diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-05-18 21:26:17 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-05-18 21:26:17 +0200 |
| commit | 91c5db736a4d3f2290a0cc5698fb4e35ae7bda59 (patch) | |
| tree | 8e9e34d18f055936172329c1248e6e2ff136bff9 /docs/articles/web_only | |
| parent | ea57db98cef3fb882f7bd9656b44f270e7bded38 (diff) | |
Remove outdated comment in FOCUS L vignette, update docs
This also adds the first benchmark results obtained on my laptop system
Diffstat (limited to 'docs/articles/web_only')
19 files changed, 256 insertions, 216 deletions
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 43508280..0dafb98a 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -105,7 +105,7 @@ <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 2022-03-07)</h4> + <h4 data-toc-skip class="date">Last change 16 January 2018 (rebuilt 2022-05-18)</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> @@ -234,33 +234,31 @@ 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$bparms.ode, :</span> <span class="co">## Observations with value of zero were removed from the data</span></code></pre> -<pre><code><span class="co">## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation did not converge:</span> -<span class="co">## false convergence (8)</span></code></pre> -<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r"> +<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> -<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> +<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 96.838822 1.994274 48.5584 4.0280e-42 92.826981 100.850664</span> -<span class="co">## k_Z0 2.215393 0.118458 18.7019 1.0413e-23 1.989456 2.466989</span> -<span class="co">## k_Z1 0.478305 0.028258 16.9266 6.2418e-22 0.424708 0.538666</span> -<span class="co">## k_Z2 0.451627 0.042139 10.7176 1.6314e-14 0.374339 0.544872</span> -<span class="co">## k_Z3 0.058692 0.015245 3.8499 1.7803e-04 0.034808 0.098965</span> -<span class="co">## f_Z2_to_Z3 0.471502 0.058351 8.0805 9.6608e-11 0.357769 0.588274</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="cb36"><pre class="downlit sourceCode r"> +<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">## 0.4715 0.5285 </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 1.44917 4.8141</span> -<span class="co">## Z2 1.53478 5.0984</span> -<span class="co">## Z3 11.80986 39.2315</span></code></pre> +<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> <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"> @@ -268,32 +266,34 @@ </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="cb38"><pre class="downlit sourceCode r"> +<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="cb40"><pre class="downlit sourceCode r"> +<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="cb42"><pre class="downlit sourceCode r"> +<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="cb43"><pre class="downlit sourceCode r"> +<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> <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="cb45"><pre class="downlit sourceCode r"> +<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="cb47"><pre class="downlit sourceCode r"> +<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="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> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png" width="700"></p> @@ -359,11 +359,11 @@ <span class="co">## </span> <span class="co">## $SFORB</span> <span class="co">## Z0_b1 Z0_b2 Z3_b1 Z3_b2 </span> -<span class="co">## 2.4471322 0.0075125 0.0800069 0.0000000 </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 92.266 NA NA</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> @@ -398,7 +398,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</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 bc6efaf7..229bae82 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 55c1b645..e13ad9aa 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 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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 cb333a1c..250d0df5 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 db807f14..5a01c03e 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 996e5d49..df1e06db 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -43,7 +43,7 @@ <a href="../../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -105,7 +105,7 @@ <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 2022-03-02)</h4> + <h4 data-toc-skip class="date">26 February 2019 (rebuilt 2022-05-18)</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> @@ -161,7 +161,7 @@ <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 2.26e-12 5.00e-01 0.0000 Inf</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> @@ -170,7 +170,7 @@ <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 5.59e+11 3.07e+11</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> @@ -212,7 +212,7 @@ <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 8.63e-12 5.00e-01 0.0000 Inf</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> @@ -221,7 +221,7 @@ <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 1.32e+11 8.04e+10</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> @@ -263,7 +263,7 @@ <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 3.22e-11 5.00e-01 0.0000 Inf</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> @@ -272,7 +272,7 @@ <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 1.01e+10 2.15e+10</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> @@ -314,7 +314,7 @@ <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 3.63e-10 5.00e-01 0.0000 Inf</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> @@ -323,7 +323,7 @@ <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 3.77e+09 1.91e+09</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> @@ -434,7 +434,7 @@ <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 7.69e+11</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> @@ -445,17 +445,12 @@ </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">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(diag(covar_notrans)): 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="cb44"><pre class="downlit sourceCode r"> +<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> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> +<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> @@ -482,8 +477,8 @@ <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 2.23e-04 0.0255 0.0592</span> -<span class="co">## g 0.5256 NaN NA NA</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> @@ -500,7 +495,7 @@ <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="cb47"><pre class="downlit sourceCode r"> +<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> @@ -508,10 +503,10 @@ <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="cb53"><pre class="downlit sourceCode r"> +<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> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> +<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> @@ -537,8 +532,8 @@ <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 6.58e-03 0.0303 0.0809</span> -<span class="co">## k2 0.0495 2.60e-03 0.0410 0.0598</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> @@ -560,14 +555,14 @@ <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="cb56"><pre class="downlit sourceCode r"> +<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="cb59"><pre class="downlit sourceCode r"> +<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="cb60"><pre class="downlit sourceCode r"> +<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> @@ -594,7 +589,7 @@ <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 9.94e-13 5.00e-01 0.0000 Inf</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> @@ -606,7 +601,7 @@ <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] 41148170</span></code></pre> +<span class="co">## [1] 41148171</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> @@ -617,21 +612,19 @@ <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="cb62"><pre class="downlit sourceCode r"> +<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">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(diag(covar_notrans)): 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="cb70"><pre class="downlit sourceCode r"> +<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> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<div class="sourceCode" id="cb71"><pre class="downlit sourceCode r"> +<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> @@ -655,12 +648,12 @@ <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 2.74e-10 92.2366 108.805</span> -<span class="co">## k1 0.124 2.53e-05 0.0908 0.170</span> -<span class="co">## k2 0.124 2.52e-02 0.0456 0.339</span> -<span class="co">## g 0.793 NaN NA NA</span> -<span class="co">## sigma 7.048 2.50e-04 4.0349 10.061</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> @@ -675,18 +668,17 @@ <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="cb73"><pre class="downlit sourceCode r"> +<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 sqrt(diag(covar_notrans)): 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="cb80"><pre class="downlit sourceCode r"> +<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> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<div class="sourceCode" id="cb81"><pre class="downlit sourceCode r"> +<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> @@ -730,14 +722,18 @@ <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="cb83"><pre class="downlit sourceCode r"> +<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="cb86"><pre class="downlit sourceCode r"> +<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> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<div class="sourceCode" id="cb87"><pre class="downlit sourceCode r"> +<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> @@ -763,9 +759,9 @@ <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 4.14e-04 0.01611</span> -<span class="co">## k2 0.00258 NA 1.74e-03 0.00383</span> -<span class="co">## g 0.16452 NA 0.00e+00 1.00000</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> @@ -782,7 +778,7 @@ <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="cb89"><pre class="downlit sourceCode r"> +<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> @@ -790,10 +786,10 @@ <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="cb95"><pre class="downlit sourceCode r"> +<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> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb96"><pre class="downlit sourceCode r"> +<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> @@ -820,7 +816,7 @@ <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 6.08e-12 5.00e-01 0.00000 Inf</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> @@ -829,7 +825,7 @@ <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 3.05e+10 2.95e+11 1.14e+11</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> @@ -838,14 +834,18 @@ <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="cb98"><pre class="downlit sourceCode r"> +<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="cb101"><pre class="downlit sourceCode r"> +<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="cb102"><pre class="downlit sourceCode r"> +<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> @@ -871,9 +871,9 @@ <span class="co">## $DFOP</span> <span class="co">## Estimate Pr(>t) Lower Upper</span> <span class="co">## parent_0 97.96751 2.85e-13 94.21913 101.7159</span> -<span class="co">## k1 0.00952 6.28e-02 0.00250 0.0363</span> -<span class="co">## k2 0.00952 1.27e-04 0.00646 0.0140</span> -<span class="co">## g 0.21241 5.00e-01 0.00000 1.0000</span> +<span class="co">## k1 0.00952 6.28e-02 0.00260 0.0349</span> +<span class="co">## k2 0.00952 1.27e-04 0.00652 0.0139</span> +<span class="co">## g 0.21241 5.00e-01 NA NA</span> <span class="co">## sigma 4.18778 2.50e-04 2.39747 5.9781</span> <span class="co">## </span> <span class="co">## </span> @@ -885,18 +885,14 @@ <span class="co">## </span> <span class="co">## Representative half-life:</span> <span class="co">## [1] 41.33</span></code></pre> -<div class="sourceCode" id="cb104"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p15b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in cov2cor(ans$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="cb110"><pre class="downlit sourceCode r"> +<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> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<div class="sourceCode" id="cb111"><pre class="downlit sourceCode r"> +<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> @@ -916,15 +912,15 @@ <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 -1.07696 1.08</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 8.63e-04 2.73e-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 NA NA</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> @@ -941,16 +937,16 @@ <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="cb113"><pre class="downlit sourceCode r"> +<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="cb118"><pre class="downlit sourceCode r"> +<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="cb119"><pre class="downlit sourceCode r"> +<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> @@ -1026,7 +1022,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</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 75611a70..a53c48b2 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png +++ 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b/docs/articles/web_only/benchmarks.html @@ -43,7 +43,7 @@ <a href="../../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -105,7 +105,7 @@ <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 13 May 2020 (rebuilt 2022-03-02)</h4> + <h4 data-toc-skip class="date">Last change 13 May 2020 (rebuilt 2022-05-18)</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> @@ -121,7 +121,7 @@ <p>Parent only:</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">FOCUS_C</span> <span class="op"><-</span> <span class="va">FOCUS_2006_C</span> -<span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span> +<span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span> <span class="va">parent_datasets</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_C</span>, <span class="va">FOCUS_D</span><span class="op">)</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="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span><span class="op">)</span>, <span class="va">parent_datasets</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> @@ -179,74 +179,83 @@ <div class="section level2"> <h2 id="results">Results<a class="anchor" aria-label="anchor" href="#results"></a> </h2> -<p>Currently, we only have benchmark information on one system, therefore only the mkin version is shown with the results below. Timings are in seconds, shorter is better. All results were obtained by serial, i.e. not using multiple computing cores.</p> <p>Benchmarks for all available error models are shown.</p> <div class="section level3"> <h3 id="parent-only">Parent only<a class="anchor" aria-label="anchor" href="#parent-only"></a> </h3> <p>Constant variance (t1) and two-component error model (t2) for four models fitted to two datasets, i.e. eight fits for each test.</p> -<table class="table"> +<table style="width:100%;" class="table"> +<colgroup> +<col width="84%"> +<col width="7%"> +<col width="8%"> +</colgroup> <thead><tr class="header"> -<th align="left">mkin version</th> -<th align="right">t1 [s]</th> -<th align="right">t2 [s]</th> +<th align="left"></th> +<th align="right">t1</th> +<th align="right">t2</th> </tr></thead> <tbody> <tr class="odd"> -<td align="left">0.9.48.1</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1</td> <td align="right">3.610</td> <td align="right">11.019</td> </tr> <tr class="even"> -<td align="left">0.9.49.1</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1</td> <td align="right">8.184</td> <td align="right">22.889</td> </tr> <tr class="odd"> -<td align="left">0.9.49.2</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2</td> <td align="right">7.064</td> <td align="right">12.558</td> </tr> <tr class="even"> -<td align="left">0.9.49.3</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3</td> <td align="right">7.296</td> <td align="right">21.239</td> </tr> <tr class="odd"> -<td align="left">0.9.49.4</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4</td> <td align="right">5.936</td> <td align="right">20.545</td> </tr> <tr class="even"> -<td align="left">0.9.50.2</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2</td> <td align="right">1.714</td> <td align="right">3.971</td> </tr> <tr class="odd"> -<td align="left">0.9.50.3</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.3</td> <td align="right">1.752</td> <td align="right">4.156</td> </tr> <tr class="even"> -<td align="left">0.9.50.4</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.4</td> <td align="right">1.786</td> <td align="right">3.729</td> </tr> <tr class="odd"> -<td align="left">1.0.3</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.0.3</td> <td align="right">1.881</td> <td align="right">3.504</td> </tr> <tr class="even"> -<td align="left">1.0.4</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.0.4</td> <td align="right">1.867</td> <td align="right">3.450</td> </tr> <tr class="odd"> -<td align="left">1.1.0</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.1.0</td> <td align="right">1.938</td> <td align="right">3.517</td> </tr> +<tr class="even"> +<td align="left">Linux, Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz, mkin version 1.1.0</td> +<td align="right">1.621</td> +<td align="right">3.123</td> +</tr> </tbody> </table> </div> @@ -255,79 +264,91 @@ </h3> <p>Constant variance (t3), two-component error model (t4), and variance by variable (t5) for three models fitted to one dataset, i.e. three fits for each test.</p> <table class="table"> +<colgroup> +<col width="78%"> +<col width="6%"> +<col width="7%"> +<col width="6%"> +</colgroup> <thead><tr class="header"> -<th align="left">mkin version</th> -<th align="right">t3 [s]</th> -<th align="right">t4 [s]</th> -<th align="right">t5 [s]</th> +<th align="left"></th> +<th align="right">t3</th> +<th align="right">t4</th> +<th align="right">t5</th> </tr></thead> <tbody> <tr class="odd"> -<td align="left">0.9.48.1</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1</td> <td align="right">3.764</td> <td align="right">14.347</td> <td align="right">9.495</td> </tr> <tr class="even"> -<td align="left">0.9.49.1</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1</td> <td align="right">4.649</td> <td align="right">13.789</td> <td align="right">6.395</td> </tr> <tr class="odd"> -<td align="left">0.9.49.2</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2</td> <td align="right">4.786</td> <td align="right">8.461</td> <td align="right">5.675</td> </tr> <tr class="even"> -<td align="left">0.9.49.3</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3</td> <td align="right">4.510</td> <td align="right">13.805</td> <td align="right">7.386</td> </tr> <tr class="odd"> -<td align="left">0.9.49.4</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4</td> <td align="right">4.446</td> <td align="right">15.335</td> <td align="right">6.002</td> </tr> <tr class="even"> -<td align="left">0.9.50.2</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2</td> <td align="right">1.402</td> <td align="right">6.174</td> <td align="right">2.764</td> </tr> <tr class="odd"> -<td align="left">0.9.50.3</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.3</td> <td align="right">1.430</td> <td align="right">6.615</td> <td align="right">2.878</td> </tr> <tr class="even"> -<td align="left">0.9.50.4</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.4</td> <td align="right">1.397</td> <td align="right">7.251</td> <td align="right">2.810</td> </tr> <tr class="odd"> -<td align="left">1.0.3</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.0.3</td> <td align="right">1.430</td> <td align="right">6.344</td> <td align="right">2.798</td> </tr> <tr class="even"> -<td align="left">1.0.4</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.0.4</td> <td align="right">1.415</td> <td align="right">6.364</td> <td align="right">2.820</td> </tr> <tr class="odd"> -<td align="left">1.1.0</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.1.0</td> <td align="right">1.470</td> <td align="right">6.508</td> <td align="right">2.894</td> </tr> +<tr class="even"> +<td align="left">Linux, Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz, mkin version 1.1.0</td> +<td align="right">3.319</td> +<td align="right">18.209</td> +<td align="right">7.773</td> +</tr> </tbody> </table> </div> @@ -336,18 +357,27 @@ </h3> <p>Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.</p> <table class="table"> +<colgroup> +<col width="64%"> +<col width="5%"> +<col width="5%"> +<col width="5%"> +<col width="6%"> +<col width="5%"> +<col width="6%"> +</colgroup> <thead><tr class="header"> -<th align="left">mkin version</th> -<th align="right">t6 [s]</th> -<th align="right">t7 [s]</th> -<th align="right">t8 [s]</th> -<th align="right">t9 [s]</th> -<th align="right">t10 [s]</th> -<th align="right">t11 [s]</th> +<th align="left"></th> +<th align="right">t6</th> +<th align="right">t7</th> +<th align="right">t8</th> +<th align="right">t9</th> +<th align="right">t10</th> +<th align="right">t11</th> </tr></thead> <tbody> <tr class="odd"> -<td align="left">0.9.48.1</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1</td> <td align="right">2.623</td> <td align="right">4.587</td> <td align="right">7.525</td> @@ -356,7 +386,7 @@ <td align="right">31.267</td> </tr> <tr class="even"> -<td align="left">0.9.49.1</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1</td> <td align="right">2.542</td> <td align="right">4.128</td> <td align="right">4.632</td> @@ -365,7 +395,7 @@ <td align="right">5.636</td> </tr> <tr class="odd"> -<td align="left">0.9.49.2</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2</td> <td align="right">2.723</td> <td align="right">4.478</td> <td align="right">4.862</td> @@ -374,7 +404,7 @@ <td align="right">5.574</td> </tr> <tr class="even"> -<td align="left">0.9.49.3</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3</td> <td align="right">2.643</td> <td align="right">4.374</td> <td align="right">7.020</td> @@ -383,7 +413,7 @@ <td align="right">7.365</td> </tr> <tr class="odd"> -<td align="left">0.9.49.4</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4</td> <td align="right">2.635</td> <td align="right">4.259</td> <td align="right">4.737</td> @@ -392,7 +422,7 @@ <td align="right">5.626</td> </tr> <tr class="even"> -<td align="left">0.9.50.2</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2</td> <td align="right">0.777</td> <td align="right">1.236</td> <td align="right">1.332</td> @@ -401,7 +431,7 @@ <td align="right">2.987</td> </tr> <tr class="odd"> -<td align="left">0.9.50.3</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.3</td> <td align="right">0.858</td> <td align="right">1.264</td> <td align="right">1.333</td> @@ -410,7 +440,7 @@ <td align="right">3.073</td> </tr> <tr class="even"> -<td align="left">0.9.50.4</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.4</td> <td align="right">0.783</td> <td align="right">1.282</td> <td align="right">1.486</td> @@ -419,7 +449,7 @@ <td align="right">3.105</td> </tr> <tr class="odd"> -<td align="left">1.0.3</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.0.3</td> <td align="right">0.763</td> <td align="right">1.244</td> <td align="right">1.457</td> @@ -428,7 +458,7 @@ <td align="right">2.839</td> </tr> <tr class="even"> -<td align="left">1.0.4</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.0.4</td> <td align="right">0.785</td> <td align="right">1.252</td> <td align="right">1.466</td> @@ -437,7 +467,7 @@ <td align="right">2.826</td> </tr> <tr class="odd"> -<td align="left">1.1.0</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.1.0</td> <td align="right">0.810</td> <td align="right">1.264</td> <td align="right">1.503</td> @@ -445,6 +475,15 @@ <td align="right">1.984</td> <td align="right">2.847</td> </tr> +<tr class="even"> +<td align="left">Linux, Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz, mkin version 1.1.0</td> +<td align="right">2.348</td> +<td align="right">3.579</td> +<td align="right">4.254</td> +<td align="right">11.315</td> +<td align="right">5.981</td> +<td align="right">8.368</td> +</tr> </tbody> </table> </div> @@ -468,7 +507,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer> diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 35ea6f27..330c25c6 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -43,7 +43,7 @@ <a href="../../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -105,7 +105,7 @@ <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">2022-03-02</h4> + <h4 data-toc-skip class="date">2022-05-18</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> @@ -141,11 +141,11 @@ 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></code></pre></div> <pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></code></pre></div> <p>We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package. In the output of below code, the warnings about zero being removed from the FOCUS D dataset are suppressed. Since mkin version 0.9.49.11, an analytical solution is also implemented, which is included in the tests below.</p> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span> - <span class="va">b.1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span> + <span class="va">b.1</span> <span class="op"><-</span> <span class="fu">benchmark</span><span class="op">(</span> <span class="st">"deSolve, not compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, @@ -162,11 +162,7 @@ <span class="op">}</span> <span class="kw">else</span> <span class="op">{</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 class="op">}</span></code></pre></div> -<pre><code><span class="co">## test replications relative elapsed</span> -<span class="co">## 4 analytical 1 1.000 0.216</span> -<span class="co">## 3 deSolve, compiled 1 1.708 0.369</span> -<span class="co">## 2 Eigenvalue based 1 1.866 0.403</span> -<span class="co">## 1 deSolve, not compiled 1 34.009 7.346</span></code></pre> +<pre><code><span class="co">## [1] "R package rbenchmark is not available"</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"> @@ -179,7 +175,7 @@ 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>, 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 class="va">b.2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span> + <span class="va">b.2</span> <span class="op"><-</span> <span class="fu">benchmark</span><span class="op">(</span> <span class="st">"deSolve, not compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, <span class="st">"deSolve, compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, @@ -191,16 +187,14 @@ <span class="va">factor_FOMC_SFO</span> <span class="op"><-</span> <span class="cn">NA</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 benchmark is not available"</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> -<pre><code><span class="co">## test replications relative elapsed</span> -<span class="co">## 2 deSolve, compiled 1 1.000 0.533</span> -<span class="co">## 1 deSolve, not compiled 1 25.146 13.403</span></code></pre> -<p>Here we get a performance benefit of a factor of 25 using the version of the differential equation model compiled from C code!</p> +<pre><code><span class="co">## Loading required package: rbenchmark</span></code></pre> +<pre><code><span class="co">## [1] "R package benchmark is not available"</span></code></pre> +<p>Here we get a performance benefit of a factor of NA using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 1.1.0 on</p> -<pre><code><span class="co">## R version 4.1.2 (2021-11-01)</span> +<pre><code><span class="co">## R version 4.2.0 (2022-04-22)</span> <span class="co">## Platform: x86_64-pc-linux-gnu (64-bit)</span> <span class="co">## Running under: Debian GNU/Linux 11 (bullseye)</span></code></pre> -<pre><code><span class="co">## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</span></code></pre> +<pre><code><span class="co">## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz</span></code></pre> </div> </div> @@ -221,7 +215,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer> diff --git a/docs/articles/web_only/dimethenamid_2018.html b/docs/articles/web_only/dimethenamid_2018.html index 09aa5150..7650f06f 100644 --- a/docs/articles/web_only/dimethenamid_2018.html +++ b/docs/articles/web_only/dimethenamid_2018.html @@ -105,7 +105,7 @@ <h1 data-toc-skip>Example evaluations of the dimethenamid data from 2018</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 7 March 2022, built on 16 Mar 2022</h4> + <h4 data-toc-skip class="date">Last change 7 March 2022, built on 18 May 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> @@ -178,7 +178,7 @@ Status of individual fits: dataset model Calke Borstel Flaach BBA 2.2 BBA 2.3 Elliot - DFOP OK OK C OK C OK + DFOP OK OK OK OK C OK OK: No warnings C: Optimisation did not converge: @@ -231,32 +231,41 @@ 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 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 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>, +<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">saemix</span><span class="op">)</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 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>, 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 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>, 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 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>, 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></code></pre></div> <p>The convergence plot for the SFO model using constant variance is shown below.</p> -<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> <code class="sourceCode R"><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>, 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 class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_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></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="cb16"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> <code class="sourceCode R"><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>, 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 class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_sfo_tc-1.png" width="700"></p> <p>When fitting the DFOP model with constant variance (see below), parameter convergence is not as unambiguous.</p> -<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">f_parent_saemix_dfop_const</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_const</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></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="cb18"><pre class="downlit sourceCode r"> +<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">f_parent_saemix_dfop_const</span><span class="op">)</span></code></pre></div> <pre><code>Kinetic nonlinear mixed-effects model fit by SAEM Structural model: @@ -277,21 +286,23 @@ 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 1.65974 1.9831 -SD.DMTA_0 1.64787 0.45779 2.8379 +a.1 1.82141 1.60516 2.0377 +SD.DMTA_0 1.64787 0.45729 2.8384 SD.k1 0.57439 0.24731 0.9015 -SD.k2 0.03296 -2.50143 2.5673 -SD.g 1.10266 0.32371 1.8816</code></pre> +SD.k2 0.03296 -2.50524 2.5712 +SD.g 1.10266 0.32354 1.8818</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="cb20"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> <code class="sourceCode R"><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>, 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 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>, - 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 class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></code></pre></div> + control <span class="op">=</span> <span class="va">saemix_control_moreiter</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></code></pre></div> +<pre><code>Likelihood cannot be computed by Importance Sampling.</code></pre> +<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></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="cb21"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb28"><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">f_parent_saemix_dfop_tc</span><span class="op">)</span></code></pre></div> <pre><code>Kinetic nonlinear mixed-effects model fit by SAEM Structural model: @@ -307,21 +318,21 @@ Likelihood computed by importance sampling 666 664 -323 Fitted parameters: - 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> + 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> <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="cb23"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r"> <code class="sourceCode R"><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 class="va">f_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>, @@ -329,7 +340,7 @@ SD.g 1.05725 0.3808 1.7337</code></pre> <span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_parent_saemix_dfop_tc_moreiter</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></code></pre></div> <pre><code>Likelihoods calculated by importance sampling</code></pre> -<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> <code class="sourceCode R"><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 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 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></code></pre></div> @@ -337,10 +348,10 @@ SD.g 1.05725 0.3808 1.7337</code></pre> SFO const 796.38 795.34 SFO tc 798.38 797.13 DFOP const 705.75 703.88 -DFOP tc 665.65 663.57 -DFOP tc more iterations 665.88 663.80</code></pre> +DFOP tc 665.72 663.63 +DFOP tc more iterations NaN NaN</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="cb27"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span> <span class="op"><-</span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/llgq.saemix.html" class="external-link">llgq.saemix</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span> <span 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> @@ -350,9 +361,9 @@ DFOP tc more iterations 665.88 663.80</code></pre> <span class="op">)</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></code></pre></div> <pre><code> is gq lin -665.65 665.68 665.11 </code></pre> +665.72 665.88 665.15 </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. 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> -<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r"> <code class="sourceCode R"><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 class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span> <span class="op"><-</span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/llgq.saemix.html" class="external-link">llgq.saemix</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span><span class="op">)</span> @@ -363,14 +374,14 @@ DFOP tc more iterations 665.88 663.80</code></pre> <span class="op">)</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></code></pre></div> <pre><code> is gq lin -668.27 718.36 666.49 </code></pre> +668.91 663.61 667.40 </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). Note that</p> -<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">AIC_all</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span> check.names <span class="op">=</span> <span class="cn">FALSE</span>, <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>, @@ -395,7 +406,7 @@ DFOP tc more iterations 665.88 663.80</code></pre> <td align="left">SFO</td> <td align="left">const</td> <td align="right">796.60</td> -<td align="right">796.60</td> +<td align="right">794.17</td> <td align="right">796.38</td> </tr> <tr class="even"> @@ -409,15 +420,15 @@ DFOP tc more iterations 665.88 663.80</code></pre> <td align="left">DFOP</td> <td align="left">const</td> <td align="right">NA</td> -<td align="right">671.98</td> +<td align="right">704.95</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">665.11</td> -<td align="right">665.65</td> +<td align="right">665.15</td> +<td align="right">665.72</td> </tr> </tbody> </table> @@ -464,7 +475,7 @@ DFOP tc more iterations 665.88 663.80</code></pre> <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer> diff --git a/docs/articles/web_only/mkin_benchmarks.rda b/docs/articles/web_only/mkin_benchmarks.rda Binary files differnew file mode 100644 index 00000000..e26caf64 --- /dev/null +++ b/docs/articles/web_only/mkin_benchmarks.rda |
