diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2021-02-15 17:36:12 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2021-02-15 17:36:12 +0100 |
| commit | b9be19af5e3085216d0cd5af439332f631fa8b92 (patch) | |
| tree | e10511f60e7f1713b781d5ea2acf885f3d1e6767 /docs/dev/articles/web_only | |
| parent | 11c7f26dd6c532d977d9875f3c16952c7bba37ca (diff) | |
Fully rebuild docs, rerun tests and check
Diffstat (limited to 'docs/dev/articles/web_only')
39 files changed, 277 insertions, 139 deletions
diff --git a/docs/dev/articles/web_only/FOCUS_Z.html b/docs/dev/articles/web_only/FOCUS_Z.html index 15c41eb7..694b33ca 100644 --- a/docs/dev/articles/web_only/FOCUS_Z.html +++ b/docs/dev/articles/web_only/FOCUS_Z.html @@ -32,7 +32,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> </span> </div> @@ -81,7 +81,7 @@ <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin/"> - <span class="fab fa fab fa-github fa-lg"></span> + <span class="fab fa-github fa-lg"></span> </a> </li> @@ -95,14 +95,13 @@ - </header><link href="FOCUS_Z_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet"> -<script src="FOCUS_Z_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row"> + </header><script src="FOCUS_Z_files/header-attrs-2.6/header-attrs.js"></script><script src="FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Example evaluation of FOCUS dataset Z</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-11-30</h4> + <h4 class="date">Last change 16 January 2018 (rebuilt 2021-02-15)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/FOCUS_Z.rmd"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small> <div class="hidden name"><code>FOCUS_Z.rmd</code></div> @@ -239,12 +238,12 @@ <div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">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>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 96.839001 1.994273 48.5585 4.0276e-42 92.827060 100.850943 -## k_Z0 2.215367 0.118456 18.7021 1.0410e-23 1.989432 2.466960 -## k_Z1 0.478310 0.028258 16.9265 6.2430e-22 0.424712 0.538673 -## k_Z2 0.451628 0.042139 10.7176 1.6313e-14 0.374337 0.544877 -## k_Z3 0.058692 0.015245 3.8498 1.7806e-04 0.034806 0.098972 -## f_Z2_to_Z3 0.471498 0.058350 8.0805 9.6614e-11 0.357741 0.588294 +## Z0_0 96.838822 1.994274 48.5584 4.0280e-42 92.826981 100.850664 +## k_Z0 2.215393 0.118458 18.7019 1.0413e-23 1.989456 2.466989 +## k_Z1 0.478305 0.028258 16.9266 6.2418e-22 0.424708 0.538666 +## k_Z2 0.451627 0.042139 10.7176 1.6314e-14 0.374339 0.544872 +## k_Z3 0.058692 0.015245 3.8499 1.7803e-04 0.034808 0.098965 +## f_Z2_to_Z3 0.471502 0.058351 8.0805 9.6608e-11 0.357769 0.588274 ## sigma 3.984431 0.383402 10.3923 4.5575e-14 3.213126 4.755736</code></pre> <div class="sourceCode" id="cb36"><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> @@ -255,9 +254,9 @@ ## $distimes ## DT50 DT90 ## Z0 0.31288 1.0394 -## Z1 1.44916 4.8140 +## Z1 1.44917 4.8141 ## Z2 1.53478 5.0984 -## Z3 11.80983 39.2314</code></pre> +## Z3 11.80986 39.2315</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 id="using-the-sforb-model" class="section level1"> @@ -353,13 +352,13 @@ ## ## $SFORB ## Z0_b1 Z0_b2 Z3_b1 Z3_b2 -## 2.4471371 0.0075126 0.0800070 0.0000000 +## 2.4471322 0.0075125 0.0800069 0.0000000 ## ## $distimes ## DT50 DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2 -## Z0 0.3043 1.1848 0.35666 0.28325 92.265 NA NA +## Z0 0.3043 1.1848 0.35666 0.28325 92.266 NA NA ## Z1 1.5148 5.0320 NA NA NA NA NA -## Z2 1.6414 5.4525 NA NA NA NA NA +## Z2 1.6414 5.4526 NA NA NA NA NA ## Z3 NA NA NA NA NA 8.6636 Inf</code></pre> <p>It is clear the degradation rate of Z3 towards the end of the experiment is very low as DT50_Z3_b2 (the second Eigenvalue of the system of two differential equations representing the SFORB system for Z3, corresponding to the slower rate constant of the DFOP model) is reported to be infinity. However, this appears to be a feature of the data.</p> </div> @@ -367,9 +366,9 @@ <h1 class="hasAnchor"> <a href="#references" class="anchor"></a>References</h1> <!-- vim: set foldmethod=syntax: --> -<div id="refs" class="references"> +<div id="refs" class="references hanging-indent"> <div id="ref-FOCUSkinetics2014"> -<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="uri">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> +<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> </div> </div> </div> diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/dev/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/dev/articles/web_only/FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); 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We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/dev/articles/web_only/NAFTA_examples.html b/docs/dev/articles/web_only/NAFTA_examples.html index fca15672..b9784415 100644 --- a/docs/dev/articles/web_only/NAFTA_examples.html +++ b/docs/dev/articles/web_only/NAFTA_examples.html @@ -32,7 +32,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> </span> </div> @@ -81,7 +81,7 @@ <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin/"> - <span class="fab fa fab fa-github fa-lg"></span> + <span class="fab fa-github fa-lg"></span> </a> </li> @@ -95,14 +95,13 @@ - </header><link href="NAFTA_examples_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet"> -<script src="NAFTA_examples_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row"> + </header><script src="NAFTA_examples_files/header-attrs-2.6/header-attrs.js"></script><script src="NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-11-30</h4> + <h4 class="date">26 February 2019 (rebuilt 2021-02-15)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/NAFTA_examples.rmd"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small> <div class="hidden name"><code>NAFTA_examples.rmd</code></div> @@ -158,7 +157,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.99e+01 1.41e-26 98.8116 101.0810 ## k1 2.67e-02 5.05e-06 0.0243 0.0295 -## k2 2.42e-12 5.00e-01 0.0000 Inf +## k2 2.26e-12 5.00e-01 0.0000 Inf ## g 6.47e-01 3.67e-06 0.6248 0.6677 ## sigma 1.27e+00 8.91e-06 0.8395 1.6929 ## @@ -167,7 +166,7 @@ ## DT50 DT90 DT50_rep ## SFO 67.7 2.25e+02 6.77e+01 ## IORE 58.2 1.07e+03 3.22e+02 -## DFOP 55.5 5.22e+11 2.86e+11 +## DFOP 55.5 5.59e+11 3.07e+11 ## ## Representative half-life: ## [1] 321.51</code></pre> @@ -209,7 +208,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.84e+01 1.24e-27 97.8078 98.9187 ## k1 1.55e-02 4.10e-04 0.0143 0.0167 -## k2 1.10e-11 5.00e-01 0.0000 Inf +## k2 8.63e-12 5.00e-01 0.0000 Inf ## g 6.89e-01 2.92e-03 0.6626 0.7142 ## sigma 6.48e-01 2.38e-05 0.4147 0.8813 ## @@ -218,7 +217,7 @@ ## DT50 DT90 DT50_rep ## SFO 86.6 2.88e+02 8.66e+01 ## IORE 85.5 7.17e+02 2.16e+02 -## DFOP 83.6 1.03e+11 6.29e+10 +## DFOP 83.6 1.32e+11 8.04e+10 ## ## Representative half-life: ## [1] 215.87</code></pre> @@ -260,7 +259,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.66e+01 1.57e-25 95.3476 97.8979 ## k1 2.55e-02 7.33e-06 0.0233 0.0278 -## k2 3.60e-11 5.00e-01 0.0000 Inf +## k2 3.22e-11 5.00e-01 0.0000 Inf ## g 8.61e-01 7.55e-06 0.8314 0.8867 ## sigma 1.46e+00 6.93e-06 0.9661 1.9483 ## @@ -269,7 +268,7 @@ ## DT50 DT90 DT50_rep ## SFO 38.6 1.28e+02 3.86e+01 ## IORE 34.0 1.77e+02 5.32e+01 -## DFOP 34.1 9.07e+09 1.93e+10 +## DFOP 34.1 1.01e+10 2.15e+10 ## ## Representative half-life: ## [1] 53.17</code></pre> @@ -311,7 +310,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.89e+01 9.44e-49 95.4640 102.2573 ## k1 1.81e-02 1.75e-01 0.0116 0.0281 -## k2 2.89e-10 5.00e-01 0.0000 Inf +## k2 3.63e-10 5.00e-01 0.0000 Inf ## g 6.06e-01 2.19e-01 0.4826 0.7178 ## sigma 7.40e+00 2.97e-15 6.0201 8.7754 ## @@ -320,7 +319,7 @@ ## DT50 DT90 DT50_rep ## SFO 94.3 3.13e+02 9.43e+01 ## IORE 96.7 1.51e+03 4.55e+02 -## DFOP 96.4 4.75e+09 2.40e+09 +## DFOP 96.4 3.77e+09 1.91e+09 ## ## Representative half-life: ## [1] 454.55</code></pre> @@ -422,7 +421,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.85e+01 2.54e-20 97.390 99.672 ## k1 1.38e-01 3.52e-05 0.131 0.146 -## k2 9.03e-13 5.00e-01 0.000 Inf +## k2 9.02e-13 5.00e-01 0.000 Inf ## g 6.52e-01 8.13e-06 0.642 0.661 ## sigma 7.88e-01 6.13e-02 0.481 1.095 ## @@ -431,7 +430,7 @@ ## DT50 DT90 DT50_rep ## SFO 16.9 5.63e+01 1.69e+01 ## IORE 11.6 3.37e+02 1.01e+02 -## DFOP 10.5 1.38e+12 7.67e+11 +## DFOP 10.5 1.38e+12 7.69e+11 ## ## Representative half-life: ## [1] 101.43</code></pre> @@ -443,15 +442,16 @@ <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>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> +<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> <pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is ## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">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="cb44"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -475,12 +475,12 @@ ## sigma 1.288 1.76e-04 0.7456 1.830 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 94.7123 NA 93.1355 96.2891 -## k1 0.0389 NA 0.0266 0.0569 -## k2 0.0389 NA 0.0255 0.0592 -## g 0.5256 NA NA NA -## sigma 1.5957 NA 0.9135 2.2779 +## Estimate Pr(>t) Lower Upper +## parent_0 94.7123 1.61e-16 93.1355 96.2891 +## k1 0.0389 1.08e-04 0.0266 0.0569 +## k2 0.0389 2.23e-04 0.0255 0.0592 +## g 0.5256 NaN NA NA +## sigma 1.5957 2.50e-04 0.9135 2.2779 ## ## ## DTx values: @@ -496,15 +496,18 @@ <div id="example-on-page-10" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-10" class="anchor"></a>Example on page 10</h2> -<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p10</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p10"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre> +<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is +## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">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="cb51"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -530,9 +533,9 @@ ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 101.7315 1.41e-09 91.6534 111.8097 -## k1 0.0495 5.63e-03 0.0240 0.1020 -## k2 0.0495 1.93e-03 0.0272 0.0903 -## g 0.4487 NaN 0.0000 1.0000 +## k1 0.0495 6.58e-03 0.0303 0.0809 +## k2 0.0495 2.60e-03 0.0410 0.0598 +## g 0.4487 5.00e-01 NA NA ## sigma 8.0152 2.50e-04 4.5886 11.4418 ## ## @@ -553,14 +556,14 @@ <div id="example-on-page-11" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-11" class="anchor"></a>Example on page 11</h2> -<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb56"><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>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb56"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">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="cb57"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb60"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -596,10 +599,10 @@ ## DT50 DT90 DT50_rep ## SFO 2.16e+02 7.18e+02 2.16e+02 ## IORE 9.73e+02 1.37e+08 4.11e+07 -## DFOP 3.07e+11 1.93e+12 6.97e+11 +## DFOP 3.07e+11 1.93e+12 6.98e+11 ## ## Representative half-life: -## [1] 41148171</code></pre> +## [1] 41148170</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> @@ -610,19 +613,21 @@ <div id="example-on-page-12-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-upper-panel" class="anchor"></a>Example on page 12, upper panel</h2> -<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb62"><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>## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance -## matrix - -## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance ## matrix</code></pre> +<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> +<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is +## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb63"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb70"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">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="cb64"><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/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -646,12 +651,12 @@ ## sigma 3.965 NA NA NA ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 100.521 2.74e-10 NA NA -## k1 0.124 2.53e-05 NA NA -## k2 0.124 2.52e-02 NA NA -## g 0.793 5.00e-01 NA NA -## sigma 7.048 2.50e-04 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 100.521 2.74e-10 92.2366 108.805 +## k1 0.124 2.53e-05 0.0908 0.170 +## k2 0.124 2.52e-02 0.0456 0.339 +## g 0.793 NaN NA NA +## sigma 7.048 2.50e-04 4.0349 10.061 ## ## ## DTx values: @@ -666,20 +671,18 @@ <div id="example-on-page-12-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-lower-panel" class="anchor"></a>Example on page 12, lower panel</h2> -<div class="sourceCode" id="cb66"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb73"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p12b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> <pre><code>## Warning in qt(alpha/2, rdf): NaNs produced</code></pre> <pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is -## doubtful</code></pre> +<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre> +<pre><code>## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb74"><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-method.html">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="cb75"><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">print</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -704,11 +707,11 @@ ## ## $DFOP ## Estimate Pr(>t) Lower Upper -## parent_0 97.6840 NA NaN NaN -## k1 0.0589 NA NA NA -## k2 0.0589 NA NA NA -## g 0.6473 NA NA NA -## sigma 3.4323 NA NaN NaN +## parent_0 97.6840 NaN NaN NaN +## k1 0.0589 NaN NA NA +## k2 0.0589 NaN NA NA +## g 0.6473 NaN NA NA +## sigma 3.4323 NaN NaN NaN ## ## ## DTx values: @@ -723,18 +726,14 @@ <div id="example-on-page-13" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2> -<div class="sourceCode" id="cb77"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p13</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is -## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb86"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">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="cb84"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb87"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -760,9 +759,9 @@ ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 92.73500 NA 8.95e+01 95.92118 -## k1 0.00258 NA 4.25e-04 0.01569 -## k2 0.00258 NA 1.76e-03 0.00379 -## g 0.16452 NA NA NA +## k1 0.00258 NA 4.14e-04 0.01611 +## k2 0.00258 NA 1.74e-03 0.00383 +## g 0.16452 NA 0.00e+00 1.00000 ## sigma 3.41172 NA 2.02e+00 4.79960 ## ## @@ -779,7 +778,7 @@ <div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1"> <h1 class="hasAnchor"> <a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1> -<div class="sourceCode" id="cb86"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb89"><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>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> @@ -787,10 +786,10 @@ ## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb92"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">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="cb93"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb96"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -817,7 +816,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 1.00e+02 2.96e-28 99.40280 101.2768 ## k1 9.53e-03 1.20e-01 0.00638 0.0143 -## k2 5.33e-12 5.00e-01 0.00000 Inf +## k2 6.08e-12 5.00e-01 0.00000 Inf ## g 3.98e-01 2.19e-01 0.30481 0.4998 ## sigma 1.17e+00 7.68e-06 0.77406 1.5610 ## @@ -826,7 +825,7 @@ ## DT50 DT90 DT50_rep ## SFO 2.48e+02 8.25e+02 2.48e+02 ## IORE 4.34e+02 2.22e+04 6.70e+03 -## DFOP 3.48e+10 3.37e+11 1.30e+11 +## DFOP 3.05e+10 2.95e+11 1.14e+11 ## ## Representative half-life: ## [1] 6697.44</code></pre> @@ -835,14 +834,14 @@ <div id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="section level1"> <h1 class="hasAnchor"> <a href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="anchor"></a>N is less than 1 and DFOP fraction parameter is below zero</h1> -<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb98"><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>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb98"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<div class="sourceCode" id="cb99"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb102"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -866,12 +865,12 @@ ## sigma 3.105 1.78e-04 1.795 4.416 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 97.96751 NA 94.21913 101.7159 -## k1 0.00952 NA 0.00221 0.0411 -## k2 0.00952 NA 0.00626 0.0145 -## g 0.21241 NA 0.00000 1.0000 -## sigma 4.18778 NA 2.39747 5.9781 +## Estimate Pr(>t) Lower Upper +## parent_0 97.96751 2.85e-13 94.21913 101.7159 +## k1 0.00952 6.28e-02 0.00250 0.0363 +## k2 0.00952 1.27e-04 0.00646 0.0140 +## g 0.21241 5.00e-01 0.00000 1.0000 +## sigma 4.18778 2.50e-04 2.39747 5.9781 ## ## ## DTx values: @@ -882,7 +881,7 @@ ## ## Representative half-life: ## [1] 41.33</code></pre> -<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb104"><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>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> @@ -890,10 +889,10 @@ ## doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb107"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb110"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">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="cb108"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb111"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -911,7 +910,7 @@ ## ## $IORE ## Estimate Pr(>t) Lower Upper -## parent_0 99.83 1.81e-16 97.51348 102.14 +## parent_0 99.83 1.81e-16 97.51349 102.14 ## k__iore_parent 0.38 3.22e-01 0.00352 41.05 ## N_parent 0.00 5.00e-01 -1.07696 1.08 ## sigma 2.21 2.57e-04 1.23245 3.19 @@ -938,16 +937,16 @@ <div id="the-dfop-fraction-parameter-is-greater-than-1" class="section level1"> <h1 class="hasAnchor"> <a href="#the-dfop-fraction-parameter-is-greater-than-1" class="anchor"></a>The DFOP fraction parameter is greater than 1</h1> -<div class="sourceCode" id="cb110"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb113"><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>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The representative half-life of the IORE model is longer than the one corresponding</code></pre> <pre><code>## to the terminal degradation rate found with the DFOP model.</code></pre> <pre><code>## The representative half-life obtained from the DFOP model may be used</code></pre> -<div class="sourceCode" id="cb115"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb118"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">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="cb116"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb119"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP @@ -998,7 +997,7 @@ <div id="references" class="section level1 unnumbered"> <h1 class="hasAnchor"> <a href="#references" class="anchor"></a>References</h1> -<div id="refs" class="references"> +<div id="refs" class="references hanging-indent"> <div id="ref-usepa2015"> <p>US EPA. 2015. “Standard Operating Procedure for Using the NAFTA Guidance to Calculate Representative Half-Life Values and Characterizing Pesticide Degradation.”</p> </div> diff --git a/docs/dev/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/dev/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/dev/articles/web_only/NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo 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We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html index 8e157c0f..a6d52649 100644 --- a/docs/dev/articles/web_only/benchmarks.html +++ b/docs/dev/articles/web_only/benchmarks.html @@ -32,7 +32,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> </span> </div> @@ -81,7 +81,7 @@ <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin/"> - <span class="fab fa fab fa-github fa-lg"></span> + <span class="fab fa-github fa-lg"></span> </a> </li> @@ -95,14 +95,13 @@ - </header><link href="benchmarks_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet"> -<script src="benchmarks_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row"> + </header><script src="benchmarks_files/header-attrs-2.6/header-attrs.js"></script><script src="benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Benchmark timings for mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-11-30</h4> + <h4 class="date">Last change 13 May 2020 (rebuilt 2021-02-15)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/benchmarks.rmd"><code>vignettes/web_only/benchmarks.rmd</code></a></small> <div class="hidden name"><code>benchmarks.rmd</code></div> @@ -137,17 +136,11 @@ 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> <span class="va">t3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">FOCUS_D</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span> <span class="va">t4</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">FOCUS_D</span><span class="op">)</span>, - error_model <span class="op">=</span> <span class="st">"tc"</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></code></pre></div> -<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge: -## iteration limit reached without convergence (10) - -## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge: -## iteration limit reached without convergence (10)</code></pre> -<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">t5</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">FOCUS_D</span><span class="op">)</span>, + error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span> +<span class="va">t5</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOMC_SFO</span>, <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">FOCUS_D</span><span class="op">)</span>, error_model <span class="op">=</span> <span class="st">"obs"</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></code></pre></div> <p>Two metabolites, synthetic data:</p> -<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">m_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <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">"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="st">"M2"</span><span class="op">)</span>, M2 <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>, @@ -174,7 +167,7 @@ error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span> <span class="va">t11</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span><span class="va">DFOP_par_c</span><span class="op">)</span>, error_model <span class="op">=</span> <span class="st">"obs"</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></code></pre></div> -<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">mkin_benchmarks</span><span class="op">[</span><span class="va">system_string</span>, <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span><span class="op">(</span><span class="st">"t"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">11</span><span class="op">)</span><span class="op">]</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">t1</span>, <span class="va">t2</span>, <span class="va">t3</span>, <span class="va">t4</span>, <span class="va">t5</span>, <span class="va">t6</span>, <span class="va">t7</span>, <span class="va">t8</span>, <span class="va">t9</span>, <span class="va">t10</span>, <span class="va">t11</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/save.html">save</a></span><span class="op">(</span><span class="va">mkin_benchmarks</span>, file <span class="op">=</span> <span class="st">"~/git/mkin/vignettes/web_only/mkin_benchmarks.rda"</span><span class="op">)</span></code></pre></div> @@ -235,6 +228,16 @@ <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="right">1.722</td> +<td align="right">3.419</td> +</tr> +<tr class="even"> +<td align="left">1.0.3.9000</td> +<td align="right">2.770</td> +<td align="right">3.458</td> +</tr> </tbody> </table> </div> @@ -298,13 +301,25 @@ <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="right">1.402</td> +<td align="right">6.343</td> +<td align="right">2.802</td> +</tr> +<tr class="even"> +<td align="left">1.0.3.9000</td> +<td align="right">1.405</td> +<td align="right">6.417</td> +<td align="right">2.824</td> +</tr> </tbody> </table> </div> <div id="two-metabolites" class="section level3"> <h3 class="hasAnchor"> <a href="#two-metabolites" class="anchor"></a>Two metabolites</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> +<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"> <thead><tr class="header"> <th align="left">mkin version</th> @@ -388,6 +403,24 @@ <td align="right">1.958</td> <td align="right">3.105</td> </tr> +<tr class="odd"> +<td align="left">1.0.3</td> +<td align="right">0.771</td> +<td align="right">1.251</td> +<td align="right">1.464</td> +<td align="right">3.074</td> +<td align="right">1.940</td> +<td align="right">2.831</td> +</tr> +<tr class="even"> +<td align="left">1.0.3.9000</td> +<td align="right">0.772</td> +<td align="right">1.263</td> +<td align="right">1.483</td> +<td align="right">3.101</td> +<td align="right">1.958</td> +<td align="right">2.843</td> +</tr> </tbody> </table> </div> diff --git a/docs/dev/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/dev/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/dev/articles/web_only/benchmarks_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/dev/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js b/docs/dev/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/dev/articles/web_only/benchmarks_files/header-attrs-2.6/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html index a444f4bc..49a579fc 100644 --- a/docs/dev/articles/web_only/compiled_models.html +++ b/docs/dev/articles/web_only/compiled_models.html @@ -32,7 +32,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> </span> </div> @@ -81,7 +81,7 @@ <ul class="nav navbar-nav navbar-right"> <li> <a href="https://github.com/jranke/mkin/"> - <span class="fab fa fab fa-github fa-lg"></span> + <span class="fab fa-github fa-lg"></span> </a> </li> @@ -95,14 +95,13 @@ - </header><link href="compiled_models_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet"> -<script src="compiled_models_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row"> + </header><script src="compiled_models_files/header-attrs-2.6/header-attrs.js"></script><script src="compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-11-30</h4> + <h4 class="date">2021-02-15</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/compiled_models.rmd"><code>vignettes/web_only/compiled_models.rmd</code></a></small> <div class="hidden name"><code>compiled_models.rmd</code></div> @@ -160,10 +159,10 @@ <span class="fu"><a href="https://rdrr.io/r/base/print.html">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>## test replications relative elapsed -## 4 analytical 1 1.000 0.187 -## 3 deSolve, compiled 1 1.807 0.338 -## 2 Eigenvalue based 1 2.032 0.380 -## 1 deSolve, not compiled 1 43.048 8.050</code></pre> +## 4 analytical 1 1.000 0.182 +## 3 deSolve, compiled 1 1.824 0.332 +## 2 Eigenvalue based 1 2.082 0.379 +## 1 deSolve, not compiled 1 46.181 8.405</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 id="model-without-analytical-solution" class="section level2"> @@ -190,13 +189,13 @@ <span class="op">}</span></code></pre></div> <pre><code>## Temporary DLL for differentials generated and loaded</code></pre> <pre><code>## test replications relative elapsed -## 2 deSolve, compiled 1 1.000 0.483 -## 1 deSolve, not compiled 1 29.969 14.475</code></pre> -<p>Here we get a performance benefit of a factor of 30 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 0.9.50.4 on</p> +## 2 deSolve, compiled 1 1.000 0.541 +## 1 deSolve, not compiled 1 29.091 15.738</code></pre> +<p>Here we get a performance benefit of a factor of 29 using the version of the differential equation model compiled from C code!</p> +<p>This vignette was built with mkin 1.0.3.9000 on</p> <pre><code>## R version 4.0.3 (2020-10-10) ## Platform: x86_64-pc-linux-gnu (64-bit) -## Running under: Debian GNU/Linux 10 (buster)</code></pre> +## Running under: Debian GNU/Linux bullseye/sid</code></pre> <pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre> </div> </div> diff --git a/docs/dev/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js b/docs/dev/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js new file mode 100644 index 00000000..ca349fd6 --- /dev/null +++ b/docs/dev/articles/web_only/compiled_models_files/accessible-code-block-0.0.1/empty-anchor.js @@ -0,0 +1,15 @@ +// Hide empty <a> tag within highlighted CodeBlock for screen reader accessibility (see https://github.com/jgm/pandoc/issues/6352#issuecomment-626106786) --> +// v0.0.1 +// Written by JooYoung Seo (jooyoung@psu.edu) and Atsushi Yasumoto on June 1st, 2020. + +document.addEventListener('DOMContentLoaded', function() { + const codeList = document.getElementsByClassName("sourceCode"); + for (var i = 0; i < codeList.length; i++) { + var linkList = codeList[i].getElementsByTagName('a'); + for (var j = 0; j < linkList.length; j++) { + if (linkList[j].innerHTML === "") { + linkList[j].setAttribute('aria-hidden', 'true'); + } + } + } +}); diff --git a/docs/dev/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js b/docs/dev/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js new file mode 100644 index 00000000..dd57d92e --- /dev/null +++ b/docs/dev/articles/web_only/compiled_models_files/header-attrs-2.6/header-attrs.js @@ -0,0 +1,12 @@ +// Pandoc 2.9 adds attributes on both header and div. We remove the former (to +// be compatible with the behavior of Pandoc < 2.8). +document.addEventListener('DOMContentLoaded', function(e) { + var hs = document.querySelectorAll("div.section[class*='level'] > :first-child"); + var i, h, a; + for (i = 0; i < hs.length; i++) { + h = hs[i]; + if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6 + a = h.attributes; + while (a.length > 0) h.removeAttribute(a[0].name); + } +}); |
