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Diffstat (limited to 'docs/articles')
18 files changed, 347 insertions, 462 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 243ebee1..cdd85f43 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -68,9 +68,6 @@ <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> - <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> - </li> </ul> </li> <li> @@ -100,10 +97,10 @@ <h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-05-14</h4> + <h4 class="date">2020-05-27</h4> - <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.rmd"><code>vignettes/FOCUS_D.rmd</code></a></small> - <div class="hidden name"><code>FOCUS_D.rmd</code></div> + <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.Rmd"><code>vignettes/FOCUS_D.Rmd</code></a></small> + <div class="hidden name"><code>FOCUS_D.Rmd</code></div> </div> @@ -180,8 +177,8 @@ <div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">fit</span>)</pre></body></html></div> <pre><code>## mkin version used for fitting: 0.9.50.2 ## R version used for fitting: 4.0.0 -## Date of fit: Thu May 14 17:07:12 2020 -## Date of summary: Thu May 14 17:07:12 2020 +## Date of fit: Wed May 27 07:05:33 2020 +## Date of summary: Wed May 27 07:05:34 2020 ## ## Equations: ## d_parent/dt = - k_parent * parent @@ -189,7 +186,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 421 model solutions performed in 0.167 s +## Fitted using 421 model solutions performed in 0.166 s ## ## Error model: Constant variance ## @@ -228,11 +225,11 @@ ## ## Parameter correlation: ## parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma -## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -3.214e-07 +## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -3.190e-07 ## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.168e-07 -## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.410e-07 -## f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 5.093e-10 -## sigma -3.214e-07 3.168e-07 -1.410e-07 5.093e-10 1.000e+00 +## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.406e-07 +## f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 -1.587e-10 +## sigma -3.190e-07 3.168e-07 -1.406e-07 -1.587e-10 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index df5c77c4..2a58b4e5 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -68,9 +68,6 @@ <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> - <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> - </li> </ul> </li> <li> @@ -100,10 +97,10 @@ <h1 data-toc-skip>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-05-14</h4> + <h4 class="date">2020-05-27</h4> - <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_L.rmd"><code>vignettes/FOCUS_L.rmd</code></a></small> - <div class="hidden name"><code>FOCUS_L.rmd</code></div> + <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_L.Rmd"><code>vignettes/FOCUS_L.Rmd</code></a></small> + <div class="hidden name"><code>FOCUS_L.Rmd</code></div> </div> @@ -126,15 +123,15 @@ <span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.L1.SFO</span>)</pre></body></html></div> <pre><code>## mkin version used for fitting: 0.9.50.2 ## R version used for fitting: 4.0.0 -## Date of fit: Thu May 14 17:07:14 2020 -## Date of summary: Thu May 14 17:07:14 2020 +## Date of fit: Wed May 27 07:05:36 2020 +## Date of summary: Wed May 27 07:05:36 2020 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted using 133 model solutions performed in 0.032 s +## Fitted using 133 model solutions performed in 0.031 s ## ## Error model: Constant variance ## @@ -166,9 +163,9 @@ ## ## Parameter correlation: ## parent_0 log_k_parent_sink sigma -## parent_0 1.000e+00 6.186e-01 -1.516e-09 -## log_k_parent_sink 6.186e-01 1.000e+00 -3.124e-09 -## sigma -1.516e-09 -3.124e-09 1.000e+00 +## parent_0 1.000e+00 6.186e-01 -1.712e-09 +## log_k_parent_sink 6.186e-01 1.000e+00 -3.237e-09 +## sigma -1.712e-09 -3.237e-09 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -221,14 +218,14 @@ <div class="sourceCode" id="cb8"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">m.L1.FOMC</span>, <span class="kw">show_errmin</span> <span class="kw">=</span> <span class="fl">TRUE</span>, <span class="kw">main</span> <span class="kw">=</span> <span class="st">"FOCUS L1 - FOMC"</span>)</pre></body></html></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p> <div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.L1.FOMC</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</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>## mkin version used for fitting: 0.9.50.2 ## R version used for fitting: 4.0.0 -## Date of fit: Thu May 14 17:07:14 2020 -## Date of summary: Thu May 14 17:07:14 2020 +## Date of fit: Wed May 27 07:05:36 2020 +## Date of summary: Wed May 27 07:05:36 2020 ## ## ## Warning: Optimisation did not converge: @@ -240,7 +237,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 380 model solutions performed in 0.081 s +## Fitted using 899 model solutions performed in 0.204 s ## ## Error model: Constant variance ## @@ -264,31 +261,31 @@ ## Results: ## ## AIC BIC logLik -## 95.88778 99.44927 -43.94389 +## 95.88835 99.44984 -43.94418 ## ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper -## parent_0 92.47 1.2820 89.720 95.220 -## log_alpha 16.92 NaN NaN NaN -## log_beta 19.26 NaN NaN NaN -## sigma 2.78 0.4501 1.814 3.745 +## parent_0 92.47 1.2800 89.730 95.220 +## log_alpha 10.58 NaN NaN NaN +## log_beta 12.93 NaN NaN NaN +## sigma 2.78 0.4507 1.813 3.747 ## ## Parameter correlation: -## parent_0 log_alpha log_beta sigma -## parent_0 1.000000 NaN NaN 0.002218 -## log_alpha NaN 1 NaN NaN -## log_beta NaN NaN 1 NaN -## sigma 0.002218 NaN NaN 1.000000 +## parent_0 log_alpha log_beta sigma +## parent_0 1.00000 NaN NaN 0.01452 +## log_alpha NaN 1 NaN NaN +## log_beta NaN NaN 1 NaN +## sigma 0.01452 NaN NaN 1.00000 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. ## t-test (unrealistically) based on the assumption of normal distribution ## for estimators of untransformed parameters. -## Estimate t value Pr(>t) Lower Upper -## parent_0 9.247e+01 NA NA 89.720 95.220 -## alpha 2.223e+07 NA NA NA NA -## beta 2.325e+08 NA NA NA NA -## sigma 2.780e+00 NA NA 1.814 3.745 +## Estimate t value Pr(>t) Lower Upper +## parent_0 92.47 72.13000 1.052e-19 89.730 95.220 +## alpha 39440.00 0.02397 4.906e-01 NA NA +## beta 412500.00 0.02397 4.906e-01 NA NA +## sigma 2.78 6.00000 1.628e-05 1.813 3.747 ## ## FOCUS Chi2 error levels in percent: ## err.min n.optim df @@ -296,8 +293,8 @@ ## parent 3.619 3 6 ## ## Estimated disappearance times: -## DT50 DT90 DT50back -## parent 7.25 24.08 7.25</code></pre> +## DT50 DT90 DT50back +## parent 7.249 24.08 7.249</code></pre> <p>We get a warning that the default optimisation algorithm <code>Port</code> did not converge, which is an indication that the model is overparameterised, <em>i.e.</em> contains too many parameters that are ill-defined as a consequence.</p> <p>And in fact, due to the higher number of parameters, and the lower number of degrees of freedom of the fit, the <span class="math inline">\(\chi^2\)</span> error level is actually higher for the FOMC model (3.6%) than for the SFO model (3.4%). Additionally, the parameters <code>log_alpha</code> and <code>log_beta</code> internally fitted in the model have excessive confidence intervals, that span more than 25 orders of magnitude (!) when backtransformed to the scale of <code>alpha</code> and <code>beta</code>. Also, the t-test for significant difference from zero does not indicate such a significant difference, with p-values greater than 0.1, and finally, the parameter correlation of <code>log_alpha</code> and <code>log_beta</code> is 1.000, clearly indicating that the model is overparameterised.</p> <p>The <span class="math inline">\(\chi^2\)</span> error levels reported in Appendix 3 and Appendix 7 to the FOCUS kinetics report are rounded to integer percentages and partly deviate by one percentage point from the results calculated by mkin. The reason for this is not known. However, mkin gives the same <span class="math inline">\(\chi^2\)</span> error levels as the kinfit package and the calculation routines of the kinfit package have been extensively compared to the results obtained by the KinGUI software, as documented in the kinfit package vignette. KinGUI was the first widely used standard package in this field. Also, the calculation of <span class="math inline">\(\chi^2\)</span> error levels was compared with KinGUII, CAKE and DegKin manager in a project sponsored by the German Umweltbundesamt <span class="citation">(Ranke 2014)</span>.</p> @@ -335,8 +332,8 @@ <div class="sourceCode" id="cb17"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.L2.FOMC</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div> <pre><code>## mkin version used for fitting: 0.9.50.2 ## R version used for fitting: 4.0.0 -## Date of fit: Thu May 14 17:07:15 2020 -## Date of summary: Thu May 14 17:07:15 2020 +## Date of fit: Wed May 27 07:05:37 2020 +## Date of summary: Wed May 27 07:05:37 2020 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -378,10 +375,10 @@ ## ## Parameter correlation: ## parent_0 log_alpha log_beta sigma -## parent_0 1.000e+00 -1.151e-01 -2.085e-01 -7.436e-09 +## parent_0 1.000e+00 -1.151e-01 -2.085e-01 -7.637e-09 ## log_alpha -1.151e-01 1.000e+00 9.741e-01 -1.617e-07 -## log_beta -2.085e-01 9.741e-01 1.000e+00 -1.386e-07 -## sigma -7.436e-09 -1.617e-07 -1.386e-07 1.000e+00 +## log_beta -2.085e-01 9.741e-01 1.000e+00 -1.387e-07 +## sigma -7.637e-09 -1.617e-07 -1.387e-07 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -414,8 +411,8 @@ <div class="sourceCode" id="cb20"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.L2.DFOP</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div> <pre><code>## mkin version used for fitting: 0.9.50.2 ## R version used for fitting: 4.0.0 -## Date of fit: Thu May 14 17:07:15 2020 -## Date of summary: Thu May 14 17:07:15 2020 +## Date of fit: Wed May 27 07:05:37 2020 +## Date of summary: Wed May 27 07:05:37 2020 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -424,7 +421,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 572 model solutions performed in 0.131 s +## Fitted using 572 model solutions performed in 0.132 s ## ## Error model: Constant variance ## @@ -455,18 +452,18 @@ ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper ## parent_0 93.9500 9.998e-01 91.5900 96.3100 -## log_k1 3.1370 2.376e+03 -5615.0000 5622.0000 +## log_k1 3.1370 2.376e+03 -5616.0000 5622.0000 ## log_k2 -1.0880 6.285e-02 -1.2370 -0.9394 ## g_ilr -0.2821 7.033e-02 -0.4484 -0.1158 ## sigma 1.4140 2.886e-01 0.7314 2.0960 ## ## Parameter correlation: ## parent_0 log_k1 log_k2 g_ilr sigma -## parent_0 1.000e+00 5.157e-07 2.376e-09 2.665e-01 -6.837e-09 -## log_k1 5.157e-07 1.000e+00 8.434e-05 -1.659e-04 -7.786e-06 -## log_k2 2.376e-09 8.434e-05 1.000e+00 -7.903e-01 -1.263e-08 -## g_ilr 2.665e-01 -1.659e-04 -7.903e-01 1.000e+00 3.248e-08 -## sigma -6.837e-09 -7.786e-06 -1.263e-08 3.248e-08 1.000e+00 +## parent_0 1.000e+00 5.155e-07 2.371e-09 2.665e-01 -6.849e-09 +## log_k1 5.155e-07 1.000e+00 8.434e-05 -1.659e-04 -7.791e-06 +## log_k2 2.371e-09 8.434e-05 1.000e+00 -7.903e-01 -1.262e-08 +## g_ilr 2.665e-01 -1.659e-04 -7.903e-01 1.000e+00 3.241e-08 +## sigma -6.849e-09 -7.791e-06 -1.262e-08 3.241e-08 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -517,8 +514,8 @@ <div class="sourceCode" id="cb24"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">mm.L3</span><span class="kw">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span>]])</pre></body></html></div> <pre><code>## mkin version used for fitting: 0.9.50.2 ## R version used for fitting: 4.0.0 -## Date of fit: Thu May 14 17:07:16 2020 -## Date of summary: Thu May 14 17:07:16 2020 +## Date of fit: Wed May 27 07:05:38 2020 +## Date of summary: Wed May 27 07:05:38 2020 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -565,11 +562,11 @@ ## ## Parameter correlation: ## parent_0 log_k1 log_k2 g_ilr sigma -## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 -6.868e-07 -## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 3.175e-07 -## log_k2 2.282e-02 4.945e-01 1.000e+00 -6.812e-01 7.631e-07 -## g_ilr 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -8.694e-07 -## sigma -6.868e-07 3.175e-07 7.631e-07 -8.694e-07 1.000e+00 +## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 -6.872e-07 +## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 3.200e-07 +## log_k2 2.282e-02 4.945e-01 1.000e+00 -6.812e-01 7.673e-07 +## g_ilr 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -8.731e-07 +## sigma -6.872e-07 3.200e-07 7.673e-07 -8.731e-07 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -626,8 +623,8 @@ <div class="sourceCode" id="cb29"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">mm.L4</span><span class="kw">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span>]], <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div> <pre><code>## mkin version used for fitting: 0.9.50.2 ## R version used for fitting: 4.0.0 -## Date of fit: Thu May 14 17:07:16 2020 -## Date of summary: Thu May 14 17:07:16 2020 +## Date of fit: Wed May 27 07:05:38 2020 +## Date of summary: Wed May 27 07:05:38 2020 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent @@ -666,9 +663,9 @@ ## ## Parameter correlation: ## parent_0 log_k_parent_sink sigma -## parent_0 1.000e+00 5.938e-01 3.387e-07 -## log_k_parent_sink 5.938e-01 1.000e+00 5.830e-07 -## sigma 3.387e-07 5.830e-07 1.000e+00 +## parent_0 1.000e+00 5.938e-01 3.440e-07 +## log_k_parent_sink 5.938e-01 1.000e+00 5.885e-07 +## sigma 3.440e-07 5.885e-07 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -690,8 +687,8 @@ <div class="sourceCode" id="cb31"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">mm.L4</span><span class="kw">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span>]], <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)</pre></body></html></div> <pre><code>## mkin version used for fitting: 0.9.50.2 ## R version used for fitting: 4.0.0 -## Date of fit: Thu May 14 17:07:16 2020 -## Date of summary: Thu May 14 17:07:16 2020 +## Date of fit: Wed May 27 07:05:38 2020 +## Date of summary: Wed May 27 07:05:38 2020 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -733,10 +730,10 @@ ## ## Parameter correlation: ## parent_0 log_alpha log_beta sigma -## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.456e-07 -## log_alpha -4.696e-01 1.000e+00 9.889e-01 2.169e-08 -## log_beta -5.543e-01 9.889e-01 1.000e+00 4.910e-08 -## sigma -2.456e-07 2.169e-08 4.910e-08 1.000e+00 +## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.563e-07 +## log_alpha -4.696e-01 1.000e+00 9.889e-01 4.066e-08 +## log_beta -5.543e-01 9.889e-01 1.000e+00 6.818e-08 +## sigma -2.563e-07 4.066e-08 6.818e-08 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png Binary files differindex db54326e..2e5071d9 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-15-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png Binary files differindex bfa271dd..16235059 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png diff --git a/docs/articles/index.html b/docs/articles/index.html index 7b003598..6f97722c 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -71,7 +71,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.2</span> </span> </div> @@ -108,9 +108,6 @@ <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> - <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> - </li> </ul> </li> <li> @@ -157,7 +154,7 @@ <dd></dt> <dt><a href="web_only/NAFTA_examples.html">Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</a></dt> <dd></dt> - <dt><a href="web_only/benchmarks.html">Benchmark timings for mkin</a></dt> + <dt><a href="web_only/benchmarks.html">Benchmark timings for mkin on various systems</a></dt> <dd></dt> <dt><a href="web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></dt> <dd></dt> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 37b7b1a1..5f858d57 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -68,9 +68,6 @@ <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> - <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> - </li> </ul> </li> <li> @@ -100,10 +97,10 @@ <h1 data-toc-skip>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-05-14</h4> + <h4 class="date">2020-05-27</h4> - <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/mkin.rmd"><code>vignettes/mkin.rmd</code></a></small> - <div class="hidden name"><code>mkin.rmd</code></div> + <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/mkin.Rmd"><code>vignettes/mkin.Rmd</code></a></small> + <div class="hidden name"><code>mkin.Rmd</code></div> </div> @@ -142,7 +139,7 @@ <span class="co"># Plot the results separately for parent and metabolites</span> <span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">f_SFO_SFO_SFO</span>, <span class="kw">lpos</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span>))</pre></body></html></div> -<p><img src="mkin_files/figure-html/unnamed-chunk-2-1.png" width="768"></p> +<p><img src="../docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png" width="768"></p> </div> <div id="background" class="section level1"> <h1 class="hasAnchor"> diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png Binary files differdeleted file mode 100644 index bdc067c1..00000000 --- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png +++ /dev/null diff --git a/docs/articles/twa.html b/docs/articles/twa.html index c231e17d..e70205f2 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -68,9 +68,6 @@ <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> - <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> - </li> </ul> </li> <li> @@ -100,10 +97,10 @@ <h1 data-toc-skip>Calculation of time weighted average concentrations with mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-05-14</h4> + <h4 class="date">2020-05-27</h4> - <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/twa.rmd"><code>vignettes/twa.rmd</code></a></small> - <div class="hidden name"><code>twa.rmd</code></div> + <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/twa.Rmd"><code>vignettes/twa.Rmd</code></a></small> + <div class="hidden name"><code>twa.Rmd</code></div> </div> diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 3427afb6..ccbfcc86 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -68,9 +68,6 @@ <li> <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> - <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> - </li> </ul> </li> <li> @@ -100,10 +97,10 @@ <h1 data-toc-skip>Example evaluation of FOCUS dataset Z</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-05-14</h4> + <h4 class="date">2020-05-27</h4> - <small class="dont-index">Source: <a href="http://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> + <small class="dont-index">Source: <a href="http://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> </div> @@ -216,25 +213,25 @@ <div class="sourceCode" id="cb33"><html><body><pre class="r"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">m.Z.FOCUS</span>)</pre></body></html></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p> <div class="sourceCode" id="cb34"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">m.Z.FOCUS</span>, <span class="kw">data</span> <span class="kw">=</span> <span class="fl">FALSE</span>)$<span class="no">bpar</span></pre></body></html></div> -<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 96.838721 1.994275 48.5584 4.0283e-42 92.826878 100.850563 -## k_Z0 2.215400 0.118459 18.7019 1.0414e-23 1.989462 2.466998 -## k_Z1 0.478301 0.028257 16.9267 6.2411e-22 0.424705 0.538662 -## k_Z2 0.451623 0.042138 10.7176 1.6313e-14 0.374336 0.544867 -## k_Z3 0.058694 0.015246 3.8499 1.7804e-04 0.034809 0.098967 -## f_Z2_to_Z3 0.471510 0.058352 8.0804 9.6640e-11 0.357775 0.588283 -## sigma 3.984431 0.383402 10.3923 4.5575e-14 3.213126 4.755736</code></pre> +<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper +## Z0_0 96.840695 1.994285 48.5591 4.0254e-42 92.828744 100.85265 +## k_Z0 2.215467 0.118463 18.7018 1.0417e-23 1.989524 2.46707 +## k_Z1 0.478325 0.028259 16.9265 6.2441e-22 0.424725 0.53869 +## k_Z2 0.451638 0.042139 10.7177 1.6309e-14 0.374346 0.54489 +## k_Z3 0.058692 0.015245 3.8498 1.7807e-04 0.034806 0.09897 +## f_Z2_to_Z3 0.471484 0.058348 8.0805 9.6599e-11 0.357736 0.58827 +## sigma 3.984431 0.383402 10.3923 4.5576e-14 3.213126 4.75574</code></pre> <div class="sourceCode" id="cb36"><html><body><pre class="r"><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span>(<span class="no">m.Z.FOCUS</span>)</pre></body></html></div> <pre><code>## $ff ## Z2_Z3 Z2_sink -## 0.47151 0.52849 +## 0.47148 0.52852 ## ## $distimes ## DT50 DT90 -## Z0 0.31288 1.0394 -## Z1 1.44919 4.8141 -## Z2 1.53479 5.0985 -## Z3 11.80955 39.2305</code></pre> +## Z0 0.31287 1.0393 +## Z1 1.44911 4.8138 +## Z2 1.53474 5.0983 +## Z3 11.80989 39.2316</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"> @@ -313,11 +310,11 @@ ## ## $SFORB ## Z0_b1 Z0_b2 Z3_b1 Z3_b2 -## 2.4471358 0.0075126 0.0800073 0.0000000 +## 2.4471337 0.0075125 0.0800071 0.0000000 ## ## $distimes ## DT50 DT90 DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2 -## Z0 0.3043 1.1848 0.28325 92.265 NA NA +## Z0 0.3043 1.1848 0.28325 92.266 NA NA ## Z1 1.5148 5.0320 NA NA NA NA ## Z2 1.6414 5.4526 NA NA NA NA ## Z3 NA NA NA NA 8.6636 Inf</code></pre> 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 d3702fb6..96738dd0 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 4a6fce4f..4f3c2554 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png Binary files differindex dd6537b7..b8c3ed26 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png Binary files differindex b986c30b..132a7317 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png Binary files differindex 47d806c0..b25bf26a 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 0c698299..dd5d89cd 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 46cb7aa5..b91e7ee7 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -68,9 +68,6 @@ <li> <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> - <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> - </li> </ul> </li> <li> @@ -100,10 +97,10 @@ <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">2020-05-14</h4> + <h4 class="date">2020-05-27</h4> - <small class="dont-index">Source: <a href="http://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> + <small class="dont-index">Source: <a href="http://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> </div> @@ -153,7 +150,7 @@ ## 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 2.17e-12 5.00e-01 0.0000 Inf +## k2 2.86e-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 ## @@ -162,7 +159,7 @@ ## 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 5.83e+11 3.20e+11 +## DFOP 55.5 4.42e+11 2.42e+11 ## ## Representative half-life: ## [1] 321.51</code></pre> @@ -201,7 +198,7 @@ ## 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 1.04e-11 5.00e-01 0.0000 Inf +## k2 1.16e-11 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 ## @@ -210,7 +207,7 @@ ## 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 1.09e+11 6.67e+10 +## DFOP 83.6 9.80e+10 5.98e+10 ## ## Representative half-life: ## [1] 215.87</code></pre> @@ -249,7 +246,7 @@ ## 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 3.88e-11 5.00e-01 0.0000 Inf +## k2 4.90e-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 ## @@ -258,7 +255,7 @@ ## 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 8.42e+09 1.79e+10 +## DFOP 34.1 6.66e+09 1.41e+10 ## ## Representative half-life: ## [1] 53.17</code></pre> @@ -297,7 +294,7 @@ ## 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 2.30e-10 5.00e-01 0.0000 Inf +## k2 1.97e-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 ## @@ -306,7 +303,7 @@ ## 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 5.95e+09 3.01e+09 +## DFOP 96.4 6.97e+09 3.52e+09 ## ## Representative half-life: ## [1] 454.55</code></pre> @@ -402,7 +399,7 @@ ## 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 6.69e-13 5.00e-01 0.000 Inf +## k2 6.02e-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 ## @@ -411,7 +408,7 @@ ## 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 1.86e+12 1.04e+12 +## DFOP 10.5 2.07e+12 1.15e+12 ## ## Representative half-life: ## [1] 101.43</code></pre> @@ -421,11 +418,16 @@ <h2 class="hasAnchor"> <a href="#example-on-page-9-lower-panel" class="anchor"></a>Example on page 9, lower panel</h2> <div class="sourceCode" id="cb37"><html><body><pre class="r"><span class="no">p9b</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p9b"</span>]])</pre></body></html></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="cb40"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p9b</span>)</pre></body></html></div> +<div class="sourceCode" id="cb44"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p9b</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb41"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p9b</span>)</pre></body></html></div> +<div class="sourceCode" id="cb45"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p9b</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 35.64867 23.22334 35.64867 @@ -452,7 +454,7 @@ ## parent_0 94.7123 1.61e-16 93.1355 96.2891 ## k1 0.0389 1.43e-06 0.0312 0.0485 ## k2 0.0389 6.67e-03 0.0186 0.0812 -## g 0.7742 5.00e-01 0.0000 1.0000 +## g 0.7742 NaN NA NA ## sigma 1.5957 2.50e-04 0.9135 2.2779 ## ## @@ -469,12 +471,12 @@ <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="cb43"><html><body><pre class="r"><span class="no">p10</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p10"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb47"><html><body><pre class="r"><span class="no">p10</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p10"</span>]])</pre></body></html></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="cb46"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p10</span>)</pre></body></html></div> +<div class="sourceCode" id="cb50"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p10</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb47"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p10</span>)</pre></body></html></div> +<div class="sourceCode" id="cb51"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p10</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 899.4089 336.4348 899.4089 @@ -497,12 +499,12 @@ ## sigma 4.90 1.77e-04 2.837 6.968 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 101.7315 1.41e-09 91.6534 111.810 -## k1 0.0495 6.48e-04 0.0303 0.081 -## k2 0.0495 1.67e-02 0.0201 0.122 -## g 0.6634 5.00e-01 0.0000 1.000 -## sigma 8.0152 2.50e-04 4.5886 11.442 +## Estimate Pr(>t) Lower Upper +## parent_0 101.7315 1.41e-09 91.6534 111.8097 +## k1 0.0495 6.42e-04 0.0301 0.0814 +## k2 0.0495 1.66e-02 0.0200 0.1225 +## g 0.6634 5.00e-01 0.0000 1.0000 +## sigma 8.0152 2.50e-04 4.5886 11.4418 ## ## ## DTx values: @@ -522,12 +524,12 @@ <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="cb49"><html><body><pre class="r"><span class="no">p11</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p11"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb53"><html><body><pre class="r"><span class="no">p11</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p11"</span>]])</pre></body></html></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="cb52"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p11</span>)</pre></body></html></div> +<div class="sourceCode" id="cb56"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p11</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> -<div class="sourceCode" id="cb53"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p11</span>)</pre></body></html></div> +<div class="sourceCode" id="cb57"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p11</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 579.6805 204.7932 144.7783 @@ -565,7 +567,7 @@ ## DFOP 4.21e+11 2.64e+12 9.56e+11 ## ## Representative half-life: -## [1] 41148171</code></pre> +## [1] 41148169</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> @@ -576,14 +578,14 @@ <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="cb55"><html><body><pre class="r"><span class="no">p12a</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p12a"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb59"><html><body><pre class="r"><span class="no">p12a</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p12a"</span>]])</pre></body></html></div> <pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance ## matrix</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="cb59"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p12a</span>)</pre></body></html></div> +<div class="sourceCode" id="cb63"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p12a</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<div class="sourceCode" id="cb60"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p12a</span>)</pre></body></html></div> +<div class="sourceCode" id="cb64"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p12a</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 695.4440 220.0685 695.4440 @@ -608,8 +610,8 @@ ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 100.521 2.74e-10 92.2366 108.805 -## k1 0.124 5.75e-06 0.0958 0.161 -## k2 0.124 6.72e-02 0.0319 0.484 +## k1 0.124 5.74e-06 0.0958 0.161 +## k2 0.124 6.61e-02 0.0319 0.484 ## g 0.877 5.00e-01 0.0000 1.000 ## sigma 7.048 2.50e-04 4.0349 10.061 ## @@ -626,20 +628,20 @@ <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="cb62"><html><body><pre class="r"><span class="no">p12b</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p12b"</span>]])</pre></body></html></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in qt(alpha/2, rdf): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<div class="sourceCode" id="cb66"><html><body><pre class="r"><span class="no">p12b</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p12b"</span>]])</pre></body></html></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(diag(covar_notrans)): NaNs produced</code></pre> +<pre><code>## Warning in pt(abs(tval), rdf, lower.tail = FALSE): 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="cb72"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p12b</span>)</pre></body></html></div> +<div class="sourceCode" id="cb76"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p12b</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<div class="sourceCode" id="cb73"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p12b</span>)</pre></body></html></div> +<div class="sourceCode" id="cb77"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p12b</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 58.90242 19.06353 58.90242 @@ -682,12 +684,16 @@ <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="cb75"><html><body><pre class="r"><span class="no">p13</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p13"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb79"><html><body><pre class="r"><span class="no">p13</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p13"</span>]])</pre></body></html></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="cb78"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p13</span>)</pre></body></html></div> +<div class="sourceCode" id="cb85"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p13</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<div class="sourceCode" id="cb79"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p13</span>)</pre></body></html></div> +<div class="sourceCode" id="cb86"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p13</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 174.5971 142.3951 174.5971 @@ -712,9 +718,9 @@ ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 92.73500 9.25e-15 8.95e+01 9.59e+01 -## k1 0.00258 4.28e-01 1.45e-08 4.61e+02 +## k1 0.00258 4.28e-01 1.70e-08 3.92e+02 ## k2 0.00258 3.69e-08 2.20e-03 3.03e-03 -## g 0.00442 5.00e-01 0.00e+00 1.00e+00 +## g 0.00442 5.00e-01 NA NA ## sigma 3.41172 1.35e-04 2.02e+00 4.80e+00 ## ## @@ -731,16 +737,16 @@ <div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1"> <h1 class="hasAnchor"> <a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1> -<div class="sourceCode" id="cb81"><html><body><pre class="r"><span class="no">p14</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p14"</span>]])</pre></body></html></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<div class="sourceCode" id="cb88"><html><body><pre class="r"><span class="no">p14</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p14"</span>]])</pre></body></html></div> +<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> <pre><code>## Warning in cov2cor(ans$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="cb87"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p14</span>)</pre></body></html></div> +<div class="sourceCode" id="cb94"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p14</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb88"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p14</span>)</pre></body></html></div> +<div class="sourceCode" id="cb95"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p14</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 48.43249 28.67746 27.26248 @@ -766,7 +772,7 @@ ## 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 7.70e-12 5.00e-01 0.00000 Inf +## k2 7.29e-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 ## @@ -775,7 +781,7 @@ ## 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 2.41e+10 2.33e+11 9.00e+10 +## DFOP 2.54e+10 2.46e+11 9.51e+10 ## ## Representative half-life: ## [1] 6697.44</code></pre> @@ -784,16 +790,17 @@ <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="cb90"><html><body><pre class="r"><span class="no">p15a</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p15a"</span>]])</pre></body></html></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<div class="sourceCode" id="cb97"><html><body><pre class="r"><span class="no">p15a</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p15a"</span>]])</pre></body></html></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="cb96"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p15a</span>)</pre></body></html></div> +<div class="sourceCode" id="cb104"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p15a</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<div class="sourceCode" id="cb97"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p15a</span>)</pre></body></html></div> +<div class="sourceCode" id="cb105"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p15a</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 245.5248 135.0132 245.5248 @@ -816,12 +823,12 @@ ## sigma 3.105 1.78e-04 1.795 4.416 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 97.96752 NA 94.21914 101.7159 -## k1 0.00952 NA 0.00241 0.0377 -## k2 0.00952 NA 0.00747 0.0121 -## g 0.17247 NA NA NA -## sigma 4.18778 NA 2.39747 5.9781 +## Estimate Pr(>t) Lower Upper +## parent_0 97.96752 2.85e-13 94.21914 101.7159 +## k1 0.00952 6.80e-02 0.00277 0.0327 +## k2 0.00952 3.82e-06 0.00902 0.0100 +## g 0.17247 NaN NA NA +## sigma 4.18778 2.50e-04 2.39747 5.9781 ## ## ## DTx values: @@ -832,16 +839,16 @@ ## ## Representative half-life: ## [1] 41.33</code></pre> -<div class="sourceCode" id="cb99"><html><body><pre class="r"><span class="no">p15b</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p15b"</span>]])</pre></body></html></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> +<div class="sourceCode" id="cb107"><html><body><pre class="r"><span class="no">p15b</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p15b"</span>]])</pre></body></html></div> +<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> +<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> <pre><code>## Warning in cov2cor(ans$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="cb105"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p15b</span>)</pre></body></html></div> +<div class="sourceCode" id="cb113"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p15b</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<div class="sourceCode" id="cb106"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p15b</span>)</pre></body></html></div> +<div class="sourceCode" id="cb114"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p15b</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 106.91629 68.55574 106.91629 @@ -858,18 +865,18 @@ ## ## $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_sink 0.38 3.22e-01 0.00352 41.05 -## N_parent 0.00 5.00e-01 -1.07696 1.08 +## N_parent 0.00 5.00e-01 -1.07695 1.08 ## sigma 2.21 2.57e-04 1.23245 3.19 ## ## $DFOP ## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 NA 98.24464 1.04e+02 -## k1 4.86e-03 NA 0.00068 3.47e-02 -## k2 4.86e-03 NA 0.00338 6.99e-03 +## parent_0 1.01e+02 NA 9.82e+01 1.04e+02 +## k1 4.86e-03 NA 6.75e-04 3.49e-02 +## k2 4.86e-03 NA 3.37e-03 6.99e-03 ## g 1.50e-01 NA NA NA -## sigma 2.76e+00 NA 1.58208 3.94e+00 +## sigma 2.76e+00 NA 1.58e+00 3.94e+00 ## ## ## DTx values: @@ -885,14 +892,14 @@ <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="cb108"><html><body><pre class="r"><span class="no">p16</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p16"</span>]])</pre></body></html></div> +<div class="sourceCode" id="cb116"><html><body><pre class="r"><span class="no">p16</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span>(<span class="no">NAFTA_SOP_Attachment</span><span class="kw">[[</span><span class="st">"p16"</span>]])</pre></body></html></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="cb113"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p16</span>)</pre></body></html></div> +<div class="sourceCode" id="cb121"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/plot.html">plot</a></span>(<span class="no">p16</span>)</pre></body></html></div> <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> -<div class="sourceCode" id="cb114"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p16</span>)</pre></body></html></div> +<div class="sourceCode" id="cb122"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">p16</span>)</pre></body></html></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3831.804 2062.008 1550.980 @@ -917,7 +924,7 @@ ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 88.5333 7.40e-18 79.9836 97.083 -## k1 18.5560 5.00e-01 0.0000 Inf +## k1 18.5561 5.00e-01 0.0000 Inf ## k2 0.0776 1.41e-05 0.0518 0.116 ## g 0.4733 1.41e-09 0.3674 0.582 ## sigma 7.1902 2.11e-08 5.2785 9.102 diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index 97e22303..0698baf6 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -5,13 +5,13 @@ <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Benchmark timings for mkin • mkin</title> +<title>Benchmark timings for mkin on various systems • mkin</title> <!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../../bootstrap-toc.css"> <script src="../../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"> <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../../pkgdown.css" rel="stylesheet"> -<script src="../../pkgdown.js"></script><meta property="og:title" content="Benchmark timings for mkin"> +<script src="../../pkgdown.js"></script><meta property="og:title" content="Benchmark timings for mkin on various systems"> <meta property="og:description" content="mkin"> <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -68,9 +68,6 @@ <li> <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> - <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> - </li> </ul> </li> <li> @@ -97,47 +94,60 @@ </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> - <h1 data-toc-skip>Benchmark timings for mkin</h1> + <h1 data-toc-skip>Benchmark timings for mkin on various systems</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-05-14</h4> + <h4 class="date">2020-05-27</h4> - <small class="dont-index">Source: <a href="http://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> + <small class="dont-index">Source: <a href="http://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> </div> -<p>Each system is characterized by its CPU type, the operating system type and the mkin version. Currently only values for one system are available. A compiler was available, so if no analytical solution was available, compiled ODE models are used.</p> -<div id="test-cases" class="section level2"> +<div id="systems" class="section level2"> <h2 class="hasAnchor"> -<a href="#test-cases" class="anchor"></a>Test cases</h2> -<p>Parent only:</p> -<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="no">FOCUS_C</span> <span class="kw"><-</span> <span class="no">FOCUS_2006_C</span> -<span class="no">FOCUS_D</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html">subset</a></span>(<span class="no">FOCUS_2006_D</span>, <span class="no">value</span> <span class="kw">!=</span> <span class="fl">0</span>) -<span class="no">parent_datasets</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_C</span>, <span class="no">FOCUS_D</span>) +<a href="#systems" class="anchor"></a>Systems</h2> +<p>Each system is characterized by its CPU type, the operating system type and the mkin version.</p> +<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="no">cpu_model</span> <span class="kw"><-</span> <span class="kw pkg">benchmarkme</span><span class="kw ns">::</span><span class="fu"><a href="https://rdrr.io/pkg/benchmarkme/man/get_cpu.html">get_cpu</a></span>()$<span class="no">model_name</span> +<span class="no">operating_system</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html">Sys.info</a></span>()<span class="kw">[[</span><span class="st">"sysname"</span>]] +<span class="no">mkin_version</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/character.html">as.character</a></span>(<span class="fu"><a href="https://rdrr.io/r/utils/packageDescription.html">packageVersion</a></span>(<span class="st">"mkin"</span>)) +<span class="no">system_string</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(<span class="no">operating_system</span>, <span class="st">", "</span>, <span class="no">cpu_model</span>, <span class="st">", mkin version "</span>, <span class="no">mkin_version</span>) +<span class="fu"><a href="https://rdrr.io/r/base/load.html">load</a></span>(<span class="st">"~/git/mkin/vignettes/web_only/mkin_benchmarks.rda"</span>) +<span class="no">mkin_benchmarks</span>[<span class="no">system_string</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"CPU"</span>, <span class="st">"OS"</span>, <span class="st">"mkin"</span>)] <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">cpu_model</span>, <span class="no">operating_system</span>, <span class="no">mkin_version</span>) -<span class="no">t1</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="no">parent_datasets</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]] -<span class="no">t2</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="no">parent_datasets</span>, - <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]</pre></body></html></div> -<p>One metabolite:</p> -<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">SFO_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>( +<span class="kw">if</span> (<span class="no">mkin_version</span> <span class="kw">></span> <span class="st">"0.9.48.1"</span>) { + <span class="no">mmkin_bench</span> <span class="kw"><-</span> <span class="kw">function</span>(<span class="no">models</span>, <span class="no">datasets</span>, <span class="no">error_model</span> <span class="kw">=</span> <span class="st">"const"</span>) <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span>(<span class="no">models</span>, <span class="no">datasets</span>, <span class="kw">error_model</span> <span class="kw">=</span> <span class="no">error_model</span>, <span class="kw">cores</span> <span class="kw">=</span> <span class="fl">1</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>) +} <span class="kw">else</span> { + <span class="no">mmkin_bench</span> <span class="kw"><-</span> <span class="kw">function</span>(<span class="no">models</span>, <span class="no">datasets</span>, <span class="no">error_model</span> <span class="kw">=</span> <span class="kw">NULL</span>) <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span>(<span class="no">models</span>, <span class="no">datasets</span>, <span class="kw">reweight.method</span> <span class="kw">=</span> <span class="no">error_model</span>, <span class="kw">cores</span> <span class="kw">=</span> <span class="fl">1</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>) +}</pre></body></html></div> +<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">FOCUS_C</span> <span class="kw"><-</span> <span class="no">FOCUS_2006_C</span> +<span class="no">FOCUS_D</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html">subset</a></span>(<span class="no">FOCUS_2006_D</span>, <span class="no">value</span> <span class="kw">!=</span> <span class="fl">0</span>) +<span class="co"># Parent only</span> +<span class="no">t1</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_C</span>, <span class="no">FOCUS_D</span>)))<span class="kw">[[</span><span class="st">"elapsed"</span>]] +<span class="no">t2</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_C</span>, <span class="no">FOCUS_D</span>), <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]</pre></body></html></div> +<pre><code>## 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"><html><body><pre class="r"><span class="co"># One metabolite</span> +<span class="no">SFO_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>( <span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), - <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>)) -<span class="no">FOMC_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>( + <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="no">FOMC_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>( <span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>), - <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>)) -<span class="no">DFOP_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>( + <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode" id="cb8"><html><body><pre class="r"><span class="no">DFOP_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>( <span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>), - <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>)) -<span class="no">t3</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOMC_SFO</span>, <span class="no">DFOP_SFO</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_D</span>)))<span class="kw">[[</span><span class="st">"elapsed"</span>]] -<span class="no">t4</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOMC_SFO</span>, <span class="no">DFOP_SFO</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_D</span>), - <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]] -<span class="no">t5</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOMC_SFO</span>, <span class="no">DFOP_SFO</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_D</span>), - <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]</pre></body></html></div> -<p>Two metabolites, synthetic data:</p> -<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">m_synth_SFO_lin</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>), + <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div> +<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> +<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="no">t3</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOMC_SFO</span>, <span class="no">DFOP_SFO</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_D</span>)))<span class="kw">[[</span><span class="st">"elapsed"</span>]] +<span class="no">t4</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOMC_SFO</span>, <span class="no">DFOP_SFO</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_D</span>), <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]] +<span class="no">t5</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOMC_SFO</span>, <span class="no">DFOP_SFO</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">FOCUS_D</span>), <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]] + +<span class="co"># Two metabolites, synthetic data</span> +<span class="no">m_synth_SFO_lin</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>), <span class="kw">M1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>), <span class="kw">M2</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), <span class="kw">use_of_ff</span> <span class="kw">=</span> <span class="st">"max"</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>) @@ -151,194 +161,81 @@ <span class="no">DFOP_par_c</span> <span class="kw"><-</span> <span class="no">synthetic_data_for_UBA_2014</span><span class="kw">[[</span><span class="fl">12</span>]]$<span class="no">data</span> -<span class="no">t6</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>)))<span class="kw">[[</span><span class="st">"elapsed"</span>]] -<span class="no">t7</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>)))<span class="kw">[[</span><span class="st">"elapsed"</span>]] +<span class="no">t6</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>)))[<span class="st">"elapsed"</span>] +<span class="no">t7</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>)))[<span class="st">"elapsed"</span>] -<span class="no">t8</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>), - <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]] -<span class="no">t9</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>), - <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]] +<span class="no">t8</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>), <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>] +<span class="no">t9</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>), <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>] -<span class="no">t10</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>), - <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]] -<span class="no">t11</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>), - <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))<span class="kw">[[</span><span class="st">"elapsed"</span>]]</pre></body></html></div> -<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="no">mkin_benchmarks</span>[<span class="no">system_string</span>, <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(<span class="st">"t"</span>, <span class="fl">1</span>:<span class="fl">11</span>)] <span class="kw"><-</span> - <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">t1</span>, <span class="no">t2</span>, <span class="no">t3</span>, <span class="no">t4</span>, <span class="no">t5</span>, <span class="no">t6</span>, <span class="no">t7</span>, <span class="no">t8</span>, <span class="no">t9</span>, <span class="no">t10</span>, <span class="no">t11</span>) -<span class="fu"><a href="https://rdrr.io/r/base/save.html">save</a></span>(<span class="no">mkin_benchmarks</span>, <span class="kw">file</span> <span class="kw">=</span> <span class="st">"~/git/mkin/vignettes/web_only/mkin_benchmarks.rda"</span>)</pre></body></html></div> -</div> -<div id="results" class="section level2"> -<h2 class="hasAnchor"> -<a href="#results" class="anchor"></a>Results</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 id="parent-only" class="section level3"> -<h3 class="hasAnchor"> -<a href="#parent-only" class="anchor"></a>Parent only</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"> -<thead><tr class="header"> -<th align="left">mkin version</th> -<th align="right">t1 [s]</th> -<th align="right">t2 [s]</th> -</tr></thead> -<tbody> -<tr class="odd"> -<td align="left">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="right">8.184</td> -<td align="right">22.889</td> -</tr> -<tr class="odd"> -<td align="left">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="right">7.296</td> -<td align="right">21.239</td> -</tr> -<tr class="odd"> -<td align="left">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="right">1.714</td> -<td align="right">3.971</td> -</tr> -</tbody> -</table> -</div> -<div id="one-metabolite" class="section level3"> -<h3 class="hasAnchor"> -<a href="#one-metabolite" class="anchor"></a>One metabolite</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"> -<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> -</tr></thead> -<tbody> -<tr class="odd"> -<td align="left">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="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="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="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="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="right">1.402</td> -<td align="right">6.174</td> -<td align="right">2.764</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> -<table class="table"> -<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> -</tr></thead> -<tbody> -<tr class="odd"> -<td align="left">0.9.48.1</td> -<td align="right">2.623</td> -<td align="right">4.587</td> -<td align="right">7.525</td> -<td align="right">16.621</td> -<td align="right">8.576</td> -<td align="right">31.267</td> -</tr> -<tr class="even"> -<td align="left">0.9.49.1</td> -<td align="right">2.542</td> -<td align="right">4.128</td> -<td align="right">4.632</td> -<td align="right">8.171</td> -<td align="right">3.676</td> -<td align="right">5.636</td> -</tr> -<tr class="odd"> -<td align="left">0.9.49.2</td> -<td align="right">2.723</td> -<td align="right">4.478</td> -<td align="right">4.862</td> -<td align="right">7.618</td> -<td align="right">3.579</td> -<td align="right">5.574</td> -</tr> -<tr class="even"> -<td align="left">0.9.49.3</td> -<td align="right">2.643</td> -<td align="right">4.374</td> -<td align="right">7.020</td> -<td align="right">11.124</td> -<td align="right">5.388</td> -<td align="right">7.365</td> -</tr> -<tr class="odd"> -<td align="left">0.9.49.4</td> -<td align="right">2.635</td> -<td align="right">4.259</td> -<td align="right">4.737</td> -<td align="right">7.763</td> -<td align="right">3.427</td> -<td align="right">5.626</td> -</tr> -<tr class="even"> -<td align="left">0.9.50.2</td> -<td align="right">0.777</td> -<td align="right">1.236</td> -<td align="right">1.332</td> -<td align="right">2.872</td> -<td align="right">2.069</td> -<td align="right">2.987</td> -</tr> -</tbody> -</table> -</div> +<span class="no">t10</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_SFO_lin</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">SFO_lin_a</span>), <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>] +<span class="no">t11</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html">system.time</a></span>(<span class="fu">mmkin_bench</span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">m_synth_DFOP_par</span>), <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="no">DFOP_par_c</span>), <span class="kw">error_model</span> <span class="kw">=</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>] + +<span class="no">mkin_benchmarks</span>[<span class="no">system_string</span>, <span class="fu"><a href="https://rdrr.io/r/base/paste.html">paste0</a></span>(<span class="st">"t"</span>, <span class="fl">1</span>:<span class="fl">11</span>)] <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="no">t1</span>, <span class="no">t2</span>, <span class="no">t3</span>, <span class="no">t4</span>, <span class="no">t5</span>, <span class="no">t6</span>, <span class="no">t7</span>, <span class="no">t8</span>, <span class="no">t9</span>, <span class="no">t10</span>, <span class="no">t11</span>) +<span class="no">mkin_benchmarks</span>[, -<span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">1</span>:<span class="fl">3</span>)]</pre></body></html></div> +<pre><code>## t1 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.610 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.184 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2 1.679 +## t2 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2 3.613 +## t3 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2 1.366 +## t4 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 8.461 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2 6.545 +## t5 t6 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495 2.623 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395 2.542 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675 2.723 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386 2.643 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.002 2.635 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2 2.709 0.752 +## t7 t8 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587 7.525 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128 4.632 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478 4.862 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374 7.02 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259 4.737 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2 1.214 1.455 +## t9 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.171 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.618 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.763 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2 4.196 +## t10 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2 1.996 +## t11 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 5.636 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.574 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.365 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.626 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2 3.1</code></pre> +<div class="sourceCode" id="cb12"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/save.html">save</a></span>(<span class="no">mkin_benchmarks</span>, <span class="kw">file</span> <span class="kw">=</span> <span class="st">"~/git/mkin/vignettes/mkin_benchmarks.rda"</span>)</pre></body></html></div> </div> </div> diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 837b288b..5aaa09bc 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -68,9 +68,6 @@ <li> <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> - <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> - </li> </ul> </li> <li> @@ -100,10 +97,10 @@ <h1 data-toc-skip>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2020-05-14</h4> + <h4 class="date">2020-05-27</h4> - <small class="dont-index">Source: <a href="http://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> + <small class="dont-index">Source: <a href="http://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> </div> @@ -122,57 +119,56 @@ <p>into your .Rprofile startup file. This is just a text file with some R code that is executed when your R session starts. It has to be named .Rprofile and has to be located in your home directory, which will generally be your Documents folder. You can check the location of the home directory used by R by issuing</p> <div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html">Sys.getenv</a></span>(<span class="st">"HOME"</span>)</pre></body></html></div> </div> -<div id="comparison-with-other-solution-methods" class="section level2"> +<div id="comparison-with-eigenvalue-based-solutions" class="section level2"> <h2 class="hasAnchor"> -<a href="#comparison-with-other-solution-methods" class="anchor"></a>Comparison with other solution methods</h2> -<p>First, we build a simple degradation model for a parent compound with one metabolite, and we remove zero values from the dataset.</p> +<a href="#comparison-with-eigenvalue-based-solutions" class="anchor"></a>Comparison with Eigenvalue based solutions</h2> +<p>First, we build a simple degradation model for a parent compound with one metabolite.</p> <div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="st">"mkin"</span>, <span class="kw">quietly</span> <span class="kw">=</span> <span class="fl">TRUE</span>) <span class="no">SFO_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>( <span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="no">FOCUS_D</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html">subset</a></span>(<span class="no">FOCUS_2006_D</span>, <span class="no">value</span> <span class="kw">!=</span> <span class="fl">0</span>)</pre></body></html></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"><html><body><pre class="r"><span class="kw">if</span> (<span class="fu"><a href="https://rdrr.io/r/base/library.html">require</a></span>(<span class="no">rbenchmark</span>)) { +<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.</p> +<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="kw">if</span> (<span class="fu"><a href="https://rdrr.io/r/base/library.html">require</a></span>(<span class="no">rbenchmark</span>)) { <span class="no">b.1</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html">benchmark</a></span>( - <span class="st">"deSolve, not compiled"</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOCUS_D</span>, - <span class="kw">solution_type</span> <span class="kw">=</span> <span class="st">"deSolve"</span>, - <span class="kw">use_compiled</span> <span class="kw">=</span> <span class="fl">FALSE</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>), - <span class="st">"Eigenvalue based"</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOCUS_D</span>, - <span class="kw">solution_type</span> <span class="kw">=</span> <span class="st">"eigen"</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>), - <span class="st">"deSolve, compiled"</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOCUS_D</span>, - <span class="kw">solution_type</span> <span class="kw">=</span> <span class="st">"deSolve"</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>), - <span class="st">"analytical"</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOCUS_D</span>, - <span class="kw">solution_type</span> <span class="kw">=</span> <span class="st">"analytical"</span>, - <span class="kw">use_compiled</span> <span class="kw">=</span> <span class="fl">FALSE</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>), - <span class="kw">replications</span> <span class="kw">=</span> <span class="fl">1</span>, <span class="kw">order</span> <span class="kw">=</span> <span class="st">"relative"</span>, - <span class="kw">columns</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"test"</span>, <span class="st">"replications"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span>)) + <span class="st">"deSolve, not compiled"</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOCUS_2006_D</span>, + <span class="kw">solution_type</span> <span class="kw">=</span> <span class="st">"deSolve"</span>, + <span class="kw">use_compiled</span> <span class="kw">=</span> <span class="fl">FALSE</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>), + <span class="st">"Eigenvalue based"</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOCUS_2006_D</span>, + <span class="kw">solution_type</span> <span class="kw">=</span> <span class="st">"eigen"</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>), + <span class="st">"deSolve, compiled"</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOCUS_2006_D</span>, + <span class="kw">solution_type</span> <span class="kw">=</span> <span class="st">"deSolve"</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>), + <span class="kw">replications</span> <span class="kw">=</span> <span class="fl">3</span>) <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">b.1</span>) + <span class="no">factor_SFO_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/Round.html">round</a></span>(<span class="no">b.1</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>]) } <span class="kw">else</span> { + <span class="no">factor_SFO_SFO</span> <span class="kw"><-</span> <span class="fl">NA</span> <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="st">"R package rbenchmark is not available"</span>) }</pre></body></html></div> -<pre><code>## test replications relative elapsed -## 4 analytical 1 1.000 0.191 -## 3 deSolve, compiled 1 1.801 0.344 -## 2 Eigenvalue based 1 2.105 0.402 -## 1 deSolve, not compiled 1 42.864 8.187</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> +<pre><code>## test replications elapsed relative user.self sys.self +## 3 deSolve, compiled 3 0.997 1.000 0.997 0.000 +## 1 deSolve, not compiled 3 24.417 24.490 24.405 0.001 +## 2 Eigenvalue based 3 1.159 1.162 1.159 0.000 +## user.child sys.child +## 3 0 0 +## 1 0 0 +## 2 0 0</code></pre> +<p>We see that using the compiled model is by a factor of around 24 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.</p> </div> -<div id="model-without-analytical-solution" class="section level2"> +<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> <h2 class="hasAnchor"> -<a href="#model-without-analytical-solution" class="anchor"></a>Model without analytical solution</h2> -<p>This evaluation is also taken from the example section of mkinfit. No analytical solution is available for this system, and now Eigenvalue based solution is possible, so only deSolve using with or without compiled code is available.</p> -<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="kw">if</span> (<span class="fu"><a href="https://rdrr.io/r/base/library.html">require</a></span>(<span class="no">rbenchmark</span>)) { +<a href="#model-that-can-not-be-solved-with-eigenvalues" class="anchor"></a>Model that can not be solved with Eigenvalues</h2> +<p>This evaluation is also taken from the example section of mkinfit.</p> +<div class="sourceCode" id="cb8"><html><body><pre class="r"><span class="kw">if</span> (<span class="fu"><a href="https://rdrr.io/r/base/library.html">require</a></span>(<span class="no">rbenchmark</span>)) { <span class="no">FOMC_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span>( <span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>), <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinsub.html">mkinsub</a></span>( <span class="st">"SFO"</span>)) <span class="no">b.2</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html">benchmark</a></span>( - <span class="st">"deSolve, not compiled"</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">FOMC_SFO</span>, <span class="no">FOCUS_D</span>, + <span class="st">"deSolve, not compiled"</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">FOMC_SFO</span>, <span class="no">FOCUS_2006_D</span>, <span class="kw">use_compiled</span> <span class="kw">=</span> <span class="fl">FALSE</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>), - <span class="st">"deSolve, compiled"</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">FOMC_SFO</span>, <span class="no">FOCUS_D</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>), - <span class="kw">replications</span> <span class="kw">=</span> <span class="fl">1</span>, <span class="kw">order</span> <span class="kw">=</span> <span class="st">"relative"</span>, - <span class="kw">columns</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"test"</span>, <span class="st">"replications"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span>)) + <span class="st">"deSolve, compiled"</span> <span class="kw">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span>(<span class="no">FOMC_SFO</span>, <span class="no">FOCUS_2006_D</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>), + <span class="kw">replications</span> <span class="kw">=</span> <span class="fl">3</span>) <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">b.2</span>) <span class="no">factor_FOMC_SFO</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/Round.html">round</a></span>(<span class="no">b.2</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>]) } <span class="kw">else</span> { @@ -180,9 +176,12 @@ <span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="st">"R package benchmark is not available"</span>) }</pre></body></html></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<pre><code>## test replications relative elapsed -## 2 deSolve, compiled 1 1.000 0.466 -## 1 deSolve, not compiled 1 30.942 14.419</code></pre> +<pre><code>## test replications elapsed relative user.self sys.self +## 2 deSolve, compiled 3 1.392 1.000 1.391 0 +## 1 deSolve, not compiled 3 43.021 30.906 43.002 0 +## user.child sys.child +## 2 0 0 +## 1 0 0</code></pre> <p>Here we get a performance benefit of a factor of 31 using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 0.9.50.2 on</p> <pre><code>## R version 4.0.0 (2020-04-24) |
