152 2.50e-04 4.5886 11.4418</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 14.0 46.5 14.00</span></span> +<span><span class="co">## IORE 16.4 29.4 8.86</span></span> +<span><span class="co">## DFOP 14.0 46.5 14.00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 8.86</span></span></code></pre> <p>Here, a value below N is given for the IORE model, because the data suggests a faster decline towards the end of the experiment, which appears physically rather unlikely in the case of a photolysis study. It seems PestDF does not constrain N to values above zero, thus the slight difference in IORE model parameters between PestDF and mkin.</p> </div> </div> @@ -555,53 +566,53 @@ <div class="section level3"> <h3 id="example-on-page-11">Example on page 11<a class="anchor" aria-label="anchor" href="#example-on-page-11"></a> </h3> -<div class="sourceCode" id="cb52"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p11</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p11"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb55"><pre class="downlit sourceCode r"> -<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">p11</span><span class="op">)</span></code></pre></div> -<p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> <div class="sourceCode" id="cb56"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">p11</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 579.6805 204.7932 144.7783 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 251.6944</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 96.15820 4.83e-13 90.24934 1.02e+02</span> -<span class="co">## k_parent 0.00321 4.71e-05 0.00222 4.64e-03</span> -<span class="co">## sigma 6.43473 1.28e-04 3.75822 9.11e+00</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 1.05e+02 NA 9.90e+01 1.10e+02</span> -<span class="co">## k__iore_parent 3.11e-17 NA 1.35e-20 7.18e-14</span> -<span class="co">## N_parent 8.36e+00 NA 6.62e+00 1.01e+01</span> -<span class="co">## sigma 3.82e+00 NA 2.21e+00 5.44e+00</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 1.05e+02 9.47e-13 99.9990 109.1224</span> -<span class="co">## k1 4.41e-02 5.95e-03 0.0296 0.0658</span> -<span class="co">## k2 9.93e-13 5.00e-01 0.0000 Inf</span> -<span class="co">## g 3.22e-01 1.45e-03 0.2814 0.3650</span> -<span class="co">## sigma 3.22e+00 3.52e-04 1.8410 4.5906</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 2.16e+02 7.18e+02 2.16e+02</span> -<span class="co">## IORE 9.73e+02 1.37e+08 4.11e+07</span> -<span class="co">## DFOP 3.07e+11 1.93e+12 6.98e+11</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 41148171</span></code></pre> +<code class="sourceCode R"><span><span class="va">p11</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p11"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p11</span><span class="op">)</span></span></code></pre></div> +<p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> +<div class="sourceCode" id="cb60"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p11</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 579.6805 204.7932 144.7783 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 251.6944</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.15820 4.83e-13 90.24934 1.02e+02</span></span> +<span><span class="co">## k_parent 0.00321 4.71e-05 0.00222 4.64e-03</span></span> +<span><span class="co">## sigma 6.43473 1.28e-04 3.75822 9.11e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.05e+02 NA 9.90e+01 1.10e+02</span></span> +<span><span class="co">## k__iore_parent 3.11e-17 NA 1.35e-20 7.18e-14</span></span> +<span><span class="co">## N_parent 8.36e+00 NA 6.62e+00 1.01e+01</span></span> +<span><span class="co">## sigma 3.82e+00 NA 2.21e+00 5.44e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.05e+02 9.47e-13 99.9990 109.1224</span></span> +<span><span class="co">## k1 4.41e-02 5.95e-03 0.0296 0.0658</span></span> +<span><span class="co">## k2 9.94e-13 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 3.22e-01 1.45e-03 0.2814 0.3650</span></span> +<span><span class="co">## sigma 3.22e+00 3.52e-04 1.8410 4.5906</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 2.16e+02 7.18e+02 2.16e+02</span></span> +<span><span class="co">## IORE 9.73e+02 1.37e+08 4.11e+07</span></span> +<span><span class="co">## DFOP 3.07e+11 1.93e+12 6.98e+11</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 41148170</span></span></code></pre> <p>In this case, the DFOP fit reported for PestDF resulted in a negative value for the slower rate constant, which is not possible in mkin. The other results are in agreement.</p> </div> </div> @@ -612,380 +623,379 @@ <div class="section level3"> <h3 id="example-on-page-12-upper-panel">Example on page 12, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-12-upper-panel"></a> </h3> -<div class="sourceCode" id="cb58"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p12a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span> -<span class="co">## matrix</span> - -<span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span> -<span class="co">## matrix</span></code></pre> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb62"><pre class="downlit sourceCode r"> -<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">p12a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="va">p12a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span></span> +<span><span class="co">## matrix</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb70"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p12a</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<div class="sourceCode" id="cb63"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">p12a</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 695.4440 220.0685 695.4440 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 270.4679</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 100.521 8.75e-12 92.461 108.581</span> -<span class="co">## k_parent 0.124 3.61e-08 0.104 0.148</span> -<span class="co">## sigma 7.048 1.28e-04 4.116 9.980</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 96.823 NA NA NA</span> -<span class="co">## k__iore_parent 2.436 NA NA NA</span> -<span class="co">## N_parent 0.263 NA NA NA</span> -<span class="co">## sigma 3.965 NA NA NA</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 100.521 NA NA NA</span> -<span class="co">## k1 0.124 NA NA NA</span> -<span class="co">## k2 0.124 NA NA NA</span> -<span class="co">## g 0.793 NA NA NA</span> -<span class="co">## sigma 7.048 NA NA NA</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 5.58 18.5 5.58</span> -<span class="co">## IORE 6.49 13.2 3.99</span> -<span class="co">## DFOP 5.58 18.5 5.58</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 3.99</span></code></pre> +<div class="sourceCode" id="cb71"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p12a</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 695.4440 220.0685 695.4440 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 270.4679</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 100.521 8.75e-12 92.461 108.581</span></span> +<span><span class="co">## k_parent 0.124 3.61e-08 0.104 0.148</span></span> +<span><span class="co">## sigma 7.048 1.28e-04 4.116 9.980</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.823 NA NA NA</span></span> +<span><span class="co">## k__iore_parent 2.436 NA NA NA</span></span> +<span><span class="co">## N_parent 0.263 NA NA NA</span></span> +<span><span class="co">## sigma 3.965 NA NA NA</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 100.521 2.74e-10 92.2366 108.805</span></span> +<span><span class="co">## k1 0.124 2.53e-05 0.0908 0.170</span></span> +<span><span class="co">## k2 0.124 2.52e-02 0.0456 0.339</span></span> +<span><span class="co">## g 0.793 NaN NA NA</span></span> +<span><span class="co">## sigma 7.048 2.50e-04 4.0349 10.061</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 5.58 18.5 5.58</span></span> +<span><span class="co">## IORE 6.49 13.2 3.99</span></span> +<span><span class="co">## DFOP 5.58 18.5 5.58</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 3.99</span></span></code></pre> </div> <div class="section level3"> <h3 id="example-on-page-12-lower-panel">Example on page 12, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-12-lower-panel"></a> </h3> -<div class="sourceCode" id="cb65"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p12b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in qt(alpha/2, rdf): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in qt(1 - alpha/2, rdf): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</span></code></pre> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb71"><pre class="downlit sourceCode r"> -<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">p12b</span><span class="op">)</span></code></pre></div> +<div class="sourceCode" id="cb73"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">p12b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in qt(alpha/2, rdf): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in qt(1 - alpha/2, rdf): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb80"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p12b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<div class="sourceCode" id="cb72"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">p12b</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 58.90242 19.06353 58.90242 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 51.51756</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 97.6840 0.00039 85.9388 109.4292</span> -<span class="co">## k_parent 0.0589 0.00261 0.0431 0.0805</span> -<span class="co">## sigma 3.4323 0.04356 -1.2377 8.1023</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 95.523 0.0055 74.539157 116.51</span> -<span class="co">## k__iore_parent 0.333 0.1433 0.000717 154.57</span> -<span class="co">## N_parent 0.568 0.0677 -0.989464 2.13</span> -<span class="co">## sigma 1.953 0.0975 -5.893100 9.80</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 97.6840 NaN NaN NaN</span> -<span class="co">## k1 0.0589 NaN NA NA</span> -<span class="co">## k2 0.0589 NaN NA NA</span> -<span class="co">## g 0.6473 NaN NA NA</span> -<span class="co">## sigma 3.4323 NaN NaN NaN</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 11.8 39.1 11.80</span> -<span class="co">## IORE 12.9 31.4 9.46</span> -<span class="co">## DFOP 11.8 39.1 11.80</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 9.46</span></code></pre> +<div class="sourceCode" id="cb81"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p12b</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 58.90242 19.06353 58.90242 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 51.51756</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.6840 0.00039 85.9388 109.4292</span></span> +<span><span class="co">## k_parent 0.0589 0.00261 0.0431 0.0805</span></span> +<span><span class="co">## sigma 3.4323 0.04356 -1.2377 8.1023</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 95.523 0.0055 74.539157 116.51</span></span> +<span><span class="co">## k__iore_parent 0.333 0.1433 0.000717 154.57</span></span> +<span><span class="co">## N_parent 0.568 0.0677 -0.989464 2.13</span></span> +<span><span class="co">## sigma 1.953 0.0975 -5.893100 9.80</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.6840 NaN NaN NaN</span></span> +<span><span class="co">## k1 0.0589 NaN NA NA</span></span> +<span><span class="co">## k2 0.0589 NaN NA NA</span></span> +<span><span class="co">## g 0.6473 NaN NA NA</span></span> +<span><span class="co">## sigma 3.4323 NaN NaN NaN</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 11.8 39.1 11.80</span></span> +<span><span class="co">## IORE 12.9 31.4 9.46</span></span> +<span><span class="co">## DFOP 11.8 39.1 11.80</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 9.46</span></span></code></pre> </div> <div class="section level3"> <h3 id="example-on-page-13">Example on page 13<a class="anchor" aria-label="anchor" href="#example-on-page-13"></a> </h3> -<div class="sourceCode" id="cb74"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p13</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> -<span class="co">## doubtful</span></code></pre> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb80"><pre class="downlit sourceCode r"> -<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">p13</span><span class="op">)</span></code></pre></div> +<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">p13</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb86"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p13</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<div class="sourceCode" id="cb81"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">p13</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 174.5971 142.3951 174.5971 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 172.131</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 92.73500 5.99e-17 89.61936 95.85065</span> -<span class="co">## k_parent 0.00258 2.42e-09 0.00223 0.00299</span> -<span class="co">## sigma 3.41172 7.07e-05 2.05455 4.76888</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 91.6016 6.34e-16 88.53086 94.672</span> -<span class="co">## k__iore_parent 0.0396 2.36e-01 0.00207 0.759</span> -<span class="co">## N_parent 0.3541 1.46e-01 -0.35153 1.060</span> -<span class="co">## sigma 3.0811 9.64e-05 1.84296 4.319</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 92.73500 NA 8.95e+01 95.92118</span> -<span class="co">## k1 0.00258 NA 4.24e-04 0.01573</span> -<span class="co">## k2 0.00258 NA 1.76e-03 0.00379</span> -<span class="co">## g 0.16452 NA NA NA</span> -<span class="co">## sigma 3.41172 NA 2.02e+00 4.79960</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 269 892 269</span> -<span class="co">## IORE 261 560 169</span> -<span class="co">## DFOP 269 892 269</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 168.51</span></code></pre> +<div class="sourceCode" id="cb87"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p13</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 174.5971 142.3951 174.5971 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 172.131</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 92.73500 5.99e-17 89.61936 95.85065</span></span> +<span><span class="co">## k_parent 0.00258 2.42e-09 0.00223 0.00299</span></span> +<span><span class="co">## sigma 3.41172 7.07e-05 2.05455 4.76888</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 91.6016 6.34e-16 88.53086 94.672</span></span> +<span><span class="co">## k__iore_parent 0.0396 2.36e-01 0.00207 0.759</span></span> +<span><span class="co">## N_parent 0.3541 1.46e-01 -0.35153 1.060</span></span> +<span><span class="co">## sigma 3.0811 9.64e-05 1.84296 4.319</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 92.73500 NA 8.95e+01 95.92118</span></span> +<span><span class="co">## k1 0.00258 NA 4.14e-04 0.01611</span></span> +<span><span class="co">## k2 0.00258 NA 1.74e-03 0.00383</span></span> +<span><span class="co">## g 0.16452 NA 0.00e+00 1.00000</span></span> +<span><span class="co">## sigma 3.41172 NA 2.02e+00 4.79960</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 269 892 269</span></span> +<span><span class="co">## IORE 261 560 169</span></span> +<span><span class="co">## DFOP 269 892 269</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 168.51</span></span></code></pre> </div> </div> <div class="section level2"> <h2 id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf">DT50 not observed in the study and DFOP problems in PestDF<a class="anchor" aria-label="anchor" href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf"></a> </h2> -<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p14</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> -<span class="co">## doubtful</span></code></pre> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb89"><pre class="downlit sourceCode r"> -<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">p14</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="va">p14</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p14</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb90"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">p14</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 48.43249 28.67746 27.26248 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 32.83337</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 99.47124 2.06e-30 98.42254 1.01e+02</span> -<span class="co">## k_parent 0.00279 3.75e-15 0.00256 3.04e-03</span> -<span class="co">## sigma 1.55616 3.81e-06 1.03704 2.08e+00</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 1.00e+02 NA NaN NaN</span> -<span class="co">## k__iore_parent 9.44e-08 NA NaN NaN</span> -<span class="co">## N_parent 3.31e+00 NA NaN NaN</span> -<span class="co">## sigma 1.20e+00 NA 0.796 1.6</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 1.00e+02 2.96e-28 99.40280 101.2768</span> -<span class="co">## k1 9.53e-03 1.20e-01 0.00638 0.0143</span> -<span class="co">## k2 5.03e-12 5.00e-01 0.00000 Inf</span> -<span class="co">## g 3.98e-01 2.19e-01 0.30481 0.4998</span> -<span class="co">## sigma 1.17e+00 7.68e-06 0.77406 1.5610</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 2.48e+02 8.25e+02 2.48e+02</span> -<span class="co">## IORE 4.34e+02 2.22e+04 6.70e+03</span> -<span class="co">## DFOP 3.69e+10 3.57e+11 1.38e+11</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 6697.44</span></code></pre> +<div class="sourceCode" id="cb96"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p14</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 48.43249 28.67746 27.26248 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 32.83337</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 99.47124 2.06e-30 98.42254 1.01e+02</span></span> +<span><span class="co">## k_parent 0.00279 3.75e-15 0.00256 3.04e-03</span></span> +<span><span class="co">## sigma 1.55616 3.81e-06 1.03704 2.08e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.00e+02 NA NaN NaN</span></span> +<span><span class="co">## k__iore_parent 9.44e-08 NA NaN NaN</span></span> +<span><span class="co">## N_parent 3.31e+00 NA NaN NaN</span></span> +<span><span class="co">## sigma 1.20e+00 NA 0.796 1.6</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.00e+02 2.96e-28 99.40280 101.2768</span></span> +<span><span class="co">## k1 9.53e-03 1.20e-01 0.00638 0.0143</span></span> +<span><span class="co">## k2 6.08e-12 5.00e-01 0.00000 Inf</span></span> +<span><span class="co">## g 3.98e-01 2.19e-01 0.30481 0.4998</span></span> +<span><span class="co">## sigma 1.17e+00 7.68e-06 0.77406 1.5610</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 2.48e+02 8.25e+02 2.48e+02</span></span> +<span><span class="co">## IORE 4.34e+02 2.22e+04 6.70e+03</span></span> +<span><span class="co">## DFOP 3.05e+10 2.95e+11 1.14e+11</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 6697.44</span></span></code></pre> <p>The slower rate constant reported by PestDF is negative, which is not physically realistic, and not possible in mkin. The other fits give the same results in mkin and PestDF.</p> </div> <div class="section level2"> <h2 id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero">N is less than 1 and DFOP fraction parameter is below zero<a class="anchor" aria-label="anchor" href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero"></a> </h2> -<div class="sourceCode" id="cb92"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p15a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> -<span class="co">## doubtful</span></code></pre> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> <div class="sourceCode" id="cb98"><pre class="downlit sourceCode r"> -<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">p15a</span><span class="op">)</span></code></pre></div> -<p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<div class="sourceCode" id="cb99"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">p15a</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 245.5248 135.0132 245.5248 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 165.9335</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 97.96751 2.00e-15 94.32049 101.615</span> -<span class="co">## k_parent 0.00952 4.93e-09 0.00824 0.011</span> -<span class="co">## sigma 4.18778 1.28e-04 2.44588 5.930</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 95.874 2.94e-15 92.937 98.811</span> -<span class="co">## k__iore_parent 0.629 2.11e-01 0.044 8.982</span> -<span class="co">## N_parent 0.000 5.00e-01 -0.642 0.642</span> -<span class="co">## sigma 3.105 1.78e-04 1.795 4.416</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 97.96751 2.85e-13 94.21913 101.7159</span> -<span class="co">## k1 0.00952 6.28e-02 0.00260 0.0349</span> -<span class="co">## k2 0.00952 1.27e-04 0.00652 0.0139</span> -<span class="co">## g 0.21241 5.00e-01 NA NA</span> -<span class="co">## sigma 4.18778 2.50e-04 2.39747 5.9781</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 72.8 242 72.8</span> -<span class="co">## IORE 76.3 137 41.3</span> -<span class="co">## DFOP 72.8 242 72.8</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 41.33</span></code></pre> +<code class="sourceCode R"><span><span class="va">p15a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb101"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p15b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> +<code class="sourceCode R"><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">p15a</span><span class="op">)</span></span></code></pre></div> +<p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> +<div class="sourceCode" id="cb102"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p15a</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 245.5248 135.0132 245.5248 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 165.9335</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.96751 2.00e-15 94.32049 101.615</span></span> +<span><span class="co">## k_parent 0.00952 4.93e-09 0.00824 0.011</span></span> +<span><span class="co">## sigma 4.18778 1.28e-04 2.44588 5.930</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 95.874 2.94e-15 92.937 98.811</span></span> +<span><span class="co">## k__iore_parent 0.629 2.11e-01 0.044 8.982</span></span> +<span><span class="co">## N_parent 0.000 5.00e-01 -0.642 0.642</span></span> +<span><span class="co">## sigma 3.105 1.78e-04 1.795 4.416</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.96751 2.85e-13 94.21913 101.7159</span></span> +<span><span class="co">## k1 0.00952 6.28e-02 0.00250 0.0363</span></span> +<span><span class="co">## k2 0.00952 1.27e-04 0.00646 0.0140</span></span> +<span><span class="co">## g 0.21241 5.00e-01 0.00000 1.0000</span></span> +<span><span class="co">## sigma 4.18778 2.50e-04 2.39747 5.9781</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 72.8 242 72.8</span></span> +<span><span class="co">## IORE 76.3 137 41.3</span></span> +<span><span class="co">## DFOP 72.8 242 72.8</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 41.33</span></span></code></pre> <div class="sourceCode" id="cb104"><pre class="downlit sourceCode r"> -<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">p15b</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="va">p15b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> +<div class="sourceCode" id="cb110"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p15b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<div class="sourceCode" id="cb105"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">p15b</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 106.91629 68.55574 106.91629 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 84.25618</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02</span> -<span class="co">## k_parent 4.86e-03 2.48e-10 0.00435 5.42e-03</span> -<span class="co">## sigma 2.76e+00 1.28e-04 1.61402 3.91e+00</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 99.83 1.81e-16 97.51349 102.14</span> -<span class="co">## k__iore_parent 0.38 3.22e-01 0.00352 41.05</span> -<span class="co">## N_parent 0.00 5.00e-01 -1.07695 1.08</span> -<span class="co">## sigma 2.21 2.57e-04 1.23245 3.19</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 1.01e+02 NA 9.82e+01 1.04e+02</span> -<span class="co">## k1 4.86e-03 NA 8.62e-04 2.74e-02</span> -<span class="co">## k2 4.86e-03 NA 3.21e-03 7.35e-03</span> -<span class="co">## g 1.88e-01 NA 0.00e+00 1.00e+00</span> -<span class="co">## sigma 2.76e+00 NA 1.58e+00 3.94e+00</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 143 474 143.0</span> -<span class="co">## IORE 131 236 71.2</span> -<span class="co">## DFOP 143 474 143.0</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 71.18</span></code></pre> +<div class="sourceCode" id="cb111"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p15b</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 106.91629 68.55574 106.91629 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 84.25618</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02</span></span> +<span><span class="co">## k_parent 4.86e-03 2.48e-10 0.00435 5.42e-03</span></span> +<span><span class="co">## sigma 2.76e+00 1.28e-04 1.61402 3.91e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 99.83 1.81e-16 97.51349 102.14</span></span> +<span><span class="co">## k__iore_parent 0.38 3.22e-01 0.00352 41.05</span></span> +<span><span class="co">## N_parent 0.00 5.00e-01 -1.07696 1.08</span></span> +<span><span class="co">## sigma 2.21 2.57e-04 1.23245 3.19</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.01e+02 NA 9.82e+01 1.04e+02</span></span> +<span><span class="co">## k1 4.86e-03 NA 8.63e-04 2.73e-02</span></span> +<span><span class="co">## k2 4.86e-03 NA 3.21e-03 7.35e-03</span></span> +<span><span class="co">## g 1.88e-01 NA NA NA</span></span> +<span><span class="co">## sigma 2.76e+00 NA 1.58e+00 3.94e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 143 474 143.0</span></span> +<span><span class="co">## IORE 131 236 71.2</span></span> +<span><span class="co">## DFOP 143 474 143.0</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 71.18</span></span></code></pre> <p>In mkin, only the IORE fit is affected (deemed unrealistic), as the fraction parameter of the DFOP model is restricted to the interval between 0 and 1 in mkin. The SFO fits give the same results for both mkin and PestDF.</p> </div> <div class="section level2"> <h2 id="the-dfop-fraction-parameter-is-greater-than-1">The DFOP fraction parameter is greater than 1<a class="anchor" aria-label="anchor" href="#the-dfop-fraction-parameter-is-greater-than-1"></a> </h2> -<div class="sourceCode" id="cb107"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p16</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p16"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> -<pre><code><span class="co">## The representative half-life of the IORE model is longer than the one corresponding</span></code></pre> -<pre><code><span class="co">## to the terminal degradation rate found with the DFOP model.</span></code></pre> -<pre><code><span class="co">## The representative half-life obtained from the DFOP model may be used</span></code></pre> -<div class="sourceCode" id="cb112"><pre class="downlit sourceCode r"> -<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">p16</span><span class="op">)</span></code></pre></div> -<p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> <div class="sourceCode" id="cb113"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">p16</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Sums of squares:</span> -<span class="co">## SFO IORE DFOP </span> -<span class="co">## 3831.804 2062.008 1550.980 </span> -<span class="co">## </span> -<span class="co">## Critical sum of squares for checking the SFO model:</span> -<span class="co">## [1] 2247.348</span> -<span class="co">## </span> -<span class="co">## Parameters:</span> -<span class="co">## $SFO</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 71.953 2.33e-13 60.509 83.40</span> -<span class="co">## k_parent 0.159 4.86e-05 0.102 0.25</span> -<span class="co">## sigma 11.302 1.25e-08 8.308 14.30</span> -<span class="co">## </span> -<span class="co">## $IORE</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 8.74e+01 2.48e-16 7.72e+01 97.52972</span> -<span class="co">## k__iore_parent 4.55e-04 2.16e-01 3.48e-05 0.00595</span> -<span class="co">## N_parent 2.70e+00 1.21e-08 1.99e+00 3.40046</span> -<span class="co">## sigma 8.29e+00 1.61e-08 6.09e+00 10.49062</span> -<span class="co">## </span> -<span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 88.5333 7.40e-18 79.9836 97.083</span> -<span class="co">## k1 18.8461 5.00e-01 0.0000 Inf</span> -<span class="co">## k2 0.0776 1.41e-05 0.0518 0.116</span> -<span class="co">## g 0.4733 1.41e-09 0.3674 0.582</span> -<span class="co">## sigma 7.1902 2.11e-08 5.2785 9.102</span> -<span class="co">## </span> -<span class="co">## </span> -<span class="co">## DTx values:</span> -<span class="co">## DT50 DT90 DT50_rep</span> -<span class="co">## SFO 4.35 14.4 4.35</span> -<span class="co">## IORE 1.48 32.1 9.67</span> -<span class="co">## DFOP 0.67 21.4 8.93</span> -<span class="co">## </span> -<span class="co">## Representative half-life:</span> -<span class="co">## [1] 8.93</span></code></pre> +<code class="sourceCode R"><span><span class="va">p16</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p16"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The representative half-life of the IORE model is longer than the one corresponding</span></span></code></pre> +<pre><code><span><span class="co">## to the terminal degradation rate found with the DFOP model.</span></span></code></pre> +<pre><code><span><span class="co">## The representative half-life obtained from the DFOP model may be used</span></span></code></pre> +<div class="sourceCode" id="cb118"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p16</span><span class="op">)</span></span></code></pre></div> +<p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> +<div class="sourceCode" id="cb119"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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">p16</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 3831.804 2062.008 1550.980 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 2247.348</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 71.953 2.33e-13 60.509 83.40</span></span> +<span><span class="co">## k_parent 0.159 4.86e-05 0.102 0.25</span></span> +<span><span class="co">## sigma 11.302 1.25e-08 8.308 14.30</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 8.74e+01 2.48e-16 7.72e+01 97.52972</span></span> +<span><span class="co">## k__iore_parent 4.55e-04 2.16e-01 3.48e-05 0.00595</span></span> +<span><span class="co">## N_parent 2.70e+00 1.21e-08 1.99e+00 3.40046</span></span> +<span><span class="co">## sigma 8.29e+00 1.61e-08 6.09e+00 10.49062</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 88.5333 7.40e-18 79.9836 97.083</span></span> +<span><span class="co">## k1 18.8461 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## k2 0.0776 1.41e-05 0.0518 0.116</span></span> +<span><span class="co">## g 0.4733 1.41e-09 0.3674 0.582</span></span> +<span><span class="co">## sigma 7.1902 2.11e-08 5.2785 9.102</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 4.35 14.4 4.35</span></span> +<span><span class="co">## IORE 1.48 32.1 9.67</span></span> +<span><span class="co">## DFOP 0.67 21.4 8.93</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 8.93</span></span></code></pre> <p>In PestDF, the DFOP fit seems to have stuck in a local minimum, as mkin finds a solution with a much lower <span class="math inline">\(\chi^2\)</span> error level. As the half-life from the slower rate constant of the DFOP model is larger than the IORE derived half-life, the NAFTA recommendation obtained with mkin is to use the DFOP representative half-life of 8.9 days.</p> </div> <div class="section level2"> @@ -1022,7 +1032,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer> diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png Binary files differindex a53c48b2..75611a70 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png Binary files differindex fb211a8e..b6faeff9 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15a-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png Binary files differindex 9aedbf16..6b9ba98c 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p15b-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png Binary files differindex 034eed46..db90244b 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5b-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png Binary files differindex 86cd9755..a33372e8 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p6-1.png diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png Binary files differindex 10225504..d64ea98d 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png +++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p7-1.png diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index 0b14fea2..64c68ea0 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -62,19 +62,25 @@ <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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <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> <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -105,7 +111,7 @@ <h1 data-toc-skip>Benchmark timings for mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-07-22)</h4> + <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-11-17)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/benchmarks.rmd" class="external-link"><code>vignettes/web_only/benchmarks.rmd</code></a></small> <div class="hidden name"><code>benchmarks.rmd</code></div> @@ -149,7 +155,7 @@ <span> parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> <span> m1 <span class="op">=</span> <span class="fu"><a href="../../reference/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="va">DFOP_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span> parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> +<span> parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>, <span class="co"># erroneously used FOMC twice, not fixed for consistency</span></span> <span> m1 <span class="op">=</span> <span class="fu"><a href="../../reference/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="va">t3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</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 class="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</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 class="va">FOCUS_D</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> <span><span class="va">t4</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</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 class="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</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 class="va">FOCUS_D</span><span class="op">)</span>,</span> @@ -336,8 +342,16 @@ <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.2</td> -<td align="right">1.962</td> -<td align="right">3.606</td> +<td align="right">1.957</td> +<td align="right">3.633</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">2.140</td> +<td align="right">3.774</td> </tr> </tbody> </table> @@ -506,9 +520,18 @@ <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.2</td> -<td align="right">1.465</td> -<td align="right">6.184</td> -<td align="right">2.752</td> +<td align="right">1.503</td> +<td align="right">6.147</td> +<td align="right">2.803</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">1.554</td> +<td align="right">6.193</td> +<td align="right">2.843</td> </tr> </tbody> </table> @@ -728,12 +751,24 @@ <td align="left">Ryzen 7 1700</td> <td align="left">4.2.1</td> <td align="left">1.1.2</td> -<td align="right">0.857</td> -<td align="right">1.298</td> -<td align="right">1.504</td> +<td align="right">0.861</td> +<td align="right">1.295</td> +<td align="right">1.507</td> +<td align="right">3.102</td> +<td align="right">1.961</td> +<td align="right">2.852</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.0</td> +<td align="right">0.913</td> +<td align="right">1.345</td> +<td align="right">1.539</td> <td align="right">3.011</td> -<td align="right">1.888</td> -<td align="right">2.756</td> +<td align="right">1.987</td> +<td align="right">2.802</td> </tr> </tbody> </table> @@ -758,7 +793,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer> diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 0b78bb2e..d17d7aeb 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -62,19 +62,25 @@ <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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <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> <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -105,7 +111,7 @@ <h1 data-toc-skip>Performance benefit by using compiled model definitions in mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">2022-10-29</h4> + <h4 data-toc-skip class="date">2022-11-17</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/compiled_models.rmd" class="external-link"><code>vignettes/web_only/compiled_models.rmd</code></a></small> <div class="hidden name"><code>compiled_models.rmd</code></div> @@ -163,10 +169,10 @@ <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="st">"R package rbenchmark is not available"</span><span class="op">)</span></span> <span><span class="op">}</span></span></code></pre></div> <pre><code><span><span class="co">## test replications relative elapsed</span></span> -<span><span class="co">## 4 analytical 1 1.000 0.188</span></span> -<span><span class="co">## 3 deSolve, compiled 1 1.628 0.306</span></span> -<span><span class="co">## 2 Eigenvalue based 1 2.064 0.388</span></span> -<span><span class="co">## 1 deSolve, not compiled 1 38.894 7.312</span></span></code></pre> +<span><span class="co">## 4 analytical 1 1.000 0.218</span></span> +<span><span class="co">## 3 deSolve, compiled 1 1.550 0.338</span></span> +<span><span class="co">## 2 Eigenvalue based 1 1.950 0.425</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 33.041 7.203</span></span></code></pre> <p>We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.</p> </div> <div class="section level2"> @@ -193,11 +199,11 @@ <span><span class="op">}</span></span></code></pre></div> <pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <pre><code><span><span class="co">## test replications relative elapsed</span></span> -<span><span class="co">## 2 deSolve, compiled 1 1.00 0.441</span></span> -<span><span class="co">## 1 deSolve, not compiled 1 30.68 13.530</span></span></code></pre> -<p>Here we get a performance benefit of a factor of 31 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 1.1.2 on</p> -<pre><code><span><span class="co">## R version 4.2.1 (2022-06-23)</span></span> +<span><span class="co">## 2 deSolve, compiled 1 1.000 0.510</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 26.247 13.386</span></span></code></pre> +<p>Here we get a performance benefit of a factor of 26 using the version of the differential equation model compiled from C code!</p> +<p>This vignette was built with mkin 1.2.0 on</p> +<pre><code><span><span class="co">## R version 4.2.2 (2022-10-31)</span></span> <span><span class="co">## Platform: x86_64-pc-linux-gnu (64-bit)</span></span> <span><span class="co">## Running under: Debian GNU/Linux 11 (bullseye)</span></span></code></pre> <pre><code><span><span class="co">## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</span></span></code></pre> diff --git a/docs/articles/web_only/dimethenamid_2018.html b/docs/articles/web_only/dimethenamid_2018.html index b020a7b0..8c37edd6 100644 --- a/docs/articles/web_only/dimethenamid_2018.html +++ b/docs/articles/web_only/dimethenamid_2018.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.1</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -62,19 +62,25 @@ <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/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <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> <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -105,7 +111,7 @@ <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 1 July 2022, built on 08 Jul 2022</h4> + <h4 data-toc-skip class="date">Last change 1 July 2022, built on 17 Nov 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 +161,20 @@ <span> 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></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><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></span></code></pre></div> +<code class="sourceCode R"><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="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></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><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></span></code></pre></div> +<code class="sourceCode R"><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="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></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><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></span></code></pre></div> +<code class="sourceCode R"><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="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></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><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></span></code></pre></div> +<code class="sourceCode R"><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="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></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"> @@ -178,7 +184,7 @@ Status of individual fits: dataset model Calke Borstel Flaach BBA 2.2 BBA 2.3 Elliot - DFOP OK OK OK OK C OK + DFOP OK OK C OK C OK OK: No warnings C: Optimisation did not converge: @@ -222,7 +228,7 @@ 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><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></span></code></pre></div> +<code class="sourceCode R"><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_parent_nlme_dfop_tc</span><span class="op">)</span></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"> @@ -231,41 +237,32 @@ f_parent_nlme_dfop_tc 3 10 671.91 702.34 -325.96 2 vs 3 134.69 <.0001 <p>The saemix package provided the first Open Source implementation of the Stochastic Approximation to the Expectation Maximisation (SAEM) algorithm. SAEM fits of degradation models can be conveniently performed using an interface to the saemix package available in current development versions of the mkin package.</p> <p>The corresponding SAEM fits of the four combinations of degradation and error models are fitted below. As there is no convergence criterion implemented in the saemix package, the convergence plots need to be manually checked for every fit. We define control settings that work well for all the parent data fits shown in this vignette.</p> <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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></code></pre></div> -<pre><code>Loading required package: npde</code></pre> -<pre><code>Package saemix, version 3.0 - please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</code></pre> -<pre><code> -Attaching package: 'saemix'</code></pre> -<pre><code>The following objects are masked from 'package:npde': - - kurtosis, skewness</code></pre> -<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="va">saemix_control</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</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">800</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span> +<code class="sourceCode R"><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="va">saemix_control</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</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">800</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span> <span> print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> <span><span class="va">saemix_control_moreiter</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</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">1600</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span> <span> print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> <span><span class="va">saemix_control_10k</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</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">10000</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span> <span> print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> <p>The convergence plot for the SFO model using constant variance is shown below.</p> -<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_sfo_const</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</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>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> <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_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_sfo_const-1.png" width="700"></p> <p>Obviously the selected number of iterations is sufficient to reach convergence. This can also be said for the SFO fit using the two-component error model.</p> -<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_sfo_tc</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_sfo_tc-1.png" width="700"></p> <p>When fitting the DFOP model with constant variance (see below), parameter convergence is not as unambiguous.</p> -<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_const</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</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>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> <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_parent_saemix_dfop_const</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></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_dfop_const-1.png" width="700"></p> -<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> <code class="sourceCode R"><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_parent_saemix_dfop_const</span><span class="op">)</span></span></code></pre></div> <pre><code>Kinetic nonlinear mixed-effects model fit by SAEM Structural model: @@ -286,23 +283,21 @@ DMTA_0 97.99583 96.50079 99.4909 k1 0.06377 0.03432 0.0932 k2 0.00848 0.00444 0.0125 g 0.95701 0.91313 1.0009 -a.1 1.82141 1.60516 2.0377 -SD.DMTA_0 1.64787 0.45729 2.8384 +a.1 1.82141 1.65974 1.9831 +SD.DMTA_0 1.64787 0.45779 2.8379 SD.k1 0.57439 0.24731 0.9015 -SD.k2 0.03296 -2.50524 2.5712 -SD.g 1.10266 0.32354 1.8818</code></pre> +SD.k2 0.03296 -2.50143 2.5673 +SD.g 1.10266 0.32371 1.8816</code></pre> <p>While the other parameters converge to credible values, the variance of k2 (<code>omega2.k2</code>) converges to a very small value. The printout of the <code>saem.mmkin</code> model shows that the estimated standard deviation of k2 across the population of soils (<code>SD.k2</code>) is ill-defined, indicating overparameterisation of this model.</p> <p>When the DFOP model is fitted with the two-component error model, we also observe that the estimated variance of k2 becomes very small, while being ill-defined, as illustrated by the excessive confidence interval of <code>SD.k2</code>.</p> -<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_tc</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</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>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> <span><span class="va">f_parent_saemix_dfop_tc_moreiter</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</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>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> -<span> control <span class="op">=</span> <span class="va">saemix_control_moreiter</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span></code></pre></div> -<pre><code>Likelihood cannot be computed by Importance Sampling.</code></pre> -<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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_parent_saemix_dfop_tc</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></code></pre></div> +<span> control <span class="op">=</span> <span class="va">saemix_control_moreiter</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> +<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_parent_saemix_dfop_tc</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></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_dfop_tc-1.png" width="700"></p> -<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> <code class="sourceCode R"><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_parent_saemix_dfop_tc</span><span class="op">)</span></span></code></pre></div> <pre><code>Kinetic nonlinear mixed-effects model fit by SAEM Structural model: @@ -318,21 +313,21 @@ Likelihood computed by importance sampling 666 664 -323 Fitted parameters: - estimate lower upper -DMTA_0 9.82e+01 96.27937 100.1783 -k1 6.41e-02 0.03333 0.0948 -k2 8.56e-03 0.00608 0.0110 -g 9.55e-01 0.91440 0.9947 -a.1 1.07e+00 0.86542 1.2647 -b.1 2.96e-02 0.02258 0.0367 -SD.DMTA_0 2.04e+00 0.40629 3.6678 -SD.k1 5.98e-01 0.25796 0.9373 -SD.k2 5.28e-04 -58.93251 58.9336 -SD.g 1.04e+00 0.36509 1.7083</code></pre> + estimate lower upper +DMTA_0 98.27617 96.3088 100.2436 +k1 0.06437 0.0337 0.0950 +k2 0.00880 0.0063 0.0113 +g 0.95249 0.9100 0.9949 +a.1 1.06161 0.8625 1.2607 +b.1 0.02967 0.0226 0.0367 +SD.DMTA_0 2.06075 0.4187 3.7028 +SD.k1 0.59357 0.2561 0.9310 +SD.k2 0.00292 -10.2960 10.3019 +SD.g 1.05725 0.3808 1.7337</code></pre> <p>Doubling the number of iterations in the first phase of the algorithm leads to a slightly lower likelihood, and therefore to slightly higher AIC and BIC values. With even more iterations, the algorithm stops with an error message. This is related to the variance of k2 approximating zero and has been submitted as a <a href="https://github.com/saemixdevelopment/saemixextension/issues/29" class="external-link">bug to the saemix package</a>, as the algorithm does not converge in this case.</p> <p>An alternative way to fit DFOP in combination with the two-component error model is to use the model formulation with transformed parameters as used per default in mkin. When using this option, convergence is slower, but eventually the algorithm stops as well with the same error message.</p> <p>The four combinations (SFO/const, SFO/tc, DFOP/const and DFOP/tc) and the version with increased iterations can be compared using the model comparison function of the saemix package:</p> -<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">AIC_parent_saemix</span> <span class="op"><-</span> <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> <span> <span class="va">f_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>,</span> <span> <span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>,</span> @@ -340,7 +335,7 @@ SD.g 1.04e+00 0.36509 1.7083</code></pre> <span> <span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>,</span> <span> <span class="va">f_parent_saemix_dfop_tc_moreiter</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span></code></pre></div> <pre><code>Likelihoods calculated by importance sampling</code></pre> -<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">AIC_parent_saemix</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span> <span> <span class="st">"SFO const"</span>, <span class="st">"SFO tc"</span>, <span class="st">"DFOP const"</span>, <span class="st">"DFOP tc"</span>, <span class="st">"DFOP tc more iterations"</span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix</span><span class="op">)</span></span></code></pre></div> @@ -348,10 +343,10 @@ SD.g 1.04e+00 0.36509 1.7083</code></pre> SFO const 796.38 795.34 SFO tc 798.38 797.13 DFOP const 705.75 703.88 -DFOP tc 665.72 663.63 -DFOP tc more iterations NaN NaN</code></pre> +DFOP tc 665.65 663.57 +DFOP tc more iterations 665.88 663.80</code></pre> <p>In order to check the influence of the likelihood calculation algorithms implemented in saemix, the likelihood from Gaussian quadrature is added to the best fit, and the AIC values obtained from the three methods are compared.</p> -<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span> <span class="op"><-</span></span> <span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/llgq.saemix.html" class="external-link">llgq.saemix</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span> <span><span class="va">AIC_parent_saemix_methods</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> @@ -361,11 +356,11 @@ DFOP tc more iterations NaN NaN</code></pre> <span><span class="op">)</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">AIC_parent_saemix_methods</span><span class="op">)</span></span></code></pre></div> <pre><code> is gq lin -665.72 665.88 665.15 </code></pre> +665.65 665.68 665.11 </code></pre> <p>The AIC values based on importance sampling and Gaussian quadrature are very similar. Using linearisation is known to be less accurate, but still gives a similar value.</p> <p>In order to illustrate that the comparison of the three method depends on the degree of convergence obtained in the fit, the same comparison is shown below for the fit using the defaults for the number of iterations and the number of MCMC chains.</p> <p>When using OpenBlas for linear algebra, there is a large difference in the values obtained with Gaussian quadrature, so the larger number of iterations makes a lot of difference. When using the LAPACK version coming with Debian Bullseye, the AIC based on Gaussian quadrature is almost the same as the one obtained with the other methods, also when using defaults for the fit.</p> -<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_tc_defaults</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</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></span> <span><span class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span> <span class="op"><-</span></span> <span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/llgq.saemix.html" class="external-link">llgq.saemix</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span> @@ -376,14 +371,14 @@ DFOP tc more iterations NaN NaN</code></pre> <span><span class="op">)</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">AIC_parent_saemix_methods_defaults</span><span class="op">)</span></span></code></pre></div> <pre><code> is gq lin -668.91 663.61 667.40 </code></pre> +669.77 669.36 670.95 </code></pre> </div> </div> <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).</p> -<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><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></span> <span> check.names <span class="op">=</span> <span class="cn">FALSE</span>,</span> <span> <span class="st">"Degradation model"</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">"SFO"</span>, <span class="st">"DFOP"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span> @@ -408,7 +403,7 @@ DFOP tc more iterations NaN NaN</code></pre> <td align="left">SFO</td> <td align="left">const</td> <td align="right">796.60</td> -<td align="right">794.17</td> +<td align="right">796.60</td> <td align="right">796.38</td> </tr> <tr class="even"> @@ -422,15 +417,15 @@ DFOP tc more iterations NaN NaN</code></pre> <td align="left">DFOP</td> <td align="left">const</td> <td align="right">NA</td> -<td align="right">704.95</td> +<td align="right">671.98</td> <td align="right">705.75</td> </tr> <tr class="even"> <td align="left">DFOP</td> <td align="left">tc</td> <td align="right">671.91</td> -<td align="right">665.15</td> -<td align="right">665.72</td> +<td align="right">665.11</td> +<td align="right">665.65</td> </tr> </tbody> </table> @@ -445,15 +440,15 @@ DFOP tc more iterations NaN NaN</code></pre> <div class="section level2"> <h2 id="session-info">Session Info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h2> -<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> -<pre><code>R version 4.2.1 (2022-06-23) +<pre><code>R version 4.2.2 (2022-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 11 (bullseye) Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 -LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0 +BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 +LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.13.so locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -464,28 +459,27 @@ locale: [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: -[1] parallel stats graphics grDevices utils datasets methods -[8] base +[1] stats graphics grDevices utils datasets methods base other attached packages: -[1] nlme_3.1-158 mkin_1.1.1 knitr_1.39 +[1] nlme_3.1-160 mkin_1.2.0 knitr_1.40 loaded via a namespace (and not attached): - [1] deSolve_1.32 zoo_1.8-10 tidyselect_1.1.2 xfun_0.31 - [5] bslib_0.3.1 purrr_0.3.4 lattice_0.20-45 colorspace_2.0-3 - [9] vctrs_0.4.1 generics_0.1.3 htmltools_0.5.2 yaml_2.3.5 -[13] utf8_1.2.2 rlang_1.0.3 pkgdown_2.0.5 saemix_3.0 -[17] jquerylib_0.1.4 pillar_1.7.0 glue_1.6.2 lifecycle_1.0.1 -[21] stringr_1.4.0 munsell_0.5.0 gtable_0.3.0 ragg_1.2.2 -[25] memoise_2.0.1 evaluate_0.15 npde_3.2 fastmap_1.1.0 -[29] lmtest_0.9-40 fansi_1.0.3 highr_0.9 scales_1.2.0 -[33] cachem_1.0.6 desc_1.4.1 jsonlite_1.8.0 systemfonts_1.0.4 -[37] fs_1.5.2 textshaping_0.3.6 gridExtra_2.3 ggplot2_3.3.6 -[41] digest_0.6.29 stringi_1.7.6 dplyr_1.0.9 grid_4.2.1 -[45] rprojroot_2.0.3 cli_3.3.0 tools_4.2.1 magrittr_2.0.3 -[49] sass_0.4.1 tibble_3.1.7 crayon_1.5.1 pkgconfig_2.0.3 -[53] ellipsis_0.3.2 rmarkdown_2.14 R6_2.5.1 mclust_5.4.10 -[57] compiler_4.2.1 </code></pre> + [1] deSolve_1.34 zoo_1.8-11 tidyselect_1.2.0 xfun_0.33 + [5] bslib_0.4.0 purrr_0.3.5 lattice_0.20-45 colorspace_2.0-3 + [9] vctrs_0.5.0 generics_0.1.3 htmltools_0.5.3 yaml_2.3.6 +[13] utf8_1.2.2 rlang_1.0.6 pkgdown_2.0.6 saemix_3.2 +[17] jquerylib_0.1.4 pillar_1.8.1 glue_1.6.2 DBI_1.1.3 +[21] lifecycle_1.0.3 stringr_1.4.1 munsell_0.5.0 gtable_0.3.1 +[25] ragg_1.2.2 memoise_2.0.1 evaluate_0.18 npde_3.2 +[29] fastmap_1.1.0 lmtest_0.9-40 parallel_4.2.2 fansi_1.0.3 +[33] highr_0.9 scales_1.2.1 cachem_1.0.6 desc_1.4.2 +[37] jsonlite_1.8.3 systemfonts_1.0.4 fs_1.5.2 textshaping_0.3.6 +[41] gridExtra_2.3 ggplot2_3.4.0 digest_0.6.30 stringi_1.7.8 +[45] dplyr_1.0.10 grid_4.2.2 rprojroot_2.0.3 cli_3.4.1 +[49] tools_4.2.2 magrittr_2.0.3 sass_0.4.2 tibble_3.1.8 +[53] pkgconfig_2.0.3 assertthat_0.2.1 rmarkdown_2.16 R6_2.5.1 +[57] mclust_6.0.0 compiler_4.2.2 </code></pre> </div> <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> @@ -522,7 +516,7 @@ loaded via a namespace (and not attached): <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.5.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer> diff --git a/docs/articles/web_only/multistart.html b/docs/articles/web_only/multistart.html new file mode 100644 index 00000000..720c6742 --- /dev/null +++ b/docs/articles/web_only/multistart.html @@ -0,0 +1,200 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> +<meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<title>Short demo of the multistart method • mkin</title> +<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" 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href="../../index.html">mkin</a> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> + </span> + </div> + + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> +<li> + <a href="../../reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> +<li> + <a href="../../articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="../../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with 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href="https://github.com/jranke/mkin/" class="external-link"> + <span class="fab fa-github fa-lg"></span> + + </a> +</li> + </ul> +</div> +<!--/.nav-collapse --> + </div> +<!--/.container --> +</div> +<!--/.navbar --> + + + + </header><script src="multistart_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> + <div class="col-md-9 contents"> + <div class="page-header toc-ignore"> + <h1 data-toc-skip>Short demo of the multistart method</h1> + <h4 data-toc-skip class="author">Johannes Ranke</h4> + + <h4 data-toc-skip class="date">Last change 26 September 2022 (rebuilt 2022-11-17)</h4> + + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/multistart.rmd" class="external-link"><code>vignettes/web_only/multistart.rmd</code></a></small> + <div class="hidden name"><code>multistart.rmd</code></div> + + </div> + + + +<p>The dimethenamid data from 2018 from seven soils is used as example data in this vignette.</p> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span> +<span><span class="va">dmta_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="fl">1</span><span class="op">:</span><span class="fl">7</span>, <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="va">ds_i</span> <span class="op"><-</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span> +<span> <span class="va">ds_i</span><span class="op">[</span><span class="va">ds_i</span><span class="op">$</span><span class="va">name</span> <span class="op">==</span> <span class="st">"DMTAP"</span>, <span class="st">"name"</span><span class="op">]</span> <span class="op"><-</span> <span class="st">"DMTA"</span></span> +<span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op">*</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">f_time_norm</span><span class="op">[</span><span class="va">i</span><span class="op">]</span></span> +<span> <span class="va">ds_i</span></span> +<span><span class="op">}</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="va">ds</span><span class="op">$</span><span class="va">title</span><span class="op">)</span></span> +<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span>, <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span> +<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span></code></pre></div> +<p>First, we check the DFOP model with the two-component error model and random effects for all degradation parameters.</p> +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">7</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span><span class="va">f_saem_full</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_full</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## [1] "sd(log_k2)"</span></span></code></pre> +<p>We see that not all variability parameters are identifiable. The <code>illparms</code> function tells us that the confidence interval for the standard deviation of ‘log_k2’ includes zero. We check this assessment using multiple runs with different starting values.</p> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_saem_full_multi</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/multistart.html">multistart</a></span><span class="op">(</span><span class="va">f_saem_full</span>, n <span class="op">=</span> <span class="fl">16</span>, cores <span class="op">=</span> <span class="fl">16</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_full_multi</span><span class="op">)</span></span></code></pre></div> +<p><img src="multistart_files/figure-html/unnamed-chunk-3-1.png" width="700"></p> +<p>This confirms that the variance of k2 is the most problematic parameter, so we reduce the parameter distribution model by removing the intersoil variability for k2.</p> +<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_saem_reduced</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_full</span>, no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_reduced</span><span class="op">)</span></span> +<span><span class="va">f_saem_reduced_multi</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/multistart.html">multistart</a></span><span class="op">(</span><span class="va">f_saem_reduced</span>, n <span class="op">=</span> <span class="fl">16</span>, cores <span class="op">=</span> <span class="fl">16</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span><span class="op">)</span></span></code></pre></div> +<p><img src="multistart_files/figure-html/unnamed-chunk-4-1.png" width="700"></p> +<p>The results confirm that all remaining parameters can be determined with sufficient certainty.</p> +<p>We can also analyse the log-likelihoods obtained in the multiple runs:</p> +<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/llhist.html">llhist</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span><span class="op">)</span></span></code></pre></div> +<p><img src="multistart_files/figure-html/unnamed-chunk-5-1.png" width="700"></p> +<p>The parameter histograms can be further improved by excluding the result with the low likelihood.</p> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/parplot.html">parplot</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span>, lpos <span class="op">=</span> <span class="st">"topright"</span>, llmin <span class="op">=</span> <span class="op">-</span><span class="fl">326</span>, ylim <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">0.5</span>, <span class="fl">2</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<p><img src="multistart_files/figure-html/unnamed-chunk-6-1.png" width="700"></p> +<p>We can use the <code>anova</code> method to compare the models, including a likelihood ratio test if the models are nested.</p> +<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><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_full</span>, <span class="fu"><a href="../../reference/multistart.html">best</a></span><span class="op">(</span><span class="va">f_saem_reduced_multi</span><span class="op">)</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Data: 155 observations of 1 variable(s) grouped in 6 datasets</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## npar AIC BIC Lik Chisq Df Pr(>Chisq)</span></span> +<span><span class="co">## best(f_saem_reduced_multi) 9 663.69 661.82 -322.85 </span></span> +<span><span class="co">## f_saem_full 10 669.77 667.69 -324.89 0 1 1</span></span></code></pre> +<p>While AIC and BIC are lower for the reduced model, the likelihood ratio test does not indicate a significant difference between the fits.</p> + </div> + + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + + </div> + +</div> + + + + <footer><div class="copyright"> + <p></p> +<p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer> +</div> + + + + + + + </body> +</html> diff --git a/docs/articles/web_only/multistart_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/multistart_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/web_only/multistart_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo 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data-toc-skip>Benchmark timings for saem.mmkin</h1> + <h4 data-toc-skip class="author">Johannes Ranke</h4> + + <h4 data-toc-skip class="date">Last change 14 November 2022 (rebuilt 2022-11-17)</h4> + + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/saem_benchmarks.rmd" class="external-link"><code>vignettes/web_only/saem_benchmarks.rmd</code></a></small> + <div class="hidden name"><code>saem_benchmarks.rmd</code></div> + + </div> + + + +<p>Each system is characterized by operating system type, CPU type, mkin version, saemix version and R version. A compiler was available, so if no analytical solution was available, compiled ODE models are used.</p> +<p>Every fit is only performed once, so the accuracy of the benchmarks is limited.</p> +<p>For the initial mmkin fits, we use all available cores.</p> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">n_cores</span> <span class="op"><-</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<div class="section level2"> +<h2 id="test-data">Test data<a class="anchor" aria-label="anchor" href="#test-data"></a> +</h2> +<p>Please refer to the vignette <code>dimethenamid_2018</code> for an explanation of the following preprocessing.</p> +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">dmta_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="fl">1</span><span class="op">:</span><span class="fl">7</span>, <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="va">ds_i</span> <span class="op"><-</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span><span class="op">[[</span><span class="va">i</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span> +<span> <span class="va">ds_i</span><span class="op">[</span><span class="va">ds_i</span><span class="op">$</span><span class="va">name</span> <span class="op">==</span> <span class="st">"DMTAP"</span>, <span class="st">"name"</span><span class="op">]</span> <span class="op"><-</span> <span class="st">"DMTA"</span></span> +<span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="va">ds_i</span><span class="op">$</span><span class="va">time</span> <span class="op">*</span> <span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">f_time_norm</span><span class="op">[</span><span class="va">i</span><span class="op">]</span></span> +<span> <span class="va">ds_i</span></span> +<span><span class="op">}</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">dimethenamid_2018</span><span class="op">$</span><span class="va">ds</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="va">ds</span><span class="op">$</span><span class="va">title</span><span class="op">)</span></span> +<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/cbind.html" class="external-link">rbind</a></span><span class="op">(</span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span>, <span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span> +<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 1"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span> +<span><span class="va">dmta_ds</span><span class="op">[[</span><span class="st">"Elliot 2"</span><span class="op">]</span><span class="op">]</span> <span class="op"><-</span> <span class="cn">NULL</span></span></code></pre></div> +</div> +<div class="section level2"> +<h2 id="test-cases">Test cases<a class="anchor" aria-label="anchor" href="#test-cases"></a> +</h2> +<div class="section level3"> +<h3 id="parent-only">Parent only<a class="anchor" aria-label="anchor" href="#parent-only"></a> +</h3> +<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">parent_mods</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">"DFOP"</span>, <span class="st">"SFORB"</span>, <span class="st">"HS"</span><span class="op">)</span></span> +<span><span class="va">parent_sep_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">parent_mods</span>, <span class="va">dmta_ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span></span> +<span><span class="va">parent_sep_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">parent_sep_const</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> +<span></span> +<span><span class="va">t1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sfo_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">dfop_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"SFORB"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t4</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">hs_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_const</span><span class="op">[</span><span class="st">"HS"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t5</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t6</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">dfop_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t7</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"SFORB"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t8</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">hs_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">parent_sep_tc</span><span class="op">[</span><span class="st">"HS"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span></span> +<span> <span class="va">sfo_const</span>, <span class="va">dfop_const</span>, <span class="va">sforb_const</span>, <span class="va">hs_const</span>,</span> +<span> <span class="va">sfo_tc</span>, <span class="va">dfop_tc</span>, <span class="va">sforb_tc</span>, <span class="va">hs_tc</span><span class="op">)</span> <span class="op">|></span> <span class="fu">kable</span><span class="op">(</span>, digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">npar</th> +<th align="right">AIC</th> +<th align="right">BIC</th> +<th align="right">Lik</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">sfo_const</td> +<td align="right">5</td> +<td align="right">796.3</td> +<td align="right">795.3</td> +<td align="right">-393.2</td> +</tr> +<tr class="even"> +<td align="left">sfo_tc</td> +<td align="right">6</td> +<td align="right">798.3</td> +<td align="right">797.1</td> +<td align="right">-393.2</td> +</tr> +<tr class="odd"> +<td align="left">dfop_const</td> +<td align="right">9</td> +<td align="right">709.4</td> +<td align="right">707.5</td> +<td align="right">-345.7</td> +</tr> +<tr class="even"> +<td align="left">sforb_const</td> +<td align="right">9</td> +<td align="right">710.0</td> +<td align="right">708.1</td> +<td align="right">-346.0</td> +</tr> +<tr class="odd"> +<td align="left">hs_const</td> +<td align="right">9</td> +<td align="right">713.7</td> +<td align="right">711.8</td> +<td align="right">-347.8</td> +</tr> +<tr class="even"> +<td align="left">dfop_tc</td> +<td align="right">10</td> +<td align="right">669.8</td> +<td align="right">667.7</td> +<td align="right">-324.9</td> +</tr> +<tr class="odd"> +<td align="left">sforb_tc</td> +<td align="right">10</td> +<td align="right">662.8</td> +<td align="right">660.7</td> +<td align="right">-321.4</td> +</tr> +<tr class="even"> +<td align="left">hs_tc</td> +<td align="right">10</td> +<td align="right">667.3</td> +<td align="right">665.2</td> +<td align="right">-323.6</td> +</tr> +</tbody> +</table> +<p>The above model comparison suggests to use the SFORB model with two-component error. For comparison, we keep the DFOP model with two-component error, as it competes with SFORB for biphasic curves.</p> +<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">dfop_tc</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## [1] "sd(log_k2)"</span></span></code></pre> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">sforb_tc</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## [1] "sd(log_k_DMTA_bound_free)"</span></span></code></pre> +<p>For these two models, random effects for the transformed parameters <code>k2</code> and <code>k_DMTA_bound_free</code> could not be quantified.</p> +</div> +<div class="section level3"> +<h3 id="one-metabolite">One metabolite<a class="anchor" aria-label="anchor" href="#one-metabolite"></a> +</h3> +<p>We remove parameters that were found to be ill-defined in the parent only fits.</p> +<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">one_met_mods</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> DFOP_SFO <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> +<span> DMTA <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"M23"</span><span class="op">)</span>,</span> +<span> M23 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span>,</span> +<span> SFORB_SFO <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> +<span> DMTA <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"M23"</span><span class="op">)</span>,</span> +<span> M23 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> +<span></span> +<span><span class="va">one_met_sep_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">one_met_mods</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"const"</span>,</span> +<span> cores <span class="op">=</span> <span class="va">n_cores</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span><span class="va">one_met_sep_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">one_met_mods</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span> +<span> cores <span class="op">=</span> <span class="va">n_cores</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span></span> +<span><span class="va">t9</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">dfop_sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">one_met_sep_tc</span><span class="op">[</span><span class="st">"DFOP_SFO"</span>, <span class="op">]</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="st">"log_k2"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span> +<span><span class="va">t10</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_sfo_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">one_met_sep_tc</span><span class="op">[</span><span class="st">"SFORB_SFO"</span>, <span class="op">]</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="st">"log_k_DMTA_bound_free"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div> +</div> +<div class="section level3"> +<h3 id="three-metabolites">Three metabolites<a class="anchor" aria-label="anchor" href="#three-metabolites"></a> +</h3> +<p>For the case of three metabolites, we only keep the SFORB model in order to limit the time for compiling this vignette, and as fitting in parallel may disturb the benchmark. Again, we do not include random effects that were ill-defined in previous fits of subsets of the degradation model.</p> +<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">sforb_sfo_tc</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">three_met_mods</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> SFORB_SFO3_plus <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span></span> +<span> DMTA <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</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">"M23"</span>, <span class="st">"M27"</span>, <span class="st">"M31"</span><span class="op">)</span><span class="op">)</span>,</span> +<span> M23 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> +<span> M27 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> +<span> M31 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M27"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> +<span></span> +<span><span class="va">three_met_sep_tc</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="va">three_met_mods</span>, <span class="va">dmta_ds</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span> +<span> cores <span class="op">=</span> <span class="va">n_cores</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span></span> +<span><span class="va">t11</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">sforb_sfo3_plus_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">three_met_sep_tc</span><span class="op">[</span><span class="st">"SFORB_SFO3_plus"</span>, <span class="op">]</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="st">"log_k_DMTA_bound_free"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div> +</div> +</div> +<div class="section level2"> +<h2 id="results">Results<a class="anchor" aria-label="anchor" href="#results"></a> +</h2> +<p>Benchmarks for all available error models are shown. They are intended for improving mkin, not for comparing CPUs or operating systems. All trademarks belong to their respective owners.</p> +<div class="section level3"> +<h3 id="parent-only-1">Parent only<a class="anchor" aria-label="anchor" href="#parent-only-1"></a> +</h3> +<p>Constant variance for SFO, DFOP, SFORB and HS.</p> +<table class="table"> +<thead><tr class="header"> +<th align="left">CPU</th> +<th align="left">OS</th> +<th align="left">mkin</th> +<th align="left">saemix</th> +<th align="right">t1</th> +<th align="right">t2</th> +<th align="right">t3</th> +<th align="right">t4</th> +</tr></thead> +<tbody><tr class="odd"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.0</td> +<td align="left">3.2</td> +<td align="right">2.14</td> +<td align="right">4.626</td> +<td align="right">4.328</td> +<td align="right">4.998</td> +</tr></tbody> +</table> +<p>Two-component error fits for SFO, DFOP, SFORB and HS.</p> +<table class="table"> +<thead><tr class="header"> +<th align="left">CPU</th> +<th align="left">OS</th> +<th align="left">mkin</th> +<th align="left">saemix</th> +<th align="right">t5</th> +<th align="right">t6</th> +<th align="right">t7</th> +<th align="right">t8</th> +</tr></thead> +<tbody><tr class="odd"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.0</td> +<td align="left">3.2</td> +<td align="right">5.678</td> +<td align="right">7.441</td> +<td align="right">8</td> +<td align="right">7.98</td> +</tr></tbody> +</table> +</div> +<div class="section level3"> +<h3 id="one-metabolite-1">One metabolite<a class="anchor" aria-label="anchor" href="#one-metabolite-1"></a> +</h3> +<p>Two-component error for DFOP-SFO and SFORB-SFO.</p> +<table class="table"> +<thead><tr class="header"> +<th align="left">CPU</th> +<th align="left">OS</th> +<th align="left">mkin</th> +<th align="left">saemix</th> +<th align="right">t9</th> +<th align="right">t10</th> +</tr></thead> +<tbody><tr class="odd"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.0</td> +<td align="left">3.2</td> +<td align="right">24.465</td> +<td align="right">800.266</td> +</tr></tbody> +</table> +</div> +<div class="section level3"> +<h3 id="three-metabolites-1">Three metabolites<a class="anchor" aria-label="anchor" href="#three-metabolites-1"></a> +</h3> +<p>Two-component error for SFORB-SFO3-plus</p> +<table class="table"> +<thead><tr class="header"> +<th align="left">CPU</th> +<th align="left">OS</th> +<th align="left">mkin</th> +<th align="left">saemix</th> +<th align="right">t11</th> +</tr></thead> +<tbody><tr class="odd"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.0</td> +<td align="left">3.2</td> +<td align="right">1289.198</td> +</tr></tbody> +</table> +</div> +</div> + </div> + + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + + <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> + </nav> +</div> + +</div> + + + + <footer><div class="copyright"> + <p></p> +<p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer> +</div> + + + + + + + </body> +</html> diff --git a/docs/articles/web_only/saem_benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/articles/web_only/saem_benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/articles/web_only/saem_benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); |
