diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2022-05-18 21:26:17 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2022-05-18 21:26:17 +0200 |
| commit | 91c5db736a4d3f2290a0cc5698fb4e35ae7bda59 (patch) | |
| tree | 8e9e34d18f055936172329c1248e6e2ff136bff9 /docs | |
| parent | ea57db98cef3fb882f7bd9656b44f270e7bded38 (diff) | |
Remove outdated comment in FOCUS L vignette, update docs
This also adds the first benchmark results obtained on my laptop system
Diffstat (limited to 'docs')
133 files changed, 964 insertions, 953 deletions
diff --git a/docs/404.html b/docs/404.html index ea7f1350..e4837693 100644 --- a/docs/404.html +++ b/docs/404.html @@ -124,7 +124,7 @@ Content not found. Please use links in the navbar. <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer> diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 1363ef11..39cf7e1a 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -105,7 +105,7 @@ <h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 31 January 2019 (rebuilt 2022-03-07)</h4> + <h4 data-toc-skip class="date">Last change 31 January 2019 (rebuilt 2022-05-18)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_D.rmd" class="external-link"><code>vignettes/FOCUS_D.rmd</code></a></small> <div class="hidden name"><code>FOCUS_D.rmd</code></div> @@ -191,9 +191,9 @@ <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## mkin version used for fitting: 1.1.0 </span> -<span class="co">## R version used for fitting: 4.1.2 </span> -<span class="co">## Date of fit: Mon Mar 7 13:15:58 2022 </span> -<span class="co">## Date of summary: Mon Mar 7 13:15:59 2022 </span> +<span class="co">## R version used for fitting: 4.2.0 </span> +<span class="co">## Date of fit: Wed May 18 20:42:29 2022 </span> +<span class="co">## Date of summary: Wed May 18 20:42:30 2022 </span> <span class="co">## </span> <span class="co">## Equations:</span> <span class="co">## d_parent/dt = - k_parent * parent</span> @@ -201,7 +201,7 @@ <span class="co">## </span> <span class="co">## Model predictions using solution type analytical </span> <span class="co">## </span> -<span class="co">## Fitted using 401 model solutions performed in 0.165 s</span> +<span class="co">## Fitted using 401 model solutions performed in 0.144 s</span> <span class="co">## </span> <span class="co">## Error model: Constant variance </span> <span class="co">## </span> @@ -244,11 +244,11 @@ <span class="co">## </span> <span class="co">## Parameter correlation:</span> <span class="co">## parent_0 log_k_parent log_k_m1 f_parent_qlogis sigma</span> -<span class="co">## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -1.172e-06</span> -<span class="co">## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.483e-07</span> -<span class="co">## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.205e-07</span> -<span class="co">## f_parent_qlogis -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 1.305e-06</span> -<span class="co">## sigma -1.172e-06 -8.483e-07 8.205e-07 1.305e-06 1.000e+00</span> +<span class="co">## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -1.174e-06</span> +<span class="co">## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.492e-07</span> +<span class="co">## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.220e-07</span> +<span class="co">## f_parent_qlogis -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 1.307e-06</span> +<span class="co">## sigma -1.174e-06 -8.492e-07 8.220e-07 1.307e-06 1.000e+00</span> <span class="co">## </span> <span class="co">## Backtransformed parameters:</span> <span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span> @@ -334,7 +334,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer> diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index d7412a56..5f41b6a3 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -105,7 +105,7 @@ <h1 data-toc-skip>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 17 November 2016 (rebuilt 2022-03-07)</h4> + <h4 data-toc-skip class="date">Last change 17 November 2016 (rebuilt 2022-05-18)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_L.rmd" class="external-link"><code>vignettes/FOCUS_L.rmd</code></a></small> <div class="hidden name"><code>FOCUS_L.rmd</code></div> @@ -132,16 +132,16 @@ <code class="sourceCode R"><span class="va">m.L1.SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_L1_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L1.SFO</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## mkin version used for fitting: 1.1.0 </span> -<span class="co">## R version used for fitting: 4.1.2 </span> -<span class="co">## Date of fit: Mon Mar 7 13:16:01 2022 </span> -<span class="co">## Date of summary: Mon Mar 7 13:16:01 2022 </span> +<span class="co">## R version used for fitting: 4.2.0 </span> +<span class="co">## Date of fit: Wed May 18 20:42:32 2022 </span> +<span class="co">## Date of summary: Wed May 18 20:42:32 2022 </span> <span class="co">## </span> <span class="co">## Equations:</span> <span class="co">## d_parent/dt = - k_parent * parent</span> <span class="co">## </span> <span class="co">## Model predictions using solution type analytical </span> <span class="co">## </span> -<span class="co">## Fitted using 133 model solutions performed in 0.032 s</span> +<span class="co">## Fitted using 133 model solutions performed in 0.031 s</span> <span class="co">## </span> <span class="co">## Error model: Constant variance </span> <span class="co">## </span> @@ -173,9 +173,9 @@ <span class="co">## </span> <span class="co">## Parameter correlation:</span> <span class="co">## parent_0 log_k_parent sigma</span> -<span class="co">## parent_0 1.000e+00 6.186e-01 -1.516e-09</span> -<span class="co">## log_k_parent 6.186e-01 1.000e+00 -3.124e-09</span> -<span class="co">## sigma -1.516e-09 -3.124e-09 1.000e+00</span> +<span class="co">## parent_0 1.000e+00 6.186e-01 -1.712e-09</span> +<span class="co">## log_k_parent 6.186e-01 1.000e+00 -3.237e-09</span> +<span class="co">## sigma -1.712e-09 -3.237e-09 1.000e+00</span> <span class="co">## </span> <span class="co">## Backtransformed parameters:</span> <span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span> @@ -225,29 +225,26 @@ <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-5-1.png" width="576"></p> <p>For comparison, the FOMC model is fitted as well, and the <span class="math inline">\(\chi^2\)</span> error level is checked.</p> <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.L1.FOMC</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_L1_mkin</span>, quiet<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation did not converge:</span> -<span class="co">## false convergence (8)</span></code></pre> -<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L1.FOMC</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, main <span class="op">=</span> <span class="st">"FOCUS L1 - FOMC"</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="va">m.L1.FOMC</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_L1_mkin</span>, quiet<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L1.FOMC</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, main <span class="op">=</span> <span class="st">"FOCUS L1 - FOMC"</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p> -<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L1.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> <pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> <pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> <span class="co">## doubtful</span></code></pre> <pre><code><span class="co">## mkin version used for fitting: 1.1.0 </span> -<span class="co">## R version used for fitting: 4.1.2 </span> -<span class="co">## Date of fit: Mon Mar 7 13:16:02 2022 </span> -<span class="co">## Date of summary: Mon Mar 7 13:16:02 2022 </span> +<span class="co">## R version used for fitting: 4.2.0 </span> +<span class="co">## Date of fit: Wed May 18 20:42:33 2022 </span> +<span class="co">## Date of summary: Wed May 18 20:42:33 2022 </span> <span class="co">## </span> <span class="co">## Equations:</span> <span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> <span class="co">## </span> <span class="co">## Model predictions using solution type analytical </span> <span class="co">## </span> -<span class="co">## Fitted using 369 model solutions performed in 0.081 s</span> +<span class="co">## Fitted using 357 model solutions performed in 0.072 s</span> <span class="co">## </span> <span class="co">## Error model: Constant variance </span> <span class="co">## </span> @@ -268,39 +265,34 @@ <span class="co">## Fixed parameter values:</span> <span class="co">## None</span> <span class="co">## </span> -<span class="co">## </span> -<span class="co">## Warning(s): </span> -<span class="co">## Optimisation did not converge:</span> -<span class="co">## false convergence (8)</span> -<span class="co">## </span> <span class="co">## Results:</span> <span class="co">## </span> -<span class="co">## AIC BIC logLik</span> -<span class="co">## 95.88781 99.44929 -43.9439</span> +<span class="co">## AIC BIC logLik</span> +<span class="co">## 95.88804 99.44953 -43.94402</span> <span class="co">## </span> <span class="co">## Optimised, transformed parameters with symmetric confidence intervals:</span> <span class="co">## Estimate Std. Error Lower Upper</span> <span class="co">## parent_0 92.47 1.2820 89.720 95.220</span> -<span class="co">## log_alpha 13.78 NaN NaN NaN</span> -<span class="co">## log_beta 16.13 NaN NaN NaN</span> -<span class="co">## sigma 2.78 0.4598 1.794 3.766</span> +<span class="co">## log_alpha 11.37 NaN NaN NaN</span> +<span class="co">## log_beta 13.72 NaN NaN NaN</span> +<span class="co">## sigma 2.78 0.4621 1.789 3.771</span> <span class="co">## </span> <span class="co">## Parameter correlation:</span> <span class="co">## parent_0 log_alpha log_beta sigma</span> -<span class="co">## parent_0 1.0000000 NaN NaN 0.0001671</span> +<span class="co">## parent_0 1.0000000 NaN NaN 0.0005548</span> <span class="co">## log_alpha NaN 1 NaN NaN</span> <span class="co">## log_beta NaN NaN 1 NaN</span> -<span class="co">## sigma 0.0001671 NaN NaN 1.0000000</span> +<span class="co">## sigma 0.0005548 NaN NaN 1.0000000</span> <span class="co">## </span> <span class="co">## Backtransformed parameters:</span> <span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span> <span class="co">## t-test (unrealistically) based on the assumption of normal distribution</span> <span class="co">## for estimators of untransformed parameters.</span> <span class="co">## Estimate t value Pr(>t) Lower Upper</span> -<span class="co">## parent_0 9.247e+01 NA NA 89.720 95.220</span> -<span class="co">## alpha 9.658e+05 NA NA NA NA</span> -<span class="co">## beta 1.010e+07 NA NA NA NA</span> -<span class="co">## sigma 2.780e+00 NA NA 1.794 3.766</span> +<span class="co">## parent_0 92.47 NA NA 89.720 95.220</span> +<span class="co">## alpha 87110.00 NA NA NA NA</span> +<span class="co">## beta 911100.00 NA NA NA NA</span> +<span class="co">## sigma 2.78 NA NA 1.789 3.771</span> <span class="co">## </span> <span class="co">## FOCUS Chi2 error levels in percent:</span> <span class="co">## err.min n.optim df</span> @@ -308,8 +300,8 @@ <span class="co">## parent 3.619 3 6</span> <span class="co">## </span> <span class="co">## Estimated disappearance times:</span> -<span class="co">## DT50 DT90 DT50back</span> -<span class="co">## parent 7.25 24.08 7.25</span></code></pre> +<span class="co">## DT50 DT90 DT50back</span> +<span class="co">## parent 7.249 24.08 7.249</span></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> @@ -318,7 +310,7 @@ <h2 id="laboratory-data-l2">Laboratory Data L2<a class="anchor" aria-label="anchor" href="#laboratory-data-l2"></a> </h2> <p>The following code defines example dataset L2 from the FOCUS kinetics report, p. 287:</p> -<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">FOCUS_2006_L2</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span> t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span><span class="op">)</span>, each <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>, parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">96.1</span>, <span class="fl">91.8</span>, <span class="fl">41.4</span>, <span class="fl">38.7</span>, @@ -329,7 +321,7 @@ <h3 id="sfo-fit-for-l2">SFO fit for L2<a class="anchor" aria-label="anchor" href="#sfo-fit-for-l2"></a> </h3> <p>Again, the SFO model is fitted and the result is plotted. The residual plot can be obtained simply by adding the argument <code>show_residuals</code> to the plot command.</p> -<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">m.L2.SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_L2_mkin</span>, quiet<span class="op">=</span><span class="cn">TRUE</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L2.SFO</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, main <span class="op">=</span> <span class="st">"FOCUS L2 - SFO"</span><span class="op">)</span></code></pre></div> @@ -342,24 +334,24 @@ <h3 id="fomc-fit-for-l2">FOMC fit for L2<a class="anchor" aria-label="anchor" href="#fomc-fit-for-l2"></a> </h3> <p>For comparison, the FOMC model is fitted as well, and the <span class="math inline">\(\chi^2\)</span> error level is checked.</p> -<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">m.L2.FOMC</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_L2_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, main <span class="op">=</span> <span class="st">"FOCUS L2 - FOMC"</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> -<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## mkin version used for fitting: 1.1.0 </span> -<span class="co">## R version used for fitting: 4.1.2 </span> -<span class="co">## Date of fit: Mon Mar 7 13:16:03 2022 </span> -<span class="co">## Date of summary: Mon Mar 7 13:16:03 2022 </span> +<span class="co">## R version used for fitting: 4.2.0 </span> +<span class="co">## Date of fit: Wed May 18 20:42:33 2022 </span> +<span class="co">## Date of summary: Wed May 18 20:42:33 2022 </span> <span class="co">## </span> <span class="co">## Equations:</span> <span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> <span class="co">## </span> <span class="co">## Model predictions using solution type analytical </span> <span class="co">## </span> -<span class="co">## Fitted using 239 model solutions performed in 0.049 s</span> +<span class="co">## Fitted using 239 model solutions performed in 0.044 s</span> <span class="co">## </span> <span class="co">## Error model: Constant variance </span> <span class="co">## </span> @@ -394,10 +386,10 @@ <span class="co">## </span> <span class="co">## Parameter correlation:</span> <span class="co">## parent_0 log_alpha log_beta sigma</span> -<span class="co">## parent_0 1.000e+00 -1.151e-01 -2.085e-01 -7.828e-09</span> -<span class="co">## log_alpha -1.151e-01 1.000e+00 9.741e-01 -1.602e-07</span> -<span class="co">## log_beta -2.085e-01 9.741e-01 1.000e+00 -1.372e-07</span> -<span class="co">## sigma -7.828e-09 -1.602e-07 -1.372e-07 1.000e+00</span> +<span class="co">## parent_0 1.000e+00 -1.151e-01 -2.085e-01 -7.637e-09</span> +<span class="co">## log_alpha -1.151e-01 1.000e+00 9.741e-01 -1.617e-07</span> +<span class="co">## log_beta -2.085e-01 9.741e-01 1.000e+00 -1.387e-07</span> +<span class="co">## sigma -7.637e-09 -1.617e-07 -1.387e-07 1.000e+00</span> <span class="co">## </span> <span class="co">## Backtransformed parameters:</span> <span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span> @@ -423,17 +415,17 @@ <h3 id="dfop-fit-for-l2">DFOP fit for L2<a class="anchor" aria-label="anchor" href="#dfop-fit-for-l2"></a> </h3> <p>Fitting the four parameter DFOP model further reduces the <span class="math inline">\(\chi^2\)</span> error level.</p> -<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">m.L2.DFOP</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_L2_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, main <span class="op">=</span> <span class="st">"FOCUS L2 - DFOP"</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> -<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## mkin version used for fitting: 1.1.0 </span> -<span class="co">## R version used for fitting: 4.1.2 </span> -<span class="co">## Date of fit: Mon Mar 7 13:16:03 2022 </span> -<span class="co">## Date of summary: Mon Mar 7 13:16:03 2022 </span> +<span class="co">## R version used for fitting: 4.2.0 </span> +<span class="co">## Date of fit: Wed May 18 20:42:34 2022 </span> +<span class="co">## Date of summary: Wed May 18 20:42:34 2022 </span> <span class="co">## </span> <span class="co">## Equations:</span> <span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -442,7 +434,7 @@ <span class="co">## </span> <span class="co">## Model predictions using solution type analytical </span> <span class="co">## </span> -<span class="co">## Fitted using 581 model solutions performed in 0.132 s</span> +<span class="co">## Fitted using 581 model solutions performed in 0.121 s</span> <span class="co">## </span> <span class="co">## Error model: Constant variance </span> <span class="co">## </span> @@ -473,18 +465,18 @@ <span class="co">## Optimised, transformed parameters with symmetric confidence intervals:</span> <span class="co">## Estimate Std. Error Lower Upper</span> <span class="co">## parent_0 93.950 9.998e-01 91.5900 96.3100</span> -<span class="co">## log_k1 3.112 1.842e+03 -4353.0000 4359.0000</span> +<span class="co">## log_k1 3.113 1.845e+03 -4360.0000 4367.0000</span> <span class="co">## log_k2 -1.088 6.285e-02 -1.2370 -0.9394</span> <span class="co">## g_qlogis -0.399 9.946e-02 -0.6342 -0.1638</span> <span class="co">## sigma 1.414 2.886e-01 0.7314 2.0960</span> <span class="co">## </span> <span class="co">## Parameter correlation:</span> <span class="co">## parent_0 log_k1 log_k2 g_qlogis sigma</span> -<span class="co">## parent_0 1.000e+00 6.783e-07 -3.390e-10 2.665e-01 -2.967e-10</span> -<span class="co">## log_k1 6.783e-07 1.000e+00 1.116e-04 -2.196e-04 -1.031e-05</span> -<span class="co">## log_k2 -3.390e-10 1.116e-04 1.000e+00 -7.903e-01 2.917e-09</span> -<span class="co">## g_qlogis 2.665e-01 -2.196e-04 -7.903e-01 1.000e+00 -4.408e-09</span> -<span class="co">## sigma -2.967e-10 -1.031e-05 2.917e-09 -4.408e-09 1.000e+00</span> +<span class="co">## parent_0 1.000e+00 6.784e-07 -5.188e-10 2.665e-01 -5.800e-10</span> +<span class="co">## log_k1 6.784e-07 1.000e+00 1.114e-04 -2.191e-04 -1.029e-05</span> +<span class="co">## log_k2 -5.188e-10 1.114e-04 1.000e+00 -7.903e-01 5.080e-09</span> +<span class="co">## g_qlogis 2.665e-01 -2.191e-04 -7.903e-01 1.000e+00 -7.991e-09</span> +<span class="co">## sigma -5.800e-10 -1.029e-05 5.080e-09 -7.991e-09 1.000e+00</span> <span class="co">## </span> <span class="co">## Backtransformed parameters:</span> <span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span> @@ -492,7 +484,7 @@ <span class="co">## for estimators of untransformed parameters.</span> <span class="co">## Estimate t value Pr(>t) Lower Upper</span> <span class="co">## parent_0 93.9500 9.397e+01 2.036e-12 91.5900 96.3100</span> -<span class="co">## k1 22.4800 5.553e-04 4.998e-01 0.0000 Inf</span> +<span class="co">## k1 22.4800 5.544e-04 4.998e-01 0.0000 Inf</span> <span class="co">## k2 0.3369 1.591e+01 4.697e-07 0.2904 0.3909</span> <span class="co">## g 0.4016 1.680e+01 3.238e-07 0.3466 0.4591</span> <span class="co">## sigma 1.4140 4.899e+00 8.776e-04 0.7314 2.0960</span> @@ -504,15 +496,15 @@ <span class="co">## </span> <span class="co">## Estimated disappearance times:</span> <span class="co">## DT50 DT90 DT50back DT50_k1 DT50_k2</span> -<span class="co">## parent 0.5335 5.311 1.599 0.03084 2.058</span></code></pre> -<p>Here, the DFOP model is clearly the best-fit model for dataset L2 based on the chi^2 error level criterion. However, the failure to calculate the covariance matrix indicates that the parameter estimates correlate excessively. Therefore, the FOMC model may be preferred for this dataset.</p> +<span class="co">## parent 0.5335 5.311 1.599 0.03083 2.058</span></code></pre> +<p>Here, the DFOP model is clearly the best-fit model for dataset L2 based on the chi^2 error level criterion.</p> </div> </div> <div class="section level2"> <h2 id="laboratory-data-l3">Laboratory Data L3<a class="anchor" aria-label="anchor" href="#laboratory-data-l3"></a> </h2> <p>The following code defines example dataset L3 from the FOCUS kinetics report, p. 290.</p> -<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">FOCUS_2006_L3</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span> t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">30</span>, <span class="fl">60</span>, <span class="fl">91</span>, <span class="fl">120</span><span class="op">)</span>, parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">97.8</span>, <span class="fl">60</span>, <span class="fl">51</span>, <span class="fl">43</span>, <span class="fl">35</span>, <span class="fl">22</span>, <span class="fl">15</span>, <span class="fl">12</span><span class="op">)</span><span class="op">)</span> @@ -521,7 +513,7 @@ <h3 id="fit-multiple-models">Fit multiple models<a class="anchor" aria-label="anchor" href="#fit-multiple-models"></a> </h3> <p>As of mkin version 0.9-39 (June 2015), we can fit several models to one or more datasets in one call to the function <code>mmkin</code>. The datasets have to be passed in a list, in this case a named list holding only the L3 dataset prepared above.</p> -<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="co"># Only use one core here, not to offend the CRAN checks</span> <span class="va">mm.L3</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">1</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS L3"</span> <span class="op">=</span> <span class="va">FOCUS_2006_L3_mkin</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> @@ -534,12 +526,12 @@ </h3> <p>The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.</p> <p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p> -<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## mkin version used for fitting: 1.1.0 </span> -<span class="co">## R version used for fitting: 4.1.2 </span> -<span class="co">## Date of fit: Mon Mar 7 13:16:04 2022 </span> -<span class="co">## Date of summary: Mon Mar 7 13:16:04 2022 </span> +<span class="co">## R version used for fitting: 4.2.0 </span> +<span class="co">## Date of fit: Wed May 18 20:42:34 2022 </span> +<span class="co">## Date of summary: Wed May 18 20:42:35 2022 </span> <span class="co">## </span> <span class="co">## Equations:</span> <span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -548,7 +540,7 @@ <span class="co">## </span> <span class="co">## Model predictions using solution type analytical </span> <span class="co">## </span> -<span class="co">## Fitted using 376 model solutions performed in 0.08 s</span> +<span class="co">## Fitted using 376 model solutions performed in 0.073 s</span> <span class="co">## </span> <span class="co">## Error model: Constant variance </span> <span class="co">## </span> @@ -586,11 +578,11 @@ <span class="co">## </span> <span class="co">## Parameter correlation:</span> <span class="co">## parent_0 log_k1 log_k2 g_qlogis sigma</span> -<span class="co">## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 -9.664e-08</span> -<span class="co">## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 7.147e-07</span> -<span class="co">## log_k2 2.282e-02 4.945e-01 1.000e+00 -6.812e-01 1.022e-06</span> -<span class="co">## g_qlogis 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -7.926e-07</span> -<span class="co">## sigma -9.664e-08 7.147e-07 1.022e-06 -7.926e-07 1.000e+00</span> +<span class="co">## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 -9.632e-08</span> +<span class="co">## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 7.145e-07</span> +<span class="co">## log_k2 2.282e-02 4.945e-01 1.000e+00 -6.812e-01 1.021e-06</span> +<span class="co">## g_qlogis 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -7.925e-07</span> +<span class="co">## sigma -9.632e-08 7.145e-07 1.021e-06 -7.925e-07 1.000e+00</span> <span class="co">## </span> <span class="co">## Backtransformed parameters:</span> <span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span> @@ -622,7 +614,7 @@ <span class="co">## 60 parent 22.0 23.26 -1.25919</span> <span class="co">## 91 parent 15.0 15.18 -0.18181</span> <span class="co">## 120 parent 12.0 10.19 1.81395</span></code></pre> -<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-13-1.png" width="700"></p> <p>Here, a look to the model plot, the confidence intervals of the parameters and the correlation matrix suggest that the parameter estimates are reliable, and the DFOP model can be used as the best-fit model based on the <span class="math inline">\(\chi^2\)</span> error level criterion for laboratory data L3.</p> @@ -633,13 +625,13 @@ <h2 id="laboratory-data-l4">Laboratory Data L4<a class="anchor" aria-label="anchor" href="#laboratory-data-l4"></a> </h2> <p>The following code defines example dataset L4 from the FOCUS kinetics report, p. 293:</p> -<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">FOCUS_2006_L4</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span> t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">30</span>, <span class="fl">60</span>, <span class="fl">91</span>, <span class="fl">120</span><span class="op">)</span>, parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">96.6</span>, <span class="fl">96.3</span>, <span class="fl">94.3</span>, <span class="fl">88.8</span>, <span class="fl">74.9</span>, <span class="fl">59.9</span>, <span class="fl">53.5</span>, <span class="fl">49.0</span><span class="op">)</span><span class="op">)</span> <span class="va">FOCUS_2006_L4_mkin</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">FOCUS_2006_L4</span><span class="op">)</span></code></pre></div> <p>Fits of the SFO and FOMC models, plots and summaries are produced below:</p> -<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="co"># Only use one core here, not to offend the CRAN checks</span> <span class="va">mm.L4</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">1</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS L4"</span> <span class="op">=</span> <span class="va">FOCUS_2006_L4_mkin</span><span class="op">)</span>, @@ -647,19 +639,19 @@ <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="700"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p> -<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## mkin version used for fitting: 1.1.0 </span> -<span class="co">## R version used for fitting: 4.1.2 </span> -<span class="co">## Date of fit: Mon Mar 7 13:16:04 2022 </span> -<span class="co">## Date of summary: Mon Mar 7 13:16:05 2022 </span> +<span class="co">## R version used for fitting: 4.2.0 </span> +<span class="co">## Date of fit: Wed May 18 20:42:35 2022 </span> +<span class="co">## Date of summary: Wed May 18 20:42:35 2022 </span> <span class="co">## </span> <span class="co">## Equations:</span> <span class="co">## d_parent/dt = - k_parent * parent</span> <span class="co">## </span> <span class="co">## Model predictions using solution type analytical </span> <span class="co">## </span> -<span class="co">## Fitted using 142 model solutions performed in 0.029 s</span> +<span class="co">## Fitted using 142 model solutions performed in 0.027 s</span> <span class="co">## </span> <span class="co">## Error model: Constant variance </span> <span class="co">## </span> @@ -691,9 +683,9 @@ <span class="co">## </span> <span class="co">## Parameter correlation:</span> <span class="co">## parent_0 log_k_parent sigma</span> -<span class="co">## parent_0 1.000e+00 5.938e-01 3.387e-07</span> -<span class="co">## log_k_parent 5.938e-01 1.000e+00 5.830e-07</span> -<span class="co">## sigma 3.387e-07 5.830e-07 1.000e+00</span> +<span class="co">## parent_0 1.000e+00 5.938e-01 3.440e-07</span> +<span class="co">## log_k_parent 5.938e-01 1.000e+00 5.885e-07</span> +<span class="co">## sigma 3.440e-07 5.885e-07 1.000e+00</span> <span class="co">## </span> <span class="co">## Backtransformed parameters:</span> <span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span> @@ -712,19 +704,19 @@ <span class="co">## Estimated disappearance times:</span> <span class="co">## DT50 DT90</span> <span class="co">## parent 106 352</span></code></pre> -<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## mkin version used for fitting: 1.1.0 </span> -<span class="co">## R version used for fitting: 4.1.2 </span> -<span class="co">## Date of fit: Mon Mar 7 13:16:04 2022 </span> -<span class="co">## Date of summary: Mon Mar 7 13:16:05 2022 </span> +<span class="co">## R version used for fitting: 4.2.0 </span> +<span class="co">## Date of fit: Wed May 18 20:42:35 2022 </span> +<span class="co">## Date of summary: Wed May 18 20:42:35 2022 </span> <span class="co">## </span> <span class="co">## Equations:</span> <span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> <span class="co">## </span> <span class="co">## Model predictions using solution type analytical </span> <span class="co">## </span> -<span class="co">## Fitted using 224 model solutions performed in 0.045 s</span> +<span class="co">## Fitted using 224 model solutions performed in 0.041 s</span> <span class="co">## </span> <span class="co">## Error model: Constant variance </span> <span class="co">## </span> @@ -759,10 +751,10 @@ <span class="co">## </span> <span class="co">## Parameter correlation:</span> <span class="co">## parent_0 log_alpha log_beta sigma</span> -<span class="co">## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.468e-07</span> -<span class="co">## log_alpha -4.696e-01 1.000e+00 9.889e-01 2.478e-08</span> -<span class="co">## log_beta -5.543e-01 9.889e-01 1.000e+00 5.211e-08</span> -<span class="co">## sigma -2.468e-07 2.478e-08 5.211e-08 1.000e+00</span> +<span class="co">## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.563e-07</span> +<span class="co">## log_alpha -4.696e-01 1.000e+00 9.889e-01 4.066e-08</span> +<span class="co">## log_beta -5.543e-01 9.889e-01 1.000e+00 6.818e-08</span> +<span class="co">## sigma -2.563e-07 4.066e-08 6.818e-08 1.000e+00</span> <span class="co">## </span> <span class="co">## Backtransformed parameters:</span> <span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span> @@ -811,7 +803,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer> diff --git a/docs/articles/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 b6130527..b56e91e1 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 f340896b..89eb092b 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -112,7 +112,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 60d2ef1c..a32f4b41 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -105,7 +105,7 @@ <h1 data-toc-skip>Introduction to mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 15 February 2021 (rebuilt 2022-03-07)</h4> + <h4 data-toc-skip class="date">Last change 15 February 2021 (rebuilt 2022-05-18)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/mkin.rmd" class="external-link"><code>vignettes/mkin.rmd</code></a></small> <div class="hidden name"><code>mkin.rmd</code></div> @@ -264,7 +264,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer> diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png Binary files differindex 63246387..d1e7048d 100644 --- a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png +++ b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png diff --git a/docs/articles/twa.html b/docs/articles/twa.html index d45b0ff4..dad8ee44 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -105,7 +105,7 @@ <h1 data-toc-skip>Calculation of time weighted average concentrations with mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 18 September 2019 (rebuilt 2022-03-07)</h4> + <h4 data-toc-skip class="date">Last change 18 September 2019 (rebuilt 2022-05-18)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/twa.rmd" class="external-link"><code>vignettes/twa.rmd</code></a></small> <div class="hidden name"><code>twa.rmd</code></div> @@ -168,7 +168,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer> diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 43508280..0dafb98a 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -105,7 +105,7 @@ <h1 data-toc-skip>Example evaluation of FOCUS dataset Z</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 16 January 2018 (rebuilt 2022-03-07)</h4> + <h4 data-toc-skip class="date">Last change 16 January 2018 (rebuilt 2022-05-18)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/FOCUS_Z.rmd" class="external-link"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small> <div class="hidden name"><code>FOCUS_Z.rmd</code></div> @@ -234,33 +234,31 @@ quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, :</span> <span class="co">## Observations with value of zero were removed from the data</span></code></pre> -<pre><code><span class="co">## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation did not converge:</span> -<span class="co">## false convergence (8)</span></code></pre> -<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p> -<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div> <pre><code><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span> -<span class="co">## Z0_0 96.838822 1.994274 48.5584 4.0280e-42 92.826981 100.850664</span> -<span class="co">## k_Z0 2.215393 0.118458 18.7019 1.0413e-23 1.989456 2.466989</span> -<span class="co">## k_Z1 0.478305 0.028258 16.9266 6.2418e-22 0.424708 0.538666</span> -<span class="co">## k_Z2 0.451627 0.042139 10.7176 1.6314e-14 0.374339 0.544872</span> -<span class="co">## k_Z3 0.058692 0.015245 3.8499 1.7803e-04 0.034808 0.098965</span> -<span class="co">## f_Z2_to_Z3 0.471502 0.058351 8.0805 9.6608e-11 0.357769 0.588274</span> +<span class="co">## Z0_0 96.838397 1.994270 48.5583 4.0284e-42 92.826435 100.850359</span> +<span class="co">## k_Z0 2.215406 0.118459 18.7018 1.0416e-23 1.989466 2.467005</span> +<span class="co">## k_Z1 0.478300 0.028257 16.9267 6.2409e-22 0.424702 0.538662</span> +<span class="co">## k_Z2 0.451616 0.042137 10.7178 1.6305e-14 0.374328 0.544863</span> +<span class="co">## k_Z3 0.058693 0.015245 3.8499 1.7803e-04 0.034805 0.098976</span> +<span class="co">## f_Z2_to_Z3 0.471509 0.058352 8.0804 9.6622e-11 0.357739 0.588317</span> <span class="co">## sigma 3.984431 0.383402 10.3923 4.5575e-14 3.213126 4.755736</span></code></pre> -<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## $ff</span> <span class="co">## Z2_Z3 Z2_sink </span> -<span class="co">## 0.4715 0.5285 </span> +<span class="co">## 0.47151 0.52849 </span> <span class="co">## </span> <span class="co">## $distimes</span> <span class="co">## DT50 DT90</span> <span class="co">## Z0 0.31288 1.0394</span> -<span class="co">## Z1 1.44917 4.8141</span> -<span class="co">## Z2 1.53478 5.0984</span> -<span class="co">## Z3 11.80986 39.2315</span></code></pre> +<span class="co">## Z1 1.44919 4.8141</span> +<span class="co">## Z2 1.53481 5.0985</span> +<span class="co">## Z3 11.80971 39.2310</span></code></pre> <p>This fit corresponds to the final result chosen in Appendix 7 of the FOCUS report. Confidence intervals returned by mkin are based on internally transformed parameters, however.</p> </div> <div class="section level2"> @@ -268,32 +266,34 @@ </h2> <p>As the FOCUS report states, there is a certain tailing of the time course of metabolite Z3. Also, the time course of the parent compound is not fitted very well using the SFO model, as residues at a certain low level remain.</p> <p>Therefore, an additional model is offered here, using the single first-order reversible binding (SFORB) model for metabolite Z3. As expected, the <span class="math inline">\(\chi^2\)</span> error level is lower for metabolite Z3 using this model and the graphical fit for Z3 is improved. However, the covariance matrix is not returned.</p> -<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">Z.mkin.1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>, Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> -<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">m.Z.mkin.1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.1</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span> <span class="co">## value of zero were removed from the data</span></code></pre> -<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p> -<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">cov.unscaled</span></code></pre></div> <pre><code><span class="co">## NULL</span></code></pre> <p>Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.</p> -<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">Z.mkin.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> -<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">m.Z.mkin.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span> <span class="co">## value of zero were removed from the data</span></code></pre> +<pre><code><span class="co">## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Optimisation did not converge:</span> +<span class="co">## false convergence (8)</span></code></pre> <div class="sourceCode" id="cb49"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.3</span><span class="op">)</span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png" width="700"></p> @@ -359,11 +359,11 @@ <span class="co">## </span> <span class="co">## $SFORB</span> <span class="co">## Z0_b1 Z0_b2 Z3_b1 Z3_b2 </span> -<span class="co">## 2.4471322 0.0075125 0.0800069 0.0000000 </span> +<span class="co">## 2.4471376 0.0075126 0.0800073 0.0000000 </span> <span class="co">## </span> <span class="co">## $distimes</span> <span class="co">## DT50 DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2</span> -<span class="co">## Z0 0.3043 1.1848 0.35666 0.28325 92.266 NA NA</span> +<span class="co">## Z0 0.3043 1.1848 0.35666 0.28325 92.264 NA NA</span> <span class="co">## Z1 1.5148 5.0320 NA NA NA NA NA</span> <span class="co">## Z2 1.6414 5.4526 NA NA NA NA NA</span> <span class="co">## Z3 NA NA NA NA NA 8.6636 Inf</span></code></pre> @@ -398,7 +398,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer> diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png Binary files differindex bc6efaf7..229bae82 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png Binary files differindex 55c1b645..e13ad9aa 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png 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a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -43,7 +43,7 @@ <a href="../../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -105,7 +105,7 @@ <h1 data-toc-skip>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">26 February 2019 (rebuilt 2022-03-02)</h4> + <h4 data-toc-skip class="date">26 February 2019 (rebuilt 2022-05-18)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/NAFTA_examples.rmd" class="external-link"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small> <div class="hidden name"><code>NAFTA_examples.rmd</code></div> @@ -161,7 +161,7 @@ <span class="co">## Estimate Pr(>t) Lower Upper</span> <span class="co">## parent_0 9.99e+01 1.41e-26 98.8116 101.0810</span> <span class="co">## k1 2.67e-02 5.05e-06 0.0243 0.0295</span> -<span class="co">## k2 2.26e-12 5.00e-01 0.0000 Inf</span> +<span class="co">## k2 2.95e-12 5.00e-01 0.0000 Inf</span> <span class="co">## g 6.47e-01 3.67e-06 0.6248 0.6677</span> <span class="co">## sigma 1.27e+00 8.91e-06 0.8395 1.6929</span> <span class="co">## </span> @@ -170,7 +170,7 @@ <span class="co">## DT50 DT90 DT50_rep</span> <span class="co">## SFO 67.7 2.25e+02 6.77e+01</span> <span class="co">## IORE 58.2 1.07e+03 3.22e+02</span> -<span class="co">## DFOP 55.5 5.59e+11 3.07e+11</span> +<span class="co">## DFOP 55.5 4.28e+11 2.35e+11</span> <span class="co">## </span> <span class="co">## Representative half-life:</span> <span class="co">## [1] 321.51</span></code></pre> @@ -212,7 +212,7 @@ <span class="co">## Estimate Pr(>t) Lower Upper</span> <span class="co">## parent_0 9.84e+01 1.24e-27 97.8078 98.9187</span> <span class="co">## k1 1.55e-02 4.10e-04 0.0143 0.0167</span> -<span class="co">## k2 8.63e-12 5.00e-01 0.0000 Inf</span> +<span class="co">## k2 9.41e-12 5.00e-01 0.0000 Inf</span> <span class="co">## g 6.89e-01 2.92e-03 0.6626 0.7142</span> <span class="co">## sigma 6.48e-01 2.38e-05 0.4147 0.8813</span> <span class="co">## </span> @@ -221,7 +221,7 @@ <span class="co">## DT50 DT90 DT50_rep</span> <span class="co">## SFO 86.6 2.88e+02 8.66e+01</span> <span class="co">## IORE 85.5 7.17e+02 2.16e+02</span> -<span class="co">## DFOP 83.6 1.32e+11 8.04e+10</span> +<span class="co">## DFOP 83.6 1.21e+11 7.36e+10</span> <span class="co">## </span> <span class="co">## Representative half-life:</span> <span class="co">## [1] 215.87</span></code></pre> @@ -263,7 +263,7 @@ <span class="co">## Estimate Pr(>t) Lower Upper</span> <span class="co">## parent_0 9.66e+01 1.57e-25 95.3476 97.8979</span> <span class="co">## k1 2.55e-02 7.33e-06 0.0233 0.0278</span> -<span class="co">## k2 3.22e-11 5.00e-01 0.0000 Inf</span> +<span class="co">## k2 4.40e-11 5.00e-01 0.0000 Inf</span> <span class="co">## g 8.61e-01 7.55e-06 0.8314 0.8867</span> <span class="co">## sigma 1.46e+00 6.93e-06 0.9661 1.9483</span> <span class="co">## </span> @@ -272,7 +272,7 @@ <span class="co">## DT50 DT90 DT50_rep</span> <span class="co">## SFO 38.6 1.28e+02 3.86e+01</span> <span class="co">## IORE 34.0 1.77e+02 5.32e+01</span> -<span class="co">## DFOP 34.1 1.01e+10 2.15e+10</span> +<span class="co">## DFOP 34.1 7.43e+09 1.58e+10</span> <span class="co">## </span> <span class="co">## Representative half-life:</span> <span class="co">## [1] 53.17</span></code></pre> @@ -314,7 +314,7 @@ <span class="co">## Estimate Pr(>t) Lower Upper</span> <span class="co">## parent_0 9.89e+01 9.44e-49 95.4640 102.2573</span> <span class="co">## k1 1.81e-02 1.75e-01 0.0116 0.0281</span> -<span class="co">## k2 3.63e-10 5.00e-01 0.0000 Inf</span> +<span class="co">## k2 2.81e-10 5.00e-01 0.0000 Inf</span> <span class="co">## g 6.06e-01 2.19e-01 0.4826 0.7178</span> <span class="co">## sigma 7.40e+00 2.97e-15 6.0201 8.7754</span> <span class="co">## </span> @@ -323,7 +323,7 @@ <span class="co">## DT50 DT90 DT50_rep</span> <span class="co">## SFO 94.3 3.13e+02 9.43e+01</span> <span class="co">## IORE 96.7 1.51e+03 4.55e+02</span> -<span class="co">## DFOP 96.4 3.77e+09 1.91e+09</span> +<span class="co">## DFOP 96.4 4.87e+09 2.46e+09</span> <span class="co">## </span> <span class="co">## Representative half-life:</span> <span class="co">## [1] 454.55</span></code></pre> @@ -434,7 +434,7 @@ <span class="co">## DT50 DT90 DT50_rep</span> <span class="co">## SFO 16.9 5.63e+01 1.69e+01</span> <span class="co">## IORE 11.6 3.37e+02 1.01e+02</span> -<span class="co">## DFOP 10.5 1.38e+12 7.69e+11</span> +<span class="co">## DFOP 10.5 1.38e+12 7.68e+11</span> <span class="co">## </span> <span class="co">## Representative half-life:</span> <span class="co">## [1] 101.43</span></code></pre> @@ -445,17 +445,12 @@ </h3> <div class="sourceCode" id="cb37"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p9b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> -<span class="co">## doubtful</span></code></pre> <pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> <pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Sums of squares:</span> <span class="co">## SFO IORE DFOP </span> @@ -482,8 +477,8 @@ <span class="co">## Estimate Pr(>t) Lower Upper</span> <span class="co">## parent_0 94.7123 1.61e-16 93.1355 96.2891</span> <span class="co">## k1 0.0389 1.08e-04 0.0266 0.0569</span> -<span class="co">## k2 0.0389 2.23e-04 0.0255 0.0592</span> -<span class="co">## g 0.5256 NaN NA NA</span> +<span class="co">## k2 0.0389 2.24e-04 0.0255 0.0592</span> +<span class="co">## g 0.5256 5.00e-01 0.0000 1.0000</span> <span class="co">## sigma 1.5957 2.50e-04 0.9135 2.2779</span> <span class="co">## </span> <span class="co">## </span> @@ -500,7 +495,7 @@ <div class="section level3"> <h3 id="example-on-page-10">Example on page 10<a class="anchor" aria-label="anchor" href="#example-on-page-10"></a> </h3> -<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p10</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p10"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> <pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> @@ -508,10 +503,10 @@ <span class="co">## doubtful</span></code></pre> <pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> <pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb53"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb49"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Sums of squares:</span> <span class="co">## SFO IORE DFOP </span> @@ -537,8 +532,8 @@ <span class="co">## $DFOP</span> <span class="co">## Estimate Pr(>t) Lower Upper</span> <span class="co">## parent_0 101.7315 1.41e-09 91.6534 111.8097</span> -<span class="co">## k1 0.0495 6.58e-03 0.0303 0.0809</span> -<span class="co">## k2 0.0495 2.60e-03 0.0410 0.0598</span> +<span class="co">## k1 0.0495 6.32e-03 0.0241 0.1018</span> +<span class="co">## k2 0.0495 2.41e-03 0.0272 0.0901</span> <span class="co">## g 0.4487 5.00e-01 NA NA</span> <span class="co">## sigma 8.0152 2.50e-04 4.5886 11.4418</span> <span class="co">## </span> @@ -560,14 +555,14 @@ <div class="section level3"> <h3 id="example-on-page-11">Example on page 11<a class="anchor" aria-label="anchor" href="#example-on-page-11"></a> </h3> -<div class="sourceCode" id="cb56"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb52"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p11</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p11"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> <pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb55"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> -<div class="sourceCode" id="cb60"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb56"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Sums of squares:</span> <span class="co">## SFO IORE DFOP </span> @@ -594,7 +589,7 @@ <span class="co">## Estimate Pr(>t) Lower Upper</span> <span class="co">## parent_0 1.05e+02 9.47e-13 99.9990 109.1224</span> <span class="co">## k1 4.41e-02 5.95e-03 0.0296 0.0658</span> -<span class="co">## k2 9.94e-13 5.00e-01 0.0000 Inf</span> +<span class="co">## k2 9.93e-13 5.00e-01 0.0000 Inf</span> <span class="co">## g 3.22e-01 1.45e-03 0.2814 0.3650</span> <span class="co">## sigma 3.22e+00 3.52e-04 1.8410 4.5906</span> <span class="co">## </span> @@ -606,7 +601,7 @@ <span class="co">## DFOP 3.07e+11 1.93e+12 6.98e+11</span> <span class="co">## </span> <span class="co">## Representative half-life:</span> -<span class="co">## [1] 41148170</span></code></pre> +<span class="co">## [1] 41148171</span></code></pre> <p>In this case, the DFOP fit reported for PestDF resulted in a negative value for the slower rate constant, which is not possible in mkin. The other results are in agreement.</p> </div> </div> @@ -617,21 +612,19 @@ <div class="section level3"> <h3 id="example-on-page-12-upper-panel">Example on page 12, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-12-upper-panel"></a> </h3> -<div class="sourceCode" id="cb62"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb58"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p12a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span> +<span class="co">## matrix</span> + +<span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span> <span class="co">## matrix</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> -<span class="co">## doubtful</span></code></pre> <pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> <pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb70"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb62"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<div class="sourceCode" id="cb71"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb63"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Sums of squares:</span> <span class="co">## SFO IORE DFOP </span> @@ -655,12 +648,12 @@ <span class="co">## sigma 3.965 NA NA NA</span> <span class="co">## </span> <span class="co">## $DFOP</span> -<span class="co">## Estimate Pr(>t) Lower Upper</span> -<span class="co">## parent_0 100.521 2.74e-10 92.2366 108.805</span> -<span class="co">## k1 0.124 2.53e-05 0.0908 0.170</span> -<span class="co">## k2 0.124 2.52e-02 0.0456 0.339</span> -<span class="co">## g 0.793 NaN NA NA</span> -<span class="co">## sigma 7.048 2.50e-04 4.0349 10.061</span> +<span class="co">## Estimate Pr(>t) Lower Upper</span> +<span class="co">## parent_0 100.521 NA NA NA</span> +<span class="co">## k1 0.124 NA NA NA</span> +<span class="co">## k2 0.124 NA NA NA</span> +<span class="co">## g 0.793 NA NA NA</span> +<span class="co">## sigma 7.048 NA NA NA</span> <span class="co">## </span> <span class="co">## </span> <span class="co">## DTx values:</span> @@ -675,18 +668,17 @@ <div class="section level3"> <h3 id="example-on-page-12-lower-panel">Example on page 12, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-12-lower-panel"></a> </h3> -<div class="sourceCode" id="cb73"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb65"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p12b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Warning in qt(alpha/2, rdf): NaNs produced</span></code></pre> <pre><code><span class="co">## Warning in qt(1 - alpha/2, rdf): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></code></pre> <pre><code><span class="co">## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</span></code></pre> <pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> <pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb80"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb71"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<div class="sourceCode" id="cb81"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb72"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Sums of squares:</span> <span class="co">## SFO IORE DFOP </span> @@ -730,14 +722,18 @@ <div class="section level3"> <h3 id="example-on-page-13">Example on page 13<a class="anchor" aria-label="anchor" href="#example-on-page-13"></a> </h3> -<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb74"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p13</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> +<span class="co">## doubtful</span></code></pre> <pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> <pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb86"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb80"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<div class="sourceCode" id="cb87"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb81"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Sums of squares:</span> <span class="co">## SFO IORE DFOP </span> @@ -763,9 +759,9 @@ <span class="co">## $DFOP</span> <span class="co">## Estimate Pr(>t) Lower Upper</span> <span class="co">## parent_0 92.73500 NA 8.95e+01 95.92118</span> -<span class="co">## k1 0.00258 NA 4.14e-04 0.01611</span> -<span class="co">## k2 0.00258 NA 1.74e-03 0.00383</span> -<span class="co">## g 0.16452 NA 0.00e+00 1.00000</span> +<span class="co">## k1 0.00258 NA 4.24e-04 0.01573</span> +<span class="co">## k2 0.00258 NA 1.76e-03 0.00379</span> +<span class="co">## g 0.16452 NA NA NA</span> <span class="co">## sigma 3.41172 NA 2.02e+00 4.79960</span> <span class="co">## </span> <span class="co">## </span> @@ -782,7 +778,7 @@ <div class="section level2"> <h2 id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf">DT50 not observed in the study and DFOP problems in PestDF<a class="anchor" aria-label="anchor" href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf"></a> </h2> -<div class="sourceCode" id="cb89"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p14</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> <pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> @@ -790,10 +786,10 @@ <span class="co">## doubtful</span></code></pre> <pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> <pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb95"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb89"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb96"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb90"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Sums of squares:</span> <span class="co">## SFO IORE DFOP </span> @@ -820,7 +816,7 @@ <span class="co">## Estimate Pr(>t) Lower Upper</span> <span class="co">## parent_0 1.00e+02 2.96e-28 99.40280 101.2768</span> <span class="co">## k1 9.53e-03 1.20e-01 0.00638 0.0143</span> -<span class="co">## k2 6.08e-12 5.00e-01 0.00000 Inf</span> +<span class="co">## k2 5.03e-12 5.00e-01 0.00000 Inf</span> <span class="co">## g 3.98e-01 2.19e-01 0.30481 0.4998</span> <span class="co">## sigma 1.17e+00 7.68e-06 0.77406 1.5610</span> <span class="co">## </span> @@ -829,7 +825,7 @@ <span class="co">## DT50 DT90 DT50_rep</span> <span class="co">## SFO 2.48e+02 8.25e+02 2.48e+02</span> <span class="co">## IORE 4.34e+02 2.22e+04 6.70e+03</span> -<span class="co">## DFOP 3.05e+10 2.95e+11 1.14e+11</span> +<span class="co">## DFOP 3.69e+10 3.57e+11 1.38e+11</span> <span class="co">## </span> <span class="co">## Representative half-life:</span> <span class="co">## [1] 6697.44</span></code></pre> @@ -838,14 +834,18 @@ <div class="section level2"> <h2 id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero">N is less than 1 and DFOP fraction parameter is below zero<a class="anchor" aria-label="anchor" href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero"></a> </h2> -<div class="sourceCode" id="cb98"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb92"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p15a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> +<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> +<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> +<span class="co">## doubtful</span></code></pre> <pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> <pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb98"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<div class="sourceCode" id="cb102"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb99"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Sums of squares:</span> <span class="co">## SFO IORE DFOP </span> @@ -871,9 +871,9 @@ <span class="co">## $DFOP</span> <span class="co">## Estimate Pr(>t) Lower Upper</span> <span class="co">## parent_0 97.96751 2.85e-13 94.21913 101.7159</span> -<span class="co">## k1 0.00952 6.28e-02 0.00250 0.0363</span> -<span class="co">## k2 0.00952 1.27e-04 0.00646 0.0140</span> -<span class="co">## g 0.21241 5.00e-01 0.00000 1.0000</span> +<span class="co">## k1 0.00952 6.28e-02 0.00260 0.0349</span> +<span class="co">## k2 0.00952 1.27e-04 0.00652 0.0139</span> +<span class="co">## g 0.21241 5.00e-01 NA NA</span> <span class="co">## sigma 4.18778 2.50e-04 2.39747 5.9781</span> <span class="co">## </span> <span class="co">## </span> @@ -885,18 +885,14 @@ <span class="co">## </span> <span class="co">## Representative half-life:</span> <span class="co">## [1] 41.33</span></code></pre> -<div class="sourceCode" id="cb104"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb101"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p15b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></code></pre> -<pre><code><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span> -<span class="co">## doubtful</span></code></pre> <pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> <pre><code><span class="co">## The half-life obtained from the IORE model may be used</span></code></pre> -<div class="sourceCode" id="cb110"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb104"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<div class="sourceCode" id="cb111"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb105"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Sums of squares:</span> <span class="co">## SFO IORE DFOP </span> @@ -916,15 +912,15 @@ <span class="co">## Estimate Pr(>t) Lower Upper</span> <span class="co">## parent_0 99.83 1.81e-16 97.51349 102.14</span> <span class="co">## k__iore_parent 0.38 3.22e-01 0.00352 41.05</span> -<span class="co">## N_parent 0.00 5.00e-01 -1.07696 1.08</span> +<span class="co">## N_parent 0.00 5.00e-01 -1.07695 1.08</span> <span class="co">## sigma 2.21 2.57e-04 1.23245 3.19</span> <span class="co">## </span> <span class="co">## $DFOP</span> <span class="co">## Estimate Pr(>t) Lower Upper</span> <span class="co">## parent_0 1.01e+02 NA 9.82e+01 1.04e+02</span> -<span class="co">## k1 4.86e-03 NA 8.63e-04 2.73e-02</span> +<span class="co">## k1 4.86e-03 NA 8.62e-04 2.74e-02</span> <span class="co">## k2 4.86e-03 NA 3.21e-03 7.35e-03</span> -<span class="co">## g 1.88e-01 NA NA NA</span> +<span class="co">## g 1.88e-01 NA 0.00e+00 1.00e+00</span> <span class="co">## sigma 2.76e+00 NA 1.58e+00 3.94e+00</span> <span class="co">## </span> <span class="co">## </span> @@ -941,16 +937,16 @@ <div class="section level2"> <h2 id="the-dfop-fraction-parameter-is-greater-than-1">The DFOP fraction parameter is greater than 1<a class="anchor" aria-label="anchor" href="#the-dfop-fraction-parameter-is-greater-than-1"></a> </h2> -<div class="sourceCode" id="cb113"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb107"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">p16</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p16"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></code></pre> <pre><code><span class="co">## The representative half-life of the IORE model is longer than the one corresponding</span></code></pre> <pre><code><span class="co">## to the terminal degradation rate found with the DFOP model.</span></code></pre> <pre><code><span class="co">## The representative half-life obtained from the DFOP model may be used</span></code></pre> -<div class="sourceCode" id="cb118"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb112"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> -<div class="sourceCode" id="cb119"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb113"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Sums of squares:</span> <span class="co">## SFO IORE DFOP </span> @@ -1026,7 +1022,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer> diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png Binary files differindex 75611a70..a53c48b2 100644 --- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p10-1.png +++ 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b/docs/articles/web_only/benchmarks.html @@ -43,7 +43,7 @@ <a href="../../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -105,7 +105,7 @@ <h1 data-toc-skip>Benchmark timings for mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 13 May 2020 (rebuilt 2022-03-02)</h4> + <h4 data-toc-skip class="date">Last change 13 May 2020 (rebuilt 2022-05-18)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/benchmarks.rmd" class="external-link"><code>vignettes/web_only/benchmarks.rmd</code></a></small> <div class="hidden name"><code>benchmarks.rmd</code></div> @@ -121,7 +121,7 @@ <p>Parent only:</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">FOCUS_C</span> <span class="op"><-</span> <span class="va">FOCUS_2006_C</span> -<span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span> +<span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span> <span class="va">parent_datasets</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">FOCUS_C</span>, <span class="va">FOCUS_D</span><span class="op">)</span> <span class="va">t1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="fu">mmkin_bench</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span><span class="op">)</span>, <span class="va">parent_datasets</span><span class="op">)</span><span class="op">)</span><span class="op">[[</span><span class="st">"elapsed"</span><span class="op">]</span><span class="op">]</span> @@ -179,74 +179,83 @@ <div class="section level2"> <h2 id="results">Results<a class="anchor" aria-label="anchor" href="#results"></a> </h2> -<p>Currently, we only have benchmark information on one system, therefore only the mkin version is shown with the results below. Timings are in seconds, shorter is better. All results were obtained by serial, i.e. not using multiple computing cores.</p> <p>Benchmarks for all available error models are shown.</p> <div class="section level3"> <h3 id="parent-only">Parent only<a class="anchor" aria-label="anchor" href="#parent-only"></a> </h3> <p>Constant variance (t1) and two-component error model (t2) for four models fitted to two datasets, i.e. eight fits for each test.</p> -<table class="table"> +<table style="width:100%;" class="table"> +<colgroup> +<col width="84%"> +<col width="7%"> +<col width="8%"> +</colgroup> <thead><tr class="header"> -<th align="left">mkin version</th> -<th align="right">t1 [s]</th> -<th align="right">t2 [s]</th> +<th align="left"></th> +<th align="right">t1</th> +<th align="right">t2</th> </tr></thead> <tbody> <tr class="odd"> -<td align="left">0.9.48.1</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1</td> <td align="right">3.610</td> <td align="right">11.019</td> </tr> <tr class="even"> -<td align="left">0.9.49.1</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1</td> <td align="right">8.184</td> <td align="right">22.889</td> </tr> <tr class="odd"> -<td align="left">0.9.49.2</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2</td> <td align="right">7.064</td> <td align="right">12.558</td> </tr> <tr class="even"> -<td align="left">0.9.49.3</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3</td> <td align="right">7.296</td> <td align="right">21.239</td> </tr> <tr class="odd"> -<td align="left">0.9.49.4</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4</td> <td align="right">5.936</td> <td align="right">20.545</td> </tr> <tr class="even"> -<td align="left">0.9.50.2</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2</td> <td align="right">1.714</td> <td align="right">3.971</td> </tr> <tr class="odd"> -<td align="left">0.9.50.3</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.3</td> <td align="right">1.752</td> <td align="right">4.156</td> </tr> <tr class="even"> -<td align="left">0.9.50.4</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.4</td> <td align="right">1.786</td> <td align="right">3.729</td> </tr> <tr class="odd"> -<td align="left">1.0.3</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.0.3</td> <td align="right">1.881</td> <td align="right">3.504</td> </tr> <tr class="even"> -<td align="left">1.0.4</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.0.4</td> <td align="right">1.867</td> <td align="right">3.450</td> </tr> <tr class="odd"> -<td align="left">1.1.0</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.1.0</td> <td align="right">1.938</td> <td align="right">3.517</td> </tr> +<tr class="even"> +<td align="left">Linux, Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz, mkin version 1.1.0</td> +<td align="right">1.621</td> +<td align="right">3.123</td> +</tr> </tbody> </table> </div> @@ -255,79 +264,91 @@ </h3> <p>Constant variance (t3), two-component error model (t4), and variance by variable (t5) for three models fitted to one dataset, i.e. three fits for each test.</p> <table class="table"> +<colgroup> +<col width="78%"> +<col width="6%"> +<col width="7%"> +<col width="6%"> +</colgroup> <thead><tr class="header"> -<th align="left">mkin version</th> -<th align="right">t3 [s]</th> -<th align="right">t4 [s]</th> -<th align="right">t5 [s]</th> +<th align="left"></th> +<th align="right">t3</th> +<th align="right">t4</th> +<th align="right">t5</th> </tr></thead> <tbody> <tr class="odd"> -<td align="left">0.9.48.1</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1</td> <td align="right">3.764</td> <td align="right">14.347</td> <td align="right">9.495</td> </tr> <tr class="even"> -<td align="left">0.9.49.1</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1</td> <td align="right">4.649</td> <td align="right">13.789</td> <td align="right">6.395</td> </tr> <tr class="odd"> -<td align="left">0.9.49.2</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2</td> <td align="right">4.786</td> <td align="right">8.461</td> <td align="right">5.675</td> </tr> <tr class="even"> -<td align="left">0.9.49.3</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3</td> <td align="right">4.510</td> <td align="right">13.805</td> <td align="right">7.386</td> </tr> <tr class="odd"> -<td align="left">0.9.49.4</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4</td> <td align="right">4.446</td> <td align="right">15.335</td> <td align="right">6.002</td> </tr> <tr class="even"> -<td align="left">0.9.50.2</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2</td> <td align="right">1.402</td> <td align="right">6.174</td> <td align="right">2.764</td> </tr> <tr class="odd"> -<td align="left">0.9.50.3</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.3</td> <td align="right">1.430</td> <td align="right">6.615</td> <td align="right">2.878</td> </tr> <tr class="even"> -<td align="left">0.9.50.4</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.4</td> <td align="right">1.397</td> <td align="right">7.251</td> <td align="right">2.810</td> </tr> <tr class="odd"> -<td align="left">1.0.3</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.0.3</td> <td align="right">1.430</td> <td align="right">6.344</td> <td align="right">2.798</td> </tr> <tr class="even"> -<td align="left">1.0.4</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.0.4</td> <td align="right">1.415</td> <td align="right">6.364</td> <td align="right">2.820</td> </tr> <tr class="odd"> -<td align="left">1.1.0</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.1.0</td> <td align="right">1.470</td> <td align="right">6.508</td> <td align="right">2.894</td> </tr> +<tr class="even"> +<td align="left">Linux, Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz, mkin version 1.1.0</td> +<td align="right">3.319</td> +<td align="right">18.209</td> +<td align="right">7.773</td> +</tr> </tbody> </table> </div> @@ -336,18 +357,27 @@ </h3> <p>Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.</p> <table class="table"> +<colgroup> +<col width="64%"> +<col width="5%"> +<col width="5%"> +<col width="5%"> +<col width="6%"> +<col width="5%"> +<col width="6%"> +</colgroup> <thead><tr class="header"> -<th align="left">mkin version</th> -<th align="right">t6 [s]</th> -<th align="right">t7 [s]</th> -<th align="right">t8 [s]</th> -<th align="right">t9 [s]</th> -<th align="right">t10 [s]</th> -<th align="right">t11 [s]</th> +<th align="left"></th> +<th align="right">t6</th> +<th align="right">t7</th> +<th align="right">t8</th> +<th align="right">t9</th> +<th align="right">t10</th> +<th align="right">t11</th> </tr></thead> <tbody> <tr class="odd"> -<td align="left">0.9.48.1</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1</td> <td align="right">2.623</td> <td align="right">4.587</td> <td align="right">7.525</td> @@ -356,7 +386,7 @@ <td align="right">31.267</td> </tr> <tr class="even"> -<td align="left">0.9.49.1</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1</td> <td align="right">2.542</td> <td align="right">4.128</td> <td align="right">4.632</td> @@ -365,7 +395,7 @@ <td align="right">5.636</td> </tr> <tr class="odd"> -<td align="left">0.9.49.2</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2</td> <td align="right">2.723</td> <td align="right">4.478</td> <td align="right">4.862</td> @@ -374,7 +404,7 @@ <td align="right">5.574</td> </tr> <tr class="even"> -<td align="left">0.9.49.3</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3</td> <td align="right">2.643</td> <td align="right">4.374</td> <td align="right">7.020</td> @@ -383,7 +413,7 @@ <td align="right">7.365</td> </tr> <tr class="odd"> -<td align="left">0.9.49.4</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4</td> <td align="right">2.635</td> <td align="right">4.259</td> <td align="right">4.737</td> @@ -392,7 +422,7 @@ <td align="right">5.626</td> </tr> <tr class="even"> -<td align="left">0.9.50.2</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.2</td> <td align="right">0.777</td> <td align="right">1.236</td> <td align="right">1.332</td> @@ -401,7 +431,7 @@ <td align="right">2.987</td> </tr> <tr class="odd"> -<td align="left">0.9.50.3</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.3</td> <td align="right">0.858</td> <td align="right">1.264</td> <td align="right">1.333</td> @@ -410,7 +440,7 @@ <td align="right">3.073</td> </tr> <tr class="even"> -<td align="left">0.9.50.4</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.50.4</td> <td align="right">0.783</td> <td align="right">1.282</td> <td align="right">1.486</td> @@ -419,7 +449,7 @@ <td align="right">3.105</td> </tr> <tr class="odd"> -<td align="left">1.0.3</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.0.3</td> <td align="right">0.763</td> <td align="right">1.244</td> <td align="right">1.457</td> @@ -428,7 +458,7 @@ <td align="right">2.839</td> </tr> <tr class="even"> -<td align="left">1.0.4</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.0.4</td> <td align="right">0.785</td> <td align="right">1.252</td> <td align="right">1.466</td> @@ -437,7 +467,7 @@ <td align="right">2.826</td> </tr> <tr class="odd"> -<td align="left">1.1.0</td> +<td align="left">Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 1.1.0</td> <td align="right">0.810</td> <td align="right">1.264</td> <td align="right">1.503</td> @@ -445,6 +475,15 @@ <td align="right">1.984</td> <td align="right">2.847</td> </tr> +<tr class="even"> +<td align="left">Linux, Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz, mkin version 1.1.0</td> +<td align="right">2.348</td> +<td align="right">3.579</td> +<td align="right">4.254</td> +<td align="right">11.315</td> +<td align="right">5.981</td> +<td align="right">8.368</td> +</tr> </tbody> </table> </div> @@ -468,7 +507,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer> diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 35ea6f27..330c25c6 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -43,7 +43,7 @@ <a href="../../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -105,7 +105,7 @@ <h1 data-toc-skip>Performance benefit by using compiled model definitions in mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">2022-03-02</h4> + <h4 data-toc-skip class="date">2022-05-18</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/compiled_models.rmd" class="external-link"><code>vignettes/web_only/compiled_models.rmd</code></a></small> <div class="hidden name"><code>compiled_models.rmd</code></div> @@ -141,11 +141,11 @@ m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div> <pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></code></pre></div> <p>We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package. In the output of below code, the warnings about zero being removed from the FOCUS D dataset are suppressed. Since mkin version 0.9.49.11, an analytical solution is also implemented, which is included in the tests below.</p> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span> - <span class="va">b.1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span> + <span class="va">b.1</span> <span class="op"><-</span> <span class="fu">benchmark</span><span class="op">(</span> <span class="st">"deSolve, not compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, @@ -162,11 +162,7 @@ <span class="op">}</span> <span class="kw">else</span> <span class="op">{</span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="st">"R package rbenchmark is not available"</span><span class="op">)</span> <span class="op">}</span></code></pre></div> -<pre><code><span class="co">## test replications relative elapsed</span> -<span class="co">## 4 analytical 1 1.000 0.216</span> -<span class="co">## 3 deSolve, compiled 1 1.708 0.369</span> -<span class="co">## 2 Eigenvalue based 1 1.866 0.403</span> -<span class="co">## 1 deSolve, not compiled 1 34.009 7.346</span></code></pre> +<pre><code><span class="co">## [1] "R package rbenchmark is not available"</span></code></pre> <p>We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.</p> </div> <div class="section level2"> @@ -179,7 +175,7 @@ parent <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span> <span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span> - <span class="va">b.2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span> + <span class="va">b.2</span> <span class="op"><-</span> <span class="fu">benchmark</span><span class="op">(</span> <span class="st">"deSolve, not compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, <span class="st">"deSolve, compiled"</span> <span class="op">=</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">FOMC_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, @@ -191,16 +187,14 @@ <span class="va">factor_FOMC_SFO</span> <span class="op"><-</span> <span class="cn">NA</span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="st">"R package benchmark is not available"</span><span class="op">)</span> <span class="op">}</span></code></pre></div> -<pre><code><span class="co">## Temporary DLL for differentials generated and loaded</span></code></pre> -<pre><code><span class="co">## test replications relative elapsed</span> -<span class="co">## 2 deSolve, compiled 1 1.000 0.533</span> -<span class="co">## 1 deSolve, not compiled 1 25.146 13.403</span></code></pre> -<p>Here we get a performance benefit of a factor of 25 using the version of the differential equation model compiled from C code!</p> +<pre><code><span class="co">## Loading required package: rbenchmark</span></code></pre> +<pre><code><span class="co">## [1] "R package benchmark is not available"</span></code></pre> +<p>Here we get a performance benefit of a factor of NA using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 1.1.0 on</p> -<pre><code><span class="co">## R version 4.1.2 (2021-11-01)</span> +<pre><code><span class="co">## R version 4.2.0 (2022-04-22)</span> <span class="co">## Platform: x86_64-pc-linux-gnu (64-bit)</span> <span class="co">## Running under: Debian GNU/Linux 11 (bullseye)</span></code></pre> -<pre><code><span class="co">## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</span></code></pre> +<pre><code><span class="co">## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz</span></code></pre> </div> </div> @@ -221,7 +215,7 @@ <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer> diff --git a/docs/articles/web_only/dimethenamid_2018.html b/docs/articles/web_only/dimethenamid_2018.html index 09aa5150..7650f06f 100644 --- a/docs/articles/web_only/dimethenamid_2018.html +++ b/docs/articles/web_only/dimethenamid_2018.html @@ -105,7 +105,7 @@ <h1 data-toc-skip>Example evaluations of the dimethenamid data from 2018</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 7 March 2022, built on 16 Mar 2022</h4> + <h4 data-toc-skip class="date">Last change 7 March 2022, built on 18 May 2022</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/dimethenamid_2018.rmd" class="external-link"><code>vignettes/web_only/dimethenamid_2018.rmd</code></a></small> <div class="hidden name"><code>dimethenamid_2018.rmd</code></div> @@ -178,7 +178,7 @@ Status of individual fits: dataset model Calke Borstel Flaach BBA 2.2 BBA 2.3 Elliot - DFOP OK OK C OK C OK + DFOP OK OK OK OK C OK OK: No warnings C: Optimisation did not converge: @@ -231,32 +231,41 @@ f_parent_nlme_dfop_tc 3 10 671.91 702.34 -325.96 2 vs 3 134.69 <.0001 <p>The saemix package provided the first Open Source implementation of the Stochastic Approximation to the Expectation Maximisation (SAEM) algorithm. SAEM fits of degradation models can be conveniently performed using an interface to the saemix package available in current development versions of the mkin package.</p> <p>The corresponding SAEM fits of the four combinations of degradation and error models are fitted below. As there is no convergence criterion implemented in the saemix package, the convergence plots need to be manually checked for every fit. We define control settings that work well for all the parent data fits shown in this vignette.</p> <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span> -<span class="va">saemix_control</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">800</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>, +<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></code></pre></div> +<pre><code>Loading required package: npde</code></pre> +<pre><code>Package saemix, version 3.0 + please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</code></pre> +<pre><code> +Attaching package: 'saemix'</code></pre> +<pre><code>The following objects are masked from 'package:npde': + + kurtosis, skewness</code></pre> +<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="va">saemix_control</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">800</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>, print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="va">saemix_control_moreiter</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1600</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>, print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="va">saemix_control_10k</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">10000</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>, print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></code></pre></div> <p>The convergence plot for the SFO model using constant variance is shown below.</p> -<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">f_parent_saemix_sfo_const</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_sfo_const-1.png" width="700"></p> <p>Obviously the selected number of iterations is sufficient to reach convergence. This can also be said for the SFO fit using the two-component error model.</p> -<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">f_parent_saemix_sfo_tc</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_sfo_tc-1.png" width="700"></p> <p>When fitting the DFOP model with constant variance (see below), parameter convergence is not as unambiguous.</p> -<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">f_parent_saemix_dfop_const</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_const</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_dfop_const-1.png" width="700"></p> -<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_const</span><span class="op">)</span></code></pre></div> <pre><code>Kinetic nonlinear mixed-effects model fit by SAEM Structural model: @@ -277,21 +286,23 @@ DMTA_0 97.99583 96.50079 99.4909 k1 0.06377 0.03432 0.0932 k2 0.00848 0.00444 0.0125 g 0.95701 0.91313 1.0009 -a.1 1.82141 1.65974 1.9831 -SD.DMTA_0 1.64787 0.45779 2.8379 +a.1 1.82141 1.60516 2.0377 +SD.DMTA_0 1.64787 0.45729 2.8384 SD.k1 0.57439 0.24731 0.9015 -SD.k2 0.03296 -2.50143 2.5673 -SD.g 1.10266 0.32371 1.8816</code></pre> +SD.k2 0.03296 -2.50524 2.5712 +SD.g 1.10266 0.32354 1.8818</code></pre> <p>While the other parameters converge to credible values, the variance of k2 (<code>omega2.k2</code>) converges to a very small value. The printout of the <code>saem.mmkin</code> model shows that the estimated standard deviation of k2 across the population of soils (<code>SD.k2</code>) is ill-defined, indicating overparameterisation of this model.</p> <p>When the DFOP model is fitted with the two-component error model, we also observe that the estimated variance of k2 becomes very small, while being ill-defined, as illustrated by the excessive confidence interval of <code>SD.k2</code>.</p> -<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">f_parent_saemix_dfop_tc</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span> <span class="va">f_parent_saemix_dfop_tc_moreiter</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, - control <span class="op">=</span> <span class="va">saemix_control_moreiter</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span> -<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></code></pre></div> + control <span class="op">=</span> <span class="va">saemix_control_moreiter</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></code></pre></div> +<pre><code>Likelihood cannot be computed by Importance Sampling.</code></pre> +<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_dfop_tc-1.png" width="700"></p> -<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">)</span></code></pre></div> <pre><code>Kinetic nonlinear mixed-effects model fit by SAEM Structural model: @@ -307,21 +318,21 @@ Likelihood computed by importance sampling 666 664 -323 Fitted parameters: - estimate lower upper -DMTA_0 98.27617 96.3088 100.2436 -k1 0.06437 0.0337 0.0950 -k2 0.00880 0.0063 0.0113 -g 0.95249 0.9100 0.9949 -a.1 1.06161 0.8625 1.2607 -b.1 0.02967 0.0226 0.0367 -SD.DMTA_0 2.06075 0.4187 3.7028 -SD.k1 0.59357 0.2561 0.9310 -SD.k2 0.00292 -10.2960 10.3019 -SD.g 1.05725 0.3808 1.7337</code></pre> + estimate lower upper +DMTA_0 9.82e+01 96.27937 100.1783 +k1 6.41e-02 0.03333 0.0948 +k2 8.56e-03 0.00608 0.0110 +g 9.55e-01 0.91440 0.9947 +a.1 1.07e+00 0.86542 1.2647 +b.1 2.96e-02 0.02258 0.0367 +SD.DMTA_0 2.04e+00 0.40629 3.6678 +SD.k1 5.98e-01 0.25796 0.9373 +SD.k2 5.28e-04 -58.93251 58.9336 +SD.g 1.04e+00 0.36509 1.7083</code></pre> <p>Doubling the number of iterations in the first phase of the algorithm leads to a slightly lower likelihood, and therefore to slightly higher AIC and BIC values. With even more iterations, the algorithm stops with an error message. This is related to the variance of k2 approximating zero and has been submitted as a <a href="https://github.com/saemixdevelopment/saemixextension/issues/29" class="external-link">bug to the saemix package</a>, as the algorithm does not converge in this case.</p> <p>An alternative way to fit DFOP in combination with the two-component error model is to use the model formulation with transformed parameters as used per default in mkin. When using this option, convergence is slower, but eventually the algorithm stops as well with the same error message.</p> <p>The four combinations (SFO/const, SFO/tc, DFOP/const and DFOP/tc) and the version with increased iterations can be compared using the model comparison function of the saemix package:</p> -<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">AIC_parent_saemix</span> <span class="op"><-</span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span> <span class="va">f_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>, @@ -329,7 +340,7 @@ SD.g 1.05725 0.3808 1.7337</code></pre> <span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_parent_saemix_dfop_tc_moreiter</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></code></pre></div> <pre><code>Likelihoods calculated by importance sampling</code></pre> -<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">AIC_parent_saemix</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span> <span class="st">"SFO const"</span>, <span class="st">"SFO tc"</span>, <span class="st">"DFOP const"</span>, <span class="st">"DFOP tc"</span>, <span class="st">"DFOP tc more iterations"</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix</span><span class="op">)</span></code></pre></div> @@ -337,10 +348,10 @@ SD.g 1.05725 0.3808 1.7337</code></pre> SFO const 796.38 795.34 SFO tc 798.38 797.13 DFOP const 705.75 703.88 -DFOP tc 665.65 663.57 -DFOP tc more iterations 665.88 663.80</code></pre> +DFOP tc 665.72 663.63 +DFOP tc more iterations NaN NaN</code></pre> <p>In order to check the influence of the likelihood calculation algorithms implemented in saemix, the likelihood from Gaussian quadrature is added to the best fit, and the AIC values obtained from the three methods are compared.</p> -<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span> <span class="op"><-</span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/llgq.saemix.html" class="external-link">llgq.saemix</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span> <span class="va">AIC_parent_saemix_methods</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span> @@ -350,9 +361,9 @@ DFOP tc more iterations 665.88 663.80</code></pre> <span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix_methods</span><span class="op">)</span></code></pre></div> <pre><code> is gq lin -665.65 665.68 665.11 </code></pre> +665.72 665.88 665.15 </code></pre> <p>The AIC values based on importance sampling and Gaussian quadrature are very similar. Using linearisation is known to be less accurate, but still gives a similar value. In order to illustrate that the comparison of the three method depends on the degree of convergence obtained in the fit, the same comparison is shown below for the fit using the defaults for the number of iterations and the number of MCMC chains.</p> -<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">f_parent_saemix_dfop_tc_defaults</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span> <span class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span> <span class="op"><-</span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/llgq.saemix.html" class="external-link">llgq.saemix</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span><span class="op">)</span> @@ -363,14 +374,14 @@ DFOP tc more iterations 665.88 663.80</code></pre> <span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix_methods_defaults</span><span class="op">)</span></code></pre></div> <pre><code> is gq lin -668.27 718.36 666.49 </code></pre> +668.91 663.61 667.40 </code></pre> </div> </div> <div class="section level3"> <h3 id="comparison">Comparison<a class="anchor" aria-label="anchor" href="#comparison"></a> </h3> <p>The following table gives the AIC values obtained with both backend packages using the same control parameters (800 iterations burn-in, 300 iterations second phase, 15 chains). Note that</p> -<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span class="va">AIC_all</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span> check.names <span class="op">=</span> <span class="cn">FALSE</span>, <span class="st">"Degradation model"</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"SFO"</span>, <span class="st">"DFOP"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, @@ -395,7 +406,7 @@ DFOP tc more iterations 665.88 663.80</code></pre> <td align="left">SFO</td> <td align="left">const</td> <td align="right">796.60</td> -<td align="right">796.60</td> +<td align="right">794.17</td> <td align="right">796.38</td> </tr> <tr class="even"> @@ -409,15 +420,15 @@ DFOP tc more iterations 665.88 663.80</code></pre> <td align="left">DFOP</td> <td align="left">const</td> <td align="right">NA</td> -<td align="right">671.98</td> +<td align="right">704.95</td> <td align="right">705.75</td> </tr> <tr class="even"> <td align="left">DFOP</td> <td align="left">tc</td> <td align="right">671.91</td> -<td align="right">665.11</td> -<td align="right">665.65</td> +<td align="right">665.15</td> +<td align="right">665.72</td> </tr> </tbody> </table> @@ -464,7 +475,7 @@ DFOP tc more iterations 665.88 663.80</code></pre> <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer> diff --git a/docs/articles/web_only/mkin_benchmarks.rda b/docs/articles/web_only/mkin_benchmarks.rda Binary files differnew file mode 100644 index 00000000..e26caf64 --- /dev/null +++ b/docs/articles/web_only/mkin_benchmarks.rda diff --git a/docs/authors.html b/docs/authors.html index 2f901309..70b1ce8a 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -130,7 +130,7 @@ R package version 1.1.0, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/index.html b/docs/index.html index 4491b50f..0204d944 100644 --- a/docs/index.html +++ b/docs/index.html @@ -151,7 +151,7 @@ <li>The usual one-sided t-test for significant difference from zero is nevertheless shown based on estimators for the untransformed parameters.</li> <li>Summary and plotting functions. The <code>summary</code> of an <code>mkinfit</code> object is in fact a full report that should give enough information to be able to approximately reproduce the fit with other tools.</li> <li>The chi-squared error level as defined in the FOCUS kinetics guidance (see below) is calculated for each observed variable.</li> -<li>The ‘variance by variable’ error model which is often fitted using Iteratively Reweighted Least Squares (IRLS) should now be specified as <code>error_model = "obs"</code>.</li> +<li>The ‘variance by variable’ error model which is often fitted using Iteratively Reweighted Least Squares (IRLS) can be specified as <code>error_model = "obs"</code>.</li> </ul> </div> <div class="section level3"> @@ -214,21 +214,12 @@ <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> </h2> <table class="table"> -<tr> -<td> -Ranke J, Wöltjen J, Schmidt J, and Comets E (2021) Taking kinetic evaluations of degradation data to the next level with nonlinear mixed-effects models. <i>Environments</i> <b>8</b> (8) 71 <a href="https://doi.org/10.3390/environments8080071" class="external-link">doi:10.3390/environments8080071</a> -</td> -</tr> -<tr> -<td> -Ranke J, Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data <i>Environments</i> <b>6</b> (12) 124 <a href="https://doi.org/10.3390/environments6120124" class="external-link">doi:10.3390/environments6120124</a> -</td> -</tr> -<tr> -<td> -Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic evaluation of chemical degradation data <i>Environmental Sciences Europe</i> <b>30</b> 17 <a href="https://doi.org/10.1186/s12302-018-0145-1" class="external-link">doi:10.1186/s12302-018-0145-1</a> -</td> -</tr> +<tr><td>Ranke J, Wöltjen J, Schmidt J, and Comets E (2021) Taking kinetic evaluations of degradation data to the next level with nonlinear mixed-effects models. <i>Environments</i> <b>8</b> (8) 71 <a href="https://doi.org/10.3390/environments8080071" class="external-link">doi:10.3390/environments8080071</a> +</td></tr> +<tr><td>Ranke J, Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data <i>Environments</i> <b>6</b> (12) 124 <a href="https://doi.org/10.3390/environments6120124" class="external-link">doi:10.3390/environments6120124</a> +</td></tr> +<tr><td>Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic evaluation of chemical degradation data <i>Environmental Sciences Europe</i> <b>30</b> 17 <a href="https://doi.org/10.1186/s12302-018-0145-1" class="external-link">doi:10.1186/s12302-018-0145-1</a> +</td></tr> </table> </div> <div class="section level2"> @@ -292,7 +283,7 @@ Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic <div class="pkgdown"> <p></p> -<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer> diff --git a/docs/news/index.html b/docs/news/index.html index 4776f207..3c90ccad 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -83,11 +83,14 @@ <div class="section level2"> <h2 class="page-header" data-toc-text="1.1.1" id="mkin-111">mkin 1.1.1<a class="anchor" aria-label="anchor" href="#mkin-111"></a></h2> -<ul><li><p>‘dimethenamid_2018’: Update example code to use saemix</p></li> +<ul><li><p>‘vignettes/FOCUS_L.rmd’: Remove an outdated note referring to a failure to calculate the covariance matrix for DFOP with the L2 dataset. Since 0.9.45.5 the covariance matrix is available</p></li> +<li><p>‘vignettes/web_only/benchmarks.rmd’: Add the first benchmark data using my laptop system, therefore add the CPU when showing the benchmark results.</p></li> +<li><p>‘dimethenamid_2018’: Update example code to use saemix</p></li> <li><p>‘CAKE_export’: Check for validity of the map argument, updates</p></li> <li><p>‘saem()’: Slightly improve speed in the case that no analytical solution for saemix is implemented, activate a test of the respective code</p></li> <li><p>‘mean_degparms’: New argument ‘default_log_parms’ that makes it possible to supply a surrogate value (default) for log parameters that fail the t-test</p></li> <li><p>‘plot.mixed.mmkin’: Pass the frame argument also to residual plots, take the ‘default_log_parms’ argument for ‘mean_degparms’ used for constructing approximate population curves, plot population curve last to avoid that it is covered by data</p></li> +<li><p>‘plot.mkinfit’: Respect argument ‘maxabs’ for residual plots, and make it possible to give ylim as a list, for row layouts</p></li> </ul></div> <div class="section level2"> <h2 class="page-header" data-toc-text="1.1.0" id="mkin-110-2022-03-14">mkin 1.1.0 (2022-03-14)<a class="anchor" aria-label="anchor" href="#mkin-110-2022-03-14"></a></h2> @@ -102,8 +105,7 @@ </div> <div class="section level2"> <h2 class="page-header" data-toc-text="1.0.5" id="mkin-105-2021-09-15">mkin 1.0.5 (2021-09-15)<a class="anchor" aria-label="anchor" href="#mkin-105-2021-09-15"></a></h2> -<ul><li>‘dimethenamid_2018’: Correct the data for the Borstel soil. The five observations from Staudenmaier (2013) that were previously stored as “Borstel 2” are actually just a subset of the 16 observations in “Borstel 1” which is now simply “Borstel”</li> -</ul></div> +<ul><li>‘dimethenamid_2018’: Correct the data for the Borstel soil. The five observations from Staudenmaier (2013) that were previously stored as “Borstel 2” are actually just a subset of the 16 observations in “Borstel 1” which is now simply “Borstel”</li></ul></div> <div class="section level2"> <h2 class="page-header" data-toc-text="1.0.4" id="mkin-104-2021-04-20">mkin 1.0.4 (2021-04-20)<a class="anchor" aria-label="anchor" href="#mkin-104-2021-04-20"></a></h2> <ul><li><p>All plotting functions setting graphical parameters: Use on.exit() for resetting graphical parameters</p></li> @@ -112,12 +114,10 @@ </ul></div> <div class="section level2"> <h2 class="page-header" data-toc-text="1.0.3" id="mkin-103-2021-02-15">mkin 1.0.3 (2021-02-15)<a class="anchor" aria-label="anchor" href="#mkin-103-2021-02-15"></a></h2> -<ul><li>Review and update README, the ‘Introduction to mkin’ vignette and some of the help pages</li> -</ul></div> +<ul><li>Review and update README, the ‘Introduction to mkin’ vignette and some of the help pages</li></ul></div> <div class="section level2"> <h2 class="page-header" data-toc-text="1.0.2" id="mkin-102-unreleased">mkin 1.0.2 (Unreleased)<a class="anchor" aria-label="anchor" href="#mkin-102-unreleased"></a></h2> -<ul><li>‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’</li> -</ul></div> +<ul><li>‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’</li></ul></div> <div class="section level2"> <h2 class="page-header" data-toc-text="1.0.1" id="mkin-101-2021-02-10">mkin 1.0.1 (2021-02-10)<a class="anchor" aria-label="anchor" href="#mkin-101-2021-02-10"></a></h2> <ul><li><p>‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults</p></li> @@ -172,8 +172,7 @@ </ul></div> <div class="section level2"> <h2 class="page-header" data-toc-text="0.9.49.11" id="mkin-094911-2020-04-20">mkin 0.9.49.11 (2020-04-20)<a class="anchor" aria-label="anchor" href="#mkin-094911-2020-04-20"></a></h2> -<ul><li>Increase a test tolerance to make it pass on all CRAN check machines</li> -</ul></div> +<ul><li>Increase a test tolerance to make it pass on all CRAN check machines</li></ul></div> <div class="section level2"> <h2 class="page-header" data-toc-text="0.9.49.10" id="mkin-094910-2020-04-18">mkin 0.9.49.10 (2020-04-18)<a class="anchor" aria-label="anchor" href="#mkin-094910-2020-04-18"></a></h2> <ul><li><p>‘nlme.mmkin’: An nlme method for mmkin row objects and an associated S3 class with print, plot, anova and endpoint methods</p></li> @@ -288,8 +287,7 @@ </ul></div> <div class="section level2"> <h2 class="page-header" data-toc-text="0.9.46" id="mkin-0946-2017-07-24">mkin 0.9.46 (2017-07-24)<a class="anchor" aria-label="anchor" href="#mkin-0946-2017-07-24"></a></h2> -<ul><li>Remove <code>test_FOMC_ill-defined.R</code> as it is too platform dependent</li> -</ul></div> +<ul><li>Remove <code>test_FOMC_ill-defined.R</code> as it is too platform dependent</li></ul></div> <div class="section level2"> <h2 class="page-header" data-toc-text="0.9.45.2" id="mkin-09452-2017-07-24">mkin 0.9.45.2 (2017-07-24)<a class="anchor" aria-label="anchor" href="#mkin-09452-2017-07-24"></a></h2> <ul><li><p>Rename <code>twa</code> to <code>max_twa_parent</code> to avoid conflict with <code>twa</code> from my <code>pfm</code> package</p></li> @@ -301,8 +299,7 @@ <h2 class="page-header" data-toc-text="0.9.45.1" id="mkin-09451-2016-12-20">mkin 0.9.45.1 (2016-12-20)<a class="anchor" aria-label="anchor" href="#mkin-09451-2016-12-20"></a></h2> <div class="section level3"> <h3 id="new-features-0-9-45-1">New features<a class="anchor" aria-label="anchor" href="#new-features-0-9-45-1"></a></h3> -<ul><li>A <code>twa</code> function, calculating maximum time weighted average concentrations for the parent (SFO, FOMC and DFOP).</li> -</ul></div> +<ul><li>A <code>twa</code> function, calculating maximum time weighted average concentrations for the parent (SFO, FOMC and DFOP).</li></ul></div> </div> <div class="section level2"> <h2 class="page-header" data-toc-text="0.9.45" id="mkin-0945-2016-12-08">mkin 0.9.45 (2016-12-08)<a class="anchor" aria-label="anchor" href="#mkin-0945-2016-12-08"></a></h2> @@ -317,8 +314,7 @@ <h2 class="page-header" data-toc-text="0.9.44" id="mkin-0944-2016-06-29">mkin 0.9.44 (2016-06-29)<a class="anchor" aria-label="anchor" href="#mkin-0944-2016-06-29"></a></h2> <div class="section level3"> <h3 id="bug-fixes-0-9-44">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-44"></a></h3> -<ul><li>The test <code>test_FOMC_ill-defined</code> failed on several architectures, so the test is now skipped</li> -</ul></div> +<ul><li>The test <code>test_FOMC_ill-defined</code> failed on several architectures, so the test is now skipped</li></ul></div> </div> <div class="section level2"> <h2 class="page-header" data-toc-text="0.9.43" id="mkin-0943-2016-06-28">mkin 0.9.43 (2016-06-28)<a class="anchor" aria-label="anchor" href="#mkin-0943-2016-06-28"></a></h2> @@ -352,8 +348,7 @@ <h2 class="page-header" data-toc-text="0.9.42" id="mkin-0942-2016-03-25">mkin 0.9.42 (2016-03-25)<a class="anchor" aria-label="anchor" href="#mkin-0942-2016-03-25"></a></h2> <div class="section level3"> <h3 id="major-changes-0-9-42">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-42"></a></h3> -<ul><li>Add the argument <code>from_max_mean</code> to <code>mkinfit</code>, for fitting only the decline from the maximum observed value for models with a single observed variable</li> -</ul></div> +<ul><li>Add the argument <code>from_max_mean</code> to <code>mkinfit</code>, for fitting only the decline from the maximum observed value for models with a single observed variable</li></ul></div> <div class="section level3"> <h3 id="minor-changes-0-9-42">Minor changes<a class="anchor" aria-label="anchor" href="#minor-changes-0-9-42"></a></h3> <ul><li><p>Add plots to <code>compiled_models</code> vignette</p></li> @@ -373,21 +368,18 @@ <div class="section level3"> <h3 id="bug-fixes-0-9-41">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-41"></a></h3> <ul><li> -<code><a href="../reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Avoid an error that occurred when printing summaries generated with mkin versions before 0.9-36</li> -</ul></div> +<code><a href="../reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Avoid an error that occurred when printing summaries generated with mkin versions before 0.9-36</li></ul></div> </div> <div class="section level2"> <h2 class="page-header" data-toc-text="0.9-40" id="mkin-09-40-2015-07-21">mkin 0.9-40 (2015-07-21)<a class="anchor" aria-label="anchor" href="#mkin-09-40-2015-07-21"></a></h2> <div class="section level3"> <h3 id="bug-fixes-0-9-40">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-40"></a></h3> <ul><li> -<code><a href="../reference/endpoints.html">endpoints()</a></code>: For DFOP and SFORB models, where <code><a href="https://rdrr.io/r/stats/optimize.html" class="external-link">optimize()</a></code> is used, make use of the fact that the DT50 must be between DT50_k1 and DT50_k2 (DFOP) or DT50_b1 and DT50_b2 (SFORB), as <code><a href="https://rdrr.io/r/stats/optimize.html" class="external-link">optimize()</a></code> sometimes did not find the minimum. Likewise for finding DT90 values. Also fit on the log scale to make the function more efficient.</li> -</ul></div> +<code><a href="../reference/endpoints.html">endpoints()</a></code>: For DFOP and SFORB models, where <code><a href="https://rdrr.io/r/stats/optimize.html" class="external-link">optimize()</a></code> is used, make use of the fact that the DT50 must be between DT50_k1 and DT50_k2 (DFOP) or DT50_b1 and DT50_b2 (SFORB), as <code><a href="https://rdrr.io/r/stats/optimize.html" class="external-link">optimize()</a></code> sometimes did not find the minimum. Likewise for finding DT90 values. Also fit on the log scale to make the function more efficient.</li></ul></div> <div class="section level3"> <h3 id="internal-changes-0-9-40">Internal changes<a class="anchor" aria-label="anchor" href="#internal-changes-0-9-40"></a></h3> <ul><li> -<code>DESCRIPTION</code>, <code>NAMESPACE</code>, <code>R/*.R</code>: Import (from) stats, graphics and methods packages, and qualify some function calls for non-base packages installed with R to avoid NOTES made by R CMD check –as-cran with upcoming R versions.</li> -</ul></div> +<code>DESCRIPTION</code>, <code>NAMESPACE</code>, <code>R/*.R</code>: Import (from) stats, graphics and methods packages, and qualify some function calls for non-base packages installed with R to avoid NOTES made by R CMD check –as-cran with upcoming R versions.</li></ul></div> </div> <div class="section level2"> <h2 class="page-header" data-toc-text="0.9-39" id="mkin-09-39-2015-06-26">mkin 0.9-39 (2015-06-26)<a class="anchor" aria-label="anchor" href="#mkin-09-39-2015-06-26"></a></h2> @@ -399,8 +391,7 @@ <div class="section level3"> <h3 id="bug-fixes-0-9-39">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-39"></a></h3> <ul><li> -<code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Fix the x axis scaling for rate constants and formation fractions that got confused by the introduction of the t-values of transformed parameters.</li> -</ul></div> +<code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Fix the x axis scaling for rate constants and formation fractions that got confused by the introduction of the t-values of transformed parameters.</li></ul></div> </div> <div class="section level2"> <h2 class="page-header" data-toc-text="0.9-38" id="mkin-09-38-2015-06-24">mkin 0.9-38 (2015-06-24)<a class="anchor" aria-label="anchor" href="#mkin-09-38-2015-06-24"></a></h2> @@ -412,8 +403,7 @@ <div class="section level3"> <h3 id="bug-fixes-0-9-38">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-38"></a></h3> <ul><li> -<code><a href="../reference/mkinmod.html">mkinmod()</a></code>: When generating the C code for the derivatives, only declare the time variable when it is needed and remove the ‘-W-no-unused-variable’ compiler flag as the C compiler used in the CRAN checks on Solaris does not know it.</li> -</ul></div> +<code><a href="../reference/mkinmod.html">mkinmod()</a></code>: When generating the C code for the derivatives, only declare the time variable when it is needed and remove the ‘-W-no-unused-variable’ compiler flag as the C compiler used in the CRAN checks on Solaris does not know it.</li></ul></div> </div> <div class="section level2"> <h2 class="page-header" data-toc-text="0.9-36" id="mkin-09-36-2015-06-21">mkin 0.9-36 (2015-06-21)<a class="anchor" aria-label="anchor" href="#mkin-09-36-2015-06-21"></a></h2> @@ -426,15 +416,13 @@ </ul></div> <div class="section level3"> <h3 id="minor-changes-0-9-36">Minor changes<a class="anchor" aria-label="anchor" href="#minor-changes-0-9-36"></a></h3> -<ul><li>Added a simple showcase vignette with an evaluation of FOCUS example dataset D</li> -</ul></div> +<ul><li>Added a simple showcase vignette with an evaluation of FOCUS example dataset D</li></ul></div> </div> <div class="section level2"> <h2 class="page-header" data-toc-text="0.9-35" id="mkin-09-35-2015-05-15">mkin 0.9-35 (2015-05-15)<a class="anchor" aria-label="anchor" href="#mkin-09-35-2015-05-15"></a></h2> <div class="section level3"> <h3 id="major-changes-0-9-35">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-35"></a></h3> -<ul><li>Switch from RUnit to testthat for testing</li> -</ul></div> +<ul><li>Switch from RUnit to testthat for testing</li></ul></div> <div class="section level3"> <h3 id="bug-fixes-0-9-35">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-35"></a></h3> <ul><li><p><code><a href="../reference/mkinparplot.html">mkinparplot()</a></code>: Avoid warnings that occurred when not all confidence intervals were available in the summary of the fit</p></li> @@ -516,15 +504,13 @@ <h2 class="page-header" data-toc-text="0.9-31" id="mkin-09-31-2014-07-14">mkin 0.9-31 (2014-07-14)<a class="anchor" aria-label="anchor" href="#mkin-09-31-2014-07-14"></a></h2> <div class="section level3"> <h3 id="bug-fixes-0-9-31">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-31"></a></h3> -<ul><li>The internal renaming of optimised parameters in Version 0.9-30 led to errors in the determination of the degrees of freedom for the chi2 error level calulations in <code><a href="../reference/mkinerrmin.html">mkinerrmin()</a></code> used by the summary function.</li> -</ul></div> +<ul><li>The internal renaming of optimised parameters in Version 0.9-30 led to errors in the determination of the degrees of freedom for the chi2 error level calulations in <code><a href="../reference/mkinerrmin.html">mkinerrmin()</a></code> used by the summary function.</li></ul></div> </div> <div class="section level2"> <h2 class="page-header" data-toc-text="0.9-30" id="mkin-09-30-2014-07-11">mkin 0.9-30 (2014-07-11)<a class="anchor" aria-label="anchor" href="#mkin-09-30-2014-07-11"></a></h2> <div class="section level3"> <h3 id="new-features-0-9-30">New features<a class="anchor" aria-label="anchor" href="#new-features-0-9-30"></a></h3> -<ul><li>It is now possible to use formation fractions in combination with turning off the sink in <code><a href="../reference/mkinmod.html">mkinmod()</a></code>.</li> -</ul></div> +<ul><li>It is now possible to use formation fractions in combination with turning off the sink in <code><a href="../reference/mkinmod.html">mkinmod()</a></code>.</li></ul></div> <div class="section level3"> <h3 id="major-changes-0-9-30">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-30"></a></h3> <ul><li><p>The original and the transformed parameters now have different names (e.g. <code>k_parent</code> and <code>log_k_parent</code>. They also differ in how many they are when we have formation fractions but no pathway to sink.</p></li> @@ -607,7 +593,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index b94f7f0e..e653e88e 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ pandoc: 2.9.2.1 -pkgdown: 2.0.2 +pkgdown: 2.0.3 pkgdown_sha: ~ articles: FOCUS_D: FOCUS_D.html @@ -11,7 +11,7 @@ articles: benchmarks: web_only/benchmarks.html compiled_models: web_only/compiled_models.html dimethenamid_2018: web_only/dimethenamid_2018.html -last_built: 2022-04-09T15:50Z +last_built: 2022-05-18T19:26Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index a049850d..c46824e6 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -123,6 +123,8 @@ dataframe if there are several fits in the column).</p> <span class="r-in"> <span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS A"</span> <span class="op">=</span> <span class="va">FOCUS_2006_A</span>,</span> <span class="r-in"> <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> +<span class="r-wrn co"><span class="r-pr">#></span> false convergence (8)</span> <span class="r-in"> <span class="co"># We get a warning because the FOMC model does not converge for the</span></span> <span class="r-in"> <span class="co"># FOCUS A dataset, as it is well described by SFO</span></span> <span class="r-in"></span> @@ -136,17 +138,17 @@ dataframe if there are several fits in the column).</p> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> df AIC</span> <span class="r-out co"><span class="r-pr">#></span> SFO 3 55.28197</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.28222</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.28198</span> <span class="r-out co"><span class="r-pr">#></span> DFOP 5 59.28197</span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span>, k <span class="op">=</span> <span class="fl">0</span><span class="op">)</span> <span class="co"># If we do not penalize additional parameters, we get nearly the same</span></span> <span class="r-out co"><span class="r-pr">#></span> df AIC</span> <span class="r-out co"><span class="r-pr">#></span> SFO 3 49.28197</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC 4 49.28222</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 49.28198</span> <span class="r-out co"><span class="r-pr">#></span> DFOP 5 49.28197</span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">BIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span> <span class="co"># Comparing the BIC gives a very similar picture</span></span> <span class="r-out co"><span class="r-pr">#></span> df BIC</span> <span class="r-out co"><span class="r-pr">#></span> SFO 3 55.52030</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.59999</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.59975</span> <span class="r-out co"><span class="r-pr">#></span> DFOP 5 59.67918</span> <span class="r-in"></span> <span class="r-in"> <span class="co"># For FOCUS C, the more complex models fit better</span></span> @@ -176,7 +178,7 @@ dataframe if there are several fits in the column).</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index f16a9e6c..4a0b599b 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -161,7 +161,7 @@ compatible with CAKE.</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/D24_2014.html b/docs/reference/D24_2014.html index 1c47c7f7..6e2ec0ba 100644 --- a/docs/reference/D24_2014.html +++ b/docs/reference/D24_2014.html @@ -224,7 +224,7 @@ specific pieces of information in the comments.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 86df2efc..41a7d256 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -154,7 +154,7 @@ Version 1.1, 18 December 2014 </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 7193e0f9..e00391e8 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -155,7 +155,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd> <span class="r-in"> <span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> $par</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_alpha log_beta sigma </span> -<span class="r-out co"><span class="r-pr">#></span> 99.666192 2.549850 5.050586 1.890202 </span> +<span class="r-out co"><span class="r-pr">#></span> 99.666193 2.549849 5.050586 1.890202 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $objective</span> <span class="r-out co"><span class="r-pr">#></span> [1] 28.58291</span> @@ -168,7 +168,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $evaluations</span> <span class="r-out co"><span class="r-pr">#></span> function gradient </span> -<span class="r-out co"><span class="r-pr">#></span> 25 78 </span> +<span class="r-out co"><span class="r-pr">#></span> 25 72 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $message</span> <span class="r-out co"><span class="r-pr">#></span> [1] "both X-convergence and relative convergence (5)"</span> @@ -187,7 +187,7 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 1e0e270e..aeeaf723 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -144,7 +144,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index d507b9c8..7274cadc 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -167,7 +167,7 @@ Technology</em> <b>24</b>, 1032-1038</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index d30c4e8a..03b30958 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -155,7 +155,7 @@ Version 1.1, 18 December 2014 </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index fec06e0a..0116760d 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -144,7 +144,7 @@ for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span><span class="va">fit.fomc</span><span class="op">$</span><span class="va">par</span>, <span class="va">fit.iore</span><span class="op">$</span><span class="va">par</span>, <span class="va">fit.iore.deS</span><span class="op">$</span><span class="va">par</span>, </span> <span class="r-in"> row.names <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"model par"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> fit.fomc.par fit.iore.par fit.iore.deS.par</span> -<span class="r-out co"><span class="r-pr">#></span> model par 1 85.87489063 85.874890 85.874890</span> +<span class="r-out co"><span class="r-pr">#></span> model par 1 85.87489063 85.874890 85.874891</span> <span class="r-out co"><span class="r-pr">#></span> model par 2 0.05192238 -4.826631 -4.826631</span> <span class="r-out co"><span class="r-pr">#></span> model par 3 0.65096665 1.949403 1.949403</span> <span class="r-out co"><span class="r-pr">#></span> model par 4 1.85744396 1.857444 1.857444</span> @@ -170,7 +170,7 @@ for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index ab3ae7b8..06b5bd6f 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -178,7 +178,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png Binary files differindex fa5f3834..ca982688 100644 --- a/docs/reference/Rplot001.png +++ b/docs/reference/Rplot001.png diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png Binary files differindex 3caf465f..de2d61aa 100644 --- a/docs/reference/Rplot002.png +++ b/docs/reference/Rplot002.png diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png Binary files differindex 88ebd2d4..f8bf10bb 100644 --- a/docs/reference/Rplot003.png +++ b/docs/reference/Rplot003.png diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png Binary files differindex 7e87d63d..12d337a4 100644 --- a/docs/reference/Rplot004.png +++ b/docs/reference/Rplot004.png diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png Binary files differindex 76f25647..014bf258 100644 --- a/docs/reference/Rplot005.png +++ b/docs/reference/Rplot005.png diff --git a/docs/reference/Rplot006.png b/docs/reference/Rplot006.png Binary files differindex 48f5bbd8..bc6979e9 100644 --- a/docs/reference/Rplot006.png +++ b/docs/reference/Rplot006.png diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index dfae0f69..3607a5ac 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -147,7 +147,7 @@ Version 1.1, 18 December 2014 </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 40ed1338..9b4c391c 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -161,7 +161,7 @@ Version 1.1, 18 December 2014 </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index de773982..3a129533 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -208,7 +208,7 @@ https://jrwb.de/posters/piacenza_2015.pdf</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/aw.html b/docs/reference/aw.html index 1182ab8c..1694d5f7 100644 --- a/docs/reference/aw.html +++ b/docs/reference/aw.html @@ -151,7 +151,7 @@ Inference: Understanding AIC and BIC in Model Selection. </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 806e94ca..5469f8f8 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -206,7 +206,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span class="va">f_d_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">ci_profile</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"profile"</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 4.361 0.964 3.998 </span> +<span class="r-out co"><span class="r-pr">#></span> 3.409 0.000 3.411 </span> <span class="r-in"><span class="co"># Using more cores does not save much time here, as parent_0 takes up most of the time</span></span> <span class="r-in"><span class="co"># If we additionally exclude parent_0 (the confidence of which is often of</span></span> <span class="r-in"><span class="co"># minor interest), we get a nice performance improvement if we use at least 4 cores</span></span> @@ -214,7 +214,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"k_parent_sink"</span>, <span class="st">"k_parent_m1"</span>, <span class="st">"k_m1_sink"</span>, <span class="st">"sigma"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.473 0.118 0.917 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.317 0.152 0.847 </span> <span class="r-in"><span class="va">ci_profile</span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 96.456003640 1.027703e+02</span> @@ -281,7 +281,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span class="va">ci_quadratic_transformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span> <span class="r-in"><span class="va">ci_quadratic_transformed_ff</span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833578 102.79311649</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833565 102.79311648</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.090823771 0.10725430</span> <span class="r-out co"><span class="r-pr">#></span> k_m1 0.004012219 0.00689755</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.469118824 0.55959615</span> @@ -289,7 +289,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span class="va">ci_quadratic_untransformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> <span class="r-in"><span class="va">ci_quadratic_untransformed_ff</span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833583 1.027931e+02</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833570 1.027931e+02</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.090491913 1.069035e-01</span> <span class="r-out co"><span class="r-pr">#></span> k_m1 0.003835485 6.685823e-03</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.469113477 5.598387e-01</span> @@ -309,17 +309,17 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-out co"><span class="r-pr">#></span> sigma TRUE FALSE</span> <span class="r-in"><span class="va">rel_diffs_transformed_ff</span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408690 0.0002217233</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0009598532 0.0009001864</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0307283041 0.0290588361</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046881769 0.0027780063</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408691 0.0002217232</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0009598534 0.0009001862</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0307283050 0.0290588375</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046881765 0.0027780058</span> <span class="r-out co"><span class="r-pr">#></span> sigma 0.0550252516 0.0327066836</span> <span class="r-in"><span class="va">rel_diffs_untransformed_ff</span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408689 0.0002217232</span> -<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0046102156 0.0023732281</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0146740690 0.0025291820</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046995211 0.0023457712</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408691 0.0002217231</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0046102157 0.0023732283</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0146740682 0.0025291807</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046995207 0.0023457708</span> <span class="r-out co"><span class="r-pr">#></span> sigma 0.0550252516 0.0327066836</span> <span class="r-in"></span> <span class="r-in"><span class="co"># The profiling for the following fit does not finish in a reasonable time,</span></span> @@ -333,19 +333,19 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"> error_model_algorithm <span class="op">=</span> <span class="st">"direct"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_tc_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 94.596039609 106.19954892</span> -<span class="r-out co"><span class="r-pr">#></span> k_M1 0.037605368 0.04490762</span> -<span class="r-out co"><span class="r-pr">#></span> k_M2 0.008568731 0.01087676</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.021462489 0.62023882</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.015165617 0.37975348</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.273897348 0.33388101</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.018614554 0.02250378</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.671943411 0.73583305</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.251283495 0.83992077</span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.040411024 0.07662008</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 94.596210088 106.19935874</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 0.037605436 0.04490756</span> +<span class="r-out co"><span class="r-pr">#></span> k_M2 0.008568746 0.01087674</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.021466645 0.62023879</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.015168549 0.37975352</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.273897574 0.33388069</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.018614555 0.02250379</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.671943815 0.73583258</span> +<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.251283808 0.83992121</span> +<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.040411010 0.07662004</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_tc_2</span>, <span class="st">"parent_0"</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 94.59604 106.1995</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 94.59621 106.1994</span> <span class="r-in"><span class="co"># }</span></span> </code></pre></div> </div> @@ -361,7 +361,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html index 2516edff..36b054fe 100644 --- a/docs/reference/create_deg_func.html +++ b/docs/reference/create_deg_func.html @@ -114,31 +114,21 @@ <span class="r-in"><span class="co"># \dontrun{</span></span> <span class="r-in"><span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span class="r-in"><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span></span> +<span class="r-in"> <span class="fu">benchmark</span><span class="op">(</span></span> <span class="r-in"> analytical <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"analytical"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> <span class="r-in"> deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> <span class="r-in"> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> -<span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.394 1.000 0.393 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.678 1.721 0.677 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> sys.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 0</span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>there is no package called ‘rbenchmark’</span> <span class="r-in"> <span class="va">DFOP_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> <span class="r-in"> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> <span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span></span> +<span class="r-in"> <span class="fu">benchmark</span><span class="op">(</span></span> <span class="r-in"> analytical <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"analytical"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> <span class="r-in"> deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> <span class="r-in"> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span> -<span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.829 1.000 0.829 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 1.559 1.881 1.559 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> sys.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 0</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in benchmark(analytical = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE), deSolve = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE), replications = 2):</span> could not find function "benchmark"</span> <span class="r-in"><span class="co"># }</span></span> </code></pre></div> </div> @@ -154,7 +144,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/dimethenamid_2018-1.png b/docs/reference/dimethenamid_2018-1.png Binary files differindex 4300b0c0..6e5d357d 100644 --- a/docs/reference/dimethenamid_2018-1.png +++ b/docs/reference/dimethenamid_2018-1.png diff --git a/docs/reference/dimethenamid_2018-2.png b/docs/reference/dimethenamid_2018-2.png Binary files differindex 36db063c..cf5f03f7 100644 --- a/docs/reference/dimethenamid_2018-2.png +++ b/docs/reference/dimethenamid_2018-2.png diff --git a/docs/reference/dimethenamid_2018-3.png b/docs/reference/dimethenamid_2018-3.png Binary files differindex efb89bdb..339aaef6 100644 --- a/docs/reference/dimethenamid_2018-3.png +++ b/docs/reference/dimethenamid_2018-3.png diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html index d2ed8647..a3cfc271 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -202,9 +202,9 @@ specific pieces of information in the comments.</p> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_dmta_saem_tc</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.0 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sat Apr 9 18:03:34 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sat Apr 9 18:03:34 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed May 18 20:37:14 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed May 18 20:37:14 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_DMTA/dt = - k_DMTA * DMTA</span> @@ -217,7 +217,7 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 787.836 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 1660.941 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 9 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> @@ -239,65 +239,65 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Optimised parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.5943 84.3961 92.7925</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA -3.0466 -3.5609 -2.5322</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0684 -4.9340 -3.2029</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -3.8628 -4.2627 -3.4628</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -3.9803 -4.4804 -3.4801</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1304 -0.2186 0.4795</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1490 -0.2559 0.5540</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3970 -1.6976 -1.0964</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.3098 84.1383 92.4813</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA -3.0510 -3.5659 -2.5361</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0567 -4.9178 -3.1955</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -3.8592 -4.2571 -3.4614</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -3.9685 -4.4683 -3.4686</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1382 -0.2120 0.4885</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1429 -0.2616 0.5473</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3889 -1.6943 -1.0836</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> DMTA_0 l__DMTA lg__M23 lg__M27 lg__M31 f_DMTA__1 f_DMTA__2</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA 0.0309 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0231 -0.0031 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0381 -0.0048 0.0039 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0251 -0.0031 0.0021 0.0830 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 -0.0046 -0.0006 0.0417 -0.0437 0.0328 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 -0.0008 -0.0002 0.0214 -0.0270 -0.0909 -0.0361 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -0.1832 -0.0135 0.0434 0.0804 0.0395 -0.0070 0.0059 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA 0.0315 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0237 -0.0031 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0392 -0.0048 0.0040 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0257 -0.0032 0.0022 0.0821 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 -0.0048 -0.0007 0.0415 -0.0435 0.0333 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 -0.0007 -0.0002 0.0214 -0.0270 -0.0900 -0.0372 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -0.1861 -0.0136 0.0431 0.0797 0.0382 -0.0072 0.0066 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.3651 -0.9655 7.6956</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6415 0.2774 1.0055</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0176 0.3809 1.6543</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4538 0.1522 0.7554</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5684 0.1905 0.9464</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4111 0.1524 0.6699</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4788 0.1808 0.7768</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3501 0.1316 0.5685</span> +<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.2733 -1.1098 7.6564</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6422 0.2777 1.0066</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0131 0.3797 1.6465</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4511 0.1510 0.7513</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5695 0.1923 0.9466</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4123 0.1526 0.6720</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4780 0.1804 0.7757</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3559 0.1344 0.5775</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.9349 0.8395 1.0302</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.1344 0.1176 0.1512</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.9255 0.8288 1.0221</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1365 0.1191 0.1538</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.59431 84.396147 92.79246</span> -<span class="r-out co"><span class="r-pr">#></span> k_DMTA 0.04752 0.028413 0.07948</span> -<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01710 0.007198 0.04064</span> -<span class="r-out co"><span class="r-pr">#></span> k_M27 0.02101 0.014084 0.03134</span> -<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01868 0.011329 0.03080</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.14498 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.12056 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.11015 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.30980 84.138334 92.48126</span> +<span class="r-out co"><span class="r-pr">#></span> k_DMTA 0.04731 0.028272 0.07918</span> +<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01731 0.007315 0.04095</span> +<span class="r-out co"><span class="r-pr">#></span> k_M27 0.02108 0.014164 0.03139</span> +<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01890 0.011467 0.03116</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.14626 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.12029 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.11135 NA NA</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Resulting formation fractions:</span> <span class="r-out co"><span class="r-pr">#></span> ff</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M23 0.1450</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.1206</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.1101</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.6243</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M23 0.1463</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.1203</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.1113</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.6221</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA 14.59 48.45</span> -<span class="r-out co"><span class="r-pr">#></span> M23 40.52 134.62</span> -<span class="r-out co"><span class="r-pr">#></span> M27 32.99 109.60</span> -<span class="r-out co"><span class="r-pr">#></span> M31 37.11 123.26</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA 14.65 48.67</span> +<span class="r-out co"><span class="r-pr">#></span> M23 40.05 133.05</span> +<span class="r-out co"><span class="r-pr">#></span> M27 32.88 109.21</span> +<span class="r-out co"><span class="r-pr">#></span> M31 36.67 121.81</span> <span class="r-in"><span class="co"># As the confidence interval for the random effects of DMTA_0</span></span> <span class="r-in"><span class="co"># includes zero, we could try an alternative model without</span></span> <span class="r-in"><span class="co"># such random effects</span></span> @@ -321,7 +321,7 @@ specific pieces of information in the comments.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index f764b742..883c9e5d 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -178,7 +178,7 @@ HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/experimental_data_for_UBA-1.png b/docs/reference/experimental_data_for_UBA-1.png Binary files differindex b7b4d63b..50c09278 100644 --- a/docs/reference/experimental_data_for_UBA-1.png +++ b/docs/reference/experimental_data_for_UBA-1.png diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index e87105b6..69a8baf4 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -238,7 +238,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/f_time_norm_focus.html b/docs/reference/f_time_norm_focus.html index eb0e6f73..27da5718 100644 --- a/docs/reference/f_time_norm_focus.html +++ b/docs/reference/f_time_norm_focus.html @@ -194,7 +194,7 @@ Version 1.1, 18 December 2014 </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/focus_soil_moisture.html b/docs/reference/focus_soil_moisture.html index 9189ef76..6b64ba73 100644 --- a/docs/reference/focus_soil_moisture.html +++ b/docs/reference/focus_soil_moisture.html @@ -133,7 +133,7 @@ Version 2.2, May 2014 <a href="https://esdac.jrc.ec.europa.eu/projects/ground-wa </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html index 130e786a..c63a968c 100644 --- a/docs/reference/get_deg_func.html +++ b/docs/reference/get_deg_func.html @@ -108,7 +108,7 @@ nlme.mmkin</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index d0cb6372..58ae56b0 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -170,7 +170,7 @@ Compositional Data Using Robust Methods. Math Geosci 40 233-248</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/index.html b/docs/reference/index.html index 90387a56..4d657918 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -429,7 +429,7 @@ kinetic models fitted with mkinfit</p></td> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/intervals.saem.mmkin.html b/docs/reference/intervals.saem.mmkin.html index ddc565b3..ae621adc 100644 --- a/docs/reference/intervals.saem.mmkin.html +++ b/docs/reference/intervals.saem.mmkin.html @@ -123,7 +123,7 @@ class attribute</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/loftest-3.png b/docs/reference/loftest-3.png Binary files differindex d897c363..a1a65a61 100644 --- a/docs/reference/loftest-3.png +++ b/docs/reference/loftest-3.png diff --git a/docs/reference/loftest-5.png b/docs/reference/loftest-5.png Binary files differindex 0847bbec..c441f2ed 100644 --- a/docs/reference/loftest-5.png +++ b/docs/reference/loftest-5.png diff --git a/docs/reference/loftest.html b/docs/reference/loftest.html index a96e6932..ee9b37e4 100644 --- a/docs/reference/loftest.html +++ b/docs/reference/loftest.html @@ -302,7 +302,7 @@ of replicate samples.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index c41950a3..9c34d890 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -162,7 +162,7 @@ and the fitted error model parameters.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index ed6e29dc..b09d3a69 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -176,20 +176,20 @@ Version 1.1, 18 December 2014 <span class="r-plt img"><img src="logistic.solution-2.png" alt="" width="700" height="433"></span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.057896e+02 1.9023449590 55.610120 3.768360e-16 1.016451e+02</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.057896e+02 1.9023449649 55.610120 3.768361e-16 1.016451e+02</span> <span class="r-out co"><span class="r-pr">#></span> kmax 6.398190e-02 0.0143201029 4.467978 3.841828e-04 3.929235e-02</span> -<span class="r-out co"><span class="r-pr">#></span> k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846688e-08</span> -<span class="r-out co"><span class="r-pr">#></span> r 2.263946e-01 0.1718110662 1.317695 1.061043e-01 4.335843e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846685e-08</span> +<span class="r-out co"><span class="r-pr">#></span> r 2.263946e-01 0.1718110773 1.317695 1.061044e-01 4.335843e-02</span> <span class="r-out co"><span class="r-pr">#></span> sigma 5.332935e+00 0.9145907310 5.830952 4.036926e-05 3.340213e+00</span> <span class="r-out co"><span class="r-pr">#></span> Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 109.9341588</span> <span class="r-out co"><span class="r-pr">#></span> kmax 0.1041853</span> -<span class="r-out co"><span class="r-pr">#></span> k0 0.4448749</span> -<span class="r-out co"><span class="r-pr">#></span> r 1.1821120</span> +<span class="r-out co"><span class="r-pr">#></span> k0 0.4448750</span> +<span class="r-out co"><span class="r-pr">#></span> r 1.1821121</span> <span class="r-out co"><span class="r-pr">#></span> sigma 7.3256566</span> <span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m</span><span class="op">)</span><span class="op">$</span><span class="va">distimes</span></span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50_k0 DT50_kmax</span> -<span class="r-out co"><span class="r-pr">#></span> parent 36.86533 62.41511 4297.853 10.83349</span> +<span class="r-out co"><span class="r-pr">#></span> parent 36.86533 62.41511 4297.854 10.83349</span> <span class="r-in"></span> </code></pre></div> </div> @@ -205,7 +205,7 @@ Version 1.1, 18 December 2014 </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html index 6adc1245..bc8dab67 100644 --- a/docs/reference/lrtest.mkinfit.html +++ b/docs/reference/lrtest.mkinfit.html @@ -191,7 +191,7 @@ lower number of fitted parameters (null hypothesis).</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 29b17d1a..69da881b 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -179,7 +179,7 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 9b698e64..97ac647e 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -117,7 +117,7 @@ <div id="source"> <h2>Source</h2> <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labelled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107 - doi: <a href="https://doi.org/10.1021/jf00103a026" class="external-link">10.1021/jf00103a026</a></p> + <a href="https://doi.org/10.1021/jf00103a026" class="external-link">doi:10.1021/jf00103a026</a></p> </div> <div id="ref-examples"> @@ -128,19 +128,20 @@ <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"> <span class="co"># \dontrun{</span></span> <span class="r-in"> <span class="va">fit.1</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO_SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t)</span> -<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1847074945 47.537272 4.472189e-18</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1847074929 47.537272 4.472189e-18</span> <span class="r-out co"><span class="r-pr">#></span> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13</span> -<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050581e-01 0.2986993563 1.356073 9.756989e-02</span> -<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623177e-07</span> -<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.3985340558 1.562627 6.949413e-02</span> -<span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 1.000000e+00 0.6718439825 1.488441 7.867789e-02</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.4907558883 5.123989 6.233157e-05</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050581e-01 0.2986993439 1.356073 9.756988e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623176e-07</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.3985340365 1.562627 6.949413e-02</span> +<span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 1.000000e+00 0.6718439498 1.488441 7.867788e-02</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.4907558786 5.123989 6.233156e-05</span> <span class="r-out co"><span class="r-pr">#></span> Lower Upper</span> -<span class="r-out co"><span class="r-pr">#></span> T245_0 99.246061385 1.084640e+02</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 99.246061401 1.084640e+02</span> <span class="r-out co"><span class="r-pr">#></span> k_T245 0.039631621 4.746194e-02</span> -<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.218013879 7.525762e-01</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.218013878 7.525762e-01</span> <span class="r-out co"><span class="r-pr">#></span> k_anisole 0.005370739 8.305299e-03</span> <span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 0.547559081 6.924813e-01</span> <span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 0.000000000 1.000000e+00</span> @@ -148,13 +149,13 @@ <span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> T245_phenol T245_sink phenol_anisole phenol_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 </span> +<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.195366e-10 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> <span class="r-out co"><span class="r-pr">#></span> T245 15.982025 53.09114</span> <span class="r-out co"><span class="r-pr">#></span> phenol 1.711229 5.68458</span> -<span class="r-out co"><span class="r-pr">#></span> anisole 103.784093 344.76329</span> +<span class="r-out co"><span class="r-pr">#></span> anisole 103.784092 344.76329</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"> <span class="co"># formation fraction from phenol to anisol is practically 1. As we cannot</span></span> <span class="r-in"> <span class="co"># fix formation fractions when using the ilr transformation, we can turn of</span></span> @@ -165,31 +166,32 @@ <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"> <span class="va">fit.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO_SFO_2</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>,</span> <span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span> <span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower</span> -<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1623653066 48.028439 4.993108e-19 99.271020284</span> -<span class="r-out co"><span class="r-pr">#></span> k_T245 4.337042e-02 0.0018343666 23.643268 3.573556e-14 0.039650976</span> -<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050582e-01 0.1177237473 3.440752 1.679254e-03 0.218746587</span> -<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678742e-03 0.0006829745 9.778903 1.872894e-08 0.005377083</span> -<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.0342197875 18.198824 2.039411e-12 0.547975637</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1623653038 48.028439 4.993108e-19 99.271020197</span> +<span class="r-out co"><span class="r-pr">#></span> k_T245 4.337042e-02 0.0018343667 23.643268 3.573556e-14 0.039650977</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050583e-01 0.1177237899 3.440751 1.679257e-03 0.218746592</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678741e-03 0.0006829745 9.778903 1.872895e-08 0.005377082</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.0342197865 18.198824 2.039410e-12 0.547975622</span> <span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655</span> <span class="r-out co"><span class="r-pr">#></span> Upper</span> -<span class="r-out co"><span class="r-pr">#></span> T245_0 108.43904074</span> -<span class="r-out co"><span class="r-pr">#></span> k_T245 0.04743877</span> -<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.75005585</span> -<span class="r-out co"><span class="r-pr">#></span> k_anisole 0.00829550</span> -<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 0.69212308</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 3.31827222</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 1.084390e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k_T245 4.743877e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 7.500560e-01</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 8.295499e-03</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.921231e-01</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.318272e+00</span> <span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> T245_phenol T245_sink phenol_anisole phenol_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 </span> +<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.195366e-10 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> <span class="r-out co"><span class="r-pr">#></span> T245 15.982025 53.09114</span> <span class="r-out co"><span class="r-pr">#></span> phenol 1.711229 5.68458</span> -<span class="r-out co"><span class="r-pr">#></span> anisole 103.784093 344.76329</span> +<span class="r-out co"><span class="r-pr">#></span> anisole 103.784092 344.76329</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span></span> <span class="r-plt img"><img src="mccall81_245T-1.png" alt="" width="700" height="433"></span> @@ -208,7 +210,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mean_degparms.html b/docs/reference/mean_degparms.html index efe91b6f..bea9f2d8 100644 --- a/docs/reference/mean_degparms.html +++ b/docs/reference/mean_degparms.html @@ -134,7 +134,7 @@ nlme for the case of a single grouping variable ds.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mixed-1.png b/docs/reference/mixed-1.png Binary files differindex 54b81b70..fe7e6c47 100644 --- a/docs/reference/mixed-1.png +++ b/docs/reference/mixed-1.png diff --git a/docs/reference/mixed.html b/docs/reference/mixed.html index af73f22a..dfc7a731 100644 --- a/docs/reference/mixed.html +++ b/docs/reference/mixed.html @@ -177,9 +177,9 @@ single dataframe which is convenient for plotting</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Mean fitted parameters:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 </span> -<span class="r-out co"><span class="r-pr">#></span> 100.674757 -8.761916 -0.004347 -3.348812 -3.986853 </span> +<span class="r-out co"><span class="r-pr">#></span> 100.674757 -8.762456 -0.004347 -3.348812 -3.986853 </span> <span class="r-out co"><span class="r-pr">#></span> g_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> -0.087392 </span> +<span class="r-out co"><span class="r-pr">#></span> -0.087391 </span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_mixed</span><span class="op">)</span></span> <span class="r-plt img"><img src="mixed-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span class="co"># }</span></span> @@ -197,7 +197,7 @@ single dataframe which is convenient for plotting</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index ed0abedd..ba00a80a 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -157,7 +157,7 @@ observed values called "value".</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 37c84761..0cb9ebca 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -139,7 +139,7 @@ column of observed values.</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 73a14840..bef3be93 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -145,9 +145,9 @@ and value in order to be compatible with mkinfit</p></dd> <div class="section"> <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3> -<ul><li><p><a href="#method-new"><code>mkinds$new()</code></a></p></li> -<li><p><a href="#method-clone"><code>mkinds$clone()</code></a></p></li> -</ul></div><p></p><hr><a id="method-new"></a><div class="section"> +<ul><li><p><a href="#method-mkinds-new"><code>mkinds$new()</code></a></p></li> +<li><p><a href="#method-mkinds-clone"><code>mkinds$clone()</code></a></p></li> +</ul></div><p></p><hr><a id="method-mkinds-new"></a><div class="section"> <h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> <p>Create a new mkinds object</p><div class="section"> <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> @@ -175,7 +175,7 @@ and value in order to be compatible with mkinfit</p></dd> </dl><p></p></div> </div> -</div><p></p><hr><a id="method-clone"></a><div class="section"> +</div><p></p><hr><a id="method-mkinds-clone"></a><div class="section"> <h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3> <p>The objects of this class are cloneable with this method.</p><div class="section"> <h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4> @@ -220,7 +220,7 @@ and value in order to be compatible with mkinfit</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html index 7f4ff290..ceee4f37 100644 --- a/docs/reference/mkindsg.html +++ b/docs/reference/mkindsg.html @@ -142,9 +142,9 @@ or covariates like soil pH).</p></dd> <div class="section"> <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3> -<ul><li><p><a href="#method-new"><code>mkindsg$new()</code></a></p></li> -<li><p><a href="#method-clone"><code>mkindsg$clone()</code></a></p></li> -</ul></div><p></p><hr><a id="method-new"></a><div class="section"> +<ul><li><p><a href="#method-mkindsg-new"><code>mkindsg$new()</code></a></p></li> +<li><p><a href="#method-mkindsg-clone"><code>mkindsg$clone()</code></a></p></li> +</ul></div><p></p><hr><a id="method-mkindsg-new"></a><div class="section"> <h3 id="method-new-">Method <code>new()</code><a class="anchor" aria-label="anchor" href="#method-new-"></a></h3> <p>Create a new mkindsg object</p><div class="section"> <h4 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h4> @@ -172,7 +172,7 @@ or covariates like soil pH).</p></dd> </dl><p></p></div> </div> -</div><p></p><hr><a id="method-clone"></a><div class="section"> +</div><p></p><hr><a id="method-mkindsg-clone"></a><div class="section"> <h3 id="method-clone-">Method <code>clone()</code><a class="anchor" aria-label="anchor" href="#method-clone-"></a></h3> <p>The objects of this class are cloneable with this method.</p><div class="section"> <h4 id="usage-1">Usage<a class="anchor" aria-label="anchor" href="#usage-1"></a></h4> @@ -406,7 +406,7 @@ or covariates like soil pH).</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index dc2cdab8..b6051ab8 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -139,6 +139,7 @@ Document Reference Sanco/10058/2005 version 2.0, 434 pp, <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"></span> <span class="r-in"><span class="va">fit_FOCUS_D</span> <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit_FOCUS_D</span><span class="op">)</span>, <span class="fl">4</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span> <span class="r-out co"><span class="r-pr">#></span> All data 0.0640 4 15</span> @@ -167,7 +168,7 @@ Document Reference Sanco/10058/2005 version 2.0, 434 pp, </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinerrplot-1.png b/docs/reference/mkinerrplot-1.png Binary files differindex 49bb1c0e..852da18d 100644 --- a/docs/reference/mkinerrplot-1.png +++ b/docs/reference/mkinerrplot-1.png diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 95206b61..4b78f6eb 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -164,6 +164,7 @@ lines of the mkinfit object.</p></div> <span class="r-in"><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">FOCUS_2006_D</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"><span class="fu">mkinerrplot</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> <span class="r-plt img"><img src="mkinerrplot-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span class="co"># }</span></span> @@ -182,7 +183,7 @@ lines of the mkinfit object.</p></div> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index c006ddab..e5bf1203 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -307,7 +307,7 @@ internal rate transformation.</p> for measurement error in analytical chemistry. <em>Technometrics</em> 37(2), 176-184.</p> <p>Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data. <em>Environments</em> 6(12) 124 -doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link">10.3390/environments6120124</a> +<a href="https://doi.org/10.3390/environments6120124" class="external-link">doi:10.3390/environments6120124</a> .</p> </div> <div id="see-also"> @@ -330,16 +330,16 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:11:56 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:11:56 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed May 18 20:37:57 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed May 18 20:37:57 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.045 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.041 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -374,10 +374,10 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Parameter correlation:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_alpha log_beta sigma</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.772e-08</span> -<span class="r-out co"><span class="r-pr">#></span> log_alpha -1.565e-01 1.000e+00 9.564e-01 1.005e-07</span> -<span class="r-out co"><span class="r-pr">#></span> log_beta -3.142e-01 9.564e-01 1.000e+00 8.541e-08</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 4.772e-08 1.005e-07 8.541e-08 1.000e+00</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.770e-08</span> +<span class="r-out co"><span class="r-pr">#></span> log_alpha -1.565e-01 1.000e+00 9.564e-01 9.974e-08</span> +<span class="r-out co"><span class="r-pr">#></span> log_beta -3.142e-01 9.564e-01 1.000e+00 8.468e-08</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 4.770e-08 9.974e-08 8.468e-08 1.000e+00</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> Confidence intervals for internally transformed parameters are asymmetric.</span> @@ -462,7 +462,7 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> <span class="r-out co"><span class="r-pr">#></span> parent 6.89313 22.89848</span> -<span class="r-out co"><span class="r-pr">#></span> m1 134.15634 445.65772</span> +<span class="r-out co"><span class="r-pr">#></span> m1 134.15634 445.65770</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"></span> <span class="r-in"><span class="co"># We can show a quick (only one replication) benchmark for this case, as we</span></span> @@ -471,7 +471,7 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-in"><span class="co"># benchmark vignette</span></span> <span class="r-in"><span class="co"># \dontrun{</span></span> <span class="r-in"><span class="kw">if</span><span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span>replications <span class="op">=</span> <span class="fl">1</span>, order <span class="op">=</span> <span class="st">"relative"</span>, columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"test"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span>,</span> +<span class="r-in"> <span class="fu">benchmark</span><span class="op">(</span>replications <span class="op">=</span> <span class="fl">1</span>, order <span class="op">=</span> <span class="st">"relative"</span>, columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"test"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span>,</span> <span class="r-in"> deSolve_compiled <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span> <span class="r-in"> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, use_compiled <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> <span class="r-in"> eigen <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span> @@ -479,10 +479,8 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-in"> analytical <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span> <span class="r-in"> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">)</span></span> <span class="r-in"><span class="op">}</span></span> -<span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.573</span> -<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.642 0.941</span> -<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.517 1.442</span> +<span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>there is no package called ‘rbenchmark’</span> <span class="r-in"><span class="co"># }</span></span> <span class="r-in"></span> <span class="r-in"><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span> @@ -506,10 +504,13 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-in"><span class="co"># Also, the missing standard error for log_beta and the t-tests for alpha</span></span> <span class="r-in"><span class="co"># and beta indicate overparameterisation</span></span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.FOMC_SFO.tc</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>diag(.) had 0 or NA entries; non-finite result is doubtful</span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:12:07 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:12:07 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed May 18 20:38:07 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed May 18 20:38:07 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> @@ -518,12 +519,12 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 3729 model solutions performed in 2.67 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 3924 model solutions performed in 7.107 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model algorithm: d_3 </span> -<span class="r-out co"><span class="r-pr">#></span> Direct fitting and three-step fitting yield approximately the same likelihood </span> +<span class="r-out co"><span class="r-pr">#></span> Three-step fitting yielded a higher likelihood than direct fitting </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Starting values for parameters to be optimised:</span> <span class="r-out co"><span class="r-pr">#></span> value type</span> @@ -558,7 +559,7 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 101.600000 2.6400000 96.240000 107.000000</span> <span class="r-out co"><span class="r-pr">#></span> log_k_m1 -5.284000 0.0929100 -5.474000 -5.095000</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.001426 0.0767000 -0.155000 0.157800</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.001426 0.0766900 -0.155000 0.157800</span> <span class="r-out co"><span class="r-pr">#></span> log_alpha 5.522000 0.0077320 5.506000 5.538000</span> <span class="r-out co"><span class="r-pr">#></span> log_beta 7.806000 NaN NaN NaN</span> <span class="r-out co"><span class="r-pr">#></span> sigma_low 0.002488 0.0002431 0.001992 0.002984</span> @@ -566,31 +567,31 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Parameter correlation:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_m1 f_parent_qlogis log_alpha log_beta</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000000 -0.095226 -0.76678 0.70544 NaN</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.095226 1.000000 0.51432 -0.14387 NaN</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.766780 0.514321 1.00000 -0.61396 NaN</span> -<span class="r-out co"><span class="r-pr">#></span> log_alpha 0.705444 -0.143872 -0.61396 1.00000 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000000 -0.095145 -0.76674 0.70541 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.095145 1.000000 0.51428 -0.14381 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.766743 0.514278 1.00000 -0.61392 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> log_alpha 0.705413 -0.143809 -0.61392 1.00000 NaN</span> <span class="r-out co"><span class="r-pr">#></span> log_beta NaN NaN NaN NaN 1</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.016073 0.001586 0.01548 5.87007 NaN</span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.006626 -0.011700 -0.05357 0.04849 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.016077 0.001586 0.01548 5.87034 NaN</span> +<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.006617 -0.011694 -0.05356 0.04848 NaN</span> <span class="r-out co"><span class="r-pr">#></span> sigma_low rsd_high</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 0.016073 0.006626</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 0.001586 -0.011700</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.015476 -0.053566</span> -<span class="r-out co"><span class="r-pr">#></span> log_alpha 5.870075 0.048487</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.016077 0.006617</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 0.001586 -0.011694</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.015476 -0.053560</span> +<span class="r-out co"><span class="r-pr">#></span> log_alpha 5.870339 0.048481</span> <span class="r-out co"><span class="r-pr">#></span> log_beta NaN NaN</span> -<span class="r-out co"><span class="r-pr">#></span> sigma_low 1.000000 -0.652558</span> -<span class="r-out co"><span class="r-pr">#></span> rsd_high -0.652558 1.000000</span> +<span class="r-out co"><span class="r-pr">#></span> sigma_low 1.000000 -0.652555</span> +<span class="r-out co"><span class="r-pr">#></span> rsd_high -0.652555 1.000000</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> Confidence intervals for internally transformed parameters are asymmetric.</span> <span class="r-out co"><span class="r-pr">#></span> t-test (unrealistically) based on the assumption of normal distribution</span> <span class="r-out co"><span class="r-pr">#></span> for estimators of untransformed parameters.</span> <span class="r-out co"><span class="r-pr">#></span> Estimate t value Pr(>t) Lower Upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.016e+02 32.7800 6.311e-26 9.624e+01 1.070e+02</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.016e+02 32.7800 6.312e-26 9.624e+01 1.070e+02</span> <span class="r-out co"><span class="r-pr">#></span> k_m1 5.072e-03 10.1200 1.216e-11 4.196e-03 6.130e-03</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 5.004e-01 20.8300 4.317e-20 4.613e-01 5.394e-01</span> -<span class="r-out co"><span class="r-pr">#></span> alpha 2.502e+02 0.5624 2.889e-01 2.463e+02 2.542e+02</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 5.004e-01 20.8300 4.318e-20 4.613e-01 5.394e-01</span> +<span class="r-out co"><span class="r-pr">#></span> alpha 2.502e+02 0.5624 2.890e-01 2.463e+02 2.542e+02</span> <span class="r-out co"><span class="r-pr">#></span> beta 2.455e+03 0.5549 2.915e-01 NA NA</span> <span class="r-out co"><span class="r-pr">#></span> sigma_low 2.488e-03 0.4843 3.158e-01 1.992e-03 2.984e-03</span> <span class="r-out co"><span class="r-pr">#></span> rsd_high 7.921e-02 8.4300 8.001e-10 6.018e-02 9.823e-02</span> @@ -630,7 +631,7 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 72a9ea52..3a29b39b 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -258,6 +258,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"></span> <span class="r-in"><span class="co"># \dontrun{</span></span> <span class="r-in"> <span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"></span> <span class="r-in"> <span class="co"># Now supplying compound names used for plotting, and write to user defined location</span></span> <span class="r-in"> <span class="co"># We need to choose a path outside the session tempdir because this gets removed</span></span> @@ -267,13 +268,14 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full_name <span class="op">=</span> <span class="st">"Test compound"</span><span class="op">)</span>,</span> <span class="r-in"> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span> <span class="r-in"> name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/Rtmp1TiIZY/file1180516cafe4a2.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> +<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpkcKjUM/file8dd657f864c2.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> <span class="r-in"><span class="co"># Now we can save the model and restore it in a new session</span></span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span> <span class="r-in"><span class="co"># Terminate the R session here if you would like to check, and then do</span></span> <span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span> <span class="r-in"><span class="va">SFO_SFO.3</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">readRDS</a></span><span class="op">(</span><span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span> <span class="r-in"><span class="va">fit_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.3</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"></span> <span class="r-in"><span class="co"># Show details of creating the C function</span></span> <span class="r-in"><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span></span> @@ -319,7 +321,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-out co"><span class="r-pr">#></span> })</span> <span class="r-out co"><span class="r-pr">#></span> return(predicted)</span> <span class="r-out co"><span class="r-pr">#></span> }</span> -<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55555f6c4cd8></span> +<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55cc1a5f8ad8></span> <span class="r-in"></span> <span class="r-in"><span class="co"># If we have several parallel metabolites</span></span> <span class="r-in"><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span> @@ -348,7 +350,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png Binary files differindex fff98391..69d9ac75 100644 --- a/docs/reference/mkinparplot-1.png +++ b/docs/reference/mkinparplot-1.png diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 2e787240..b9eda413 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -117,6 +117,7 @@ effect, namely to produce a plot.</p> <span class="r-in"> anisole <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"><span class="fu">mkinparplot</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> <span class="r-plt img"><img src="mkinparplot-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span class="co"># }</span></span> @@ -134,7 +135,7 @@ effect, namely to produce a plot.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 79599787..cad5b35f 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -120,7 +120,7 @@ plot.mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index c197e6dc..d888bb25 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -318,7 +318,7 @@ as these always return mapped output.</p></dd> <span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"><span class="kw">if</span><span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span>replications <span class="op">=</span> <span class="fl">10</span>, order <span class="op">=</span> <span class="st">"relative"</span>, columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"test"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span>,</span> +<span class="r-in"> <span class="fu">benchmark</span><span class="op">(</span>replications <span class="op">=</span> <span class="fl">10</span>, order <span class="op">=</span> <span class="st">"relative"</span>, columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"test"</span>, <span class="st">"relative"</span>, <span class="st">"elapsed"</span><span class="op">)</span>,</span> <span class="r-in"> eigen <span class="op">=</span> <span class="fu">mkinpredict</span><span class="op">(</span><span class="va">SFO_SFO</span>,</span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> @@ -336,11 +336,8 @@ as these always return mapped output.</p></dd> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> <span class="r-in"> solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span><span class="op">)</span></span> <span class="r-in"><span class="op">}</span></span> -<span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.00 0.004</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.50 0.006</span> -<span class="r-out co"><span class="r-pr">#></span> 1 eigen 5.25 0.021</span> -<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 52.00 0.208</span> +<span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>there is no package called ‘rbenchmark’</span> <span class="r-in"></span> <span class="r-in"><span class="co"># \dontrun{</span></span> <span class="r-in"> <span class="co"># Predict from a fitted model</span></span> @@ -370,7 +367,7 @@ as these always return mapped output.</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index cd3b4009..654b93d8 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -166,6 +166,7 @@ combining the plot of the fit and the residual plot.</p></div> <span class="r-in"><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"><span class="fu">mkinresplot</span><span class="op">(</span><span class="va">fit</span>, <span class="st">"m1"</span><span class="op">)</span></span> <span class="r-plt img"><img src="mkinresplot-1.png" alt="" width="700" height="433"></span> <span class="r-in"></span> @@ -183,7 +184,7 @@ combining the plot of the fit and the residual plot.</p></div> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png Binary files differindex 8ad9c11d..75cbc054 100644 --- a/docs/reference/mmkin-1.png +++ b/docs/reference/mmkin-1.png diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png Binary files differindex da2a48a8..76f42b73 100644 --- a/docs/reference/mmkin-2.png +++ b/docs/reference/mmkin-2.png diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png Binary files differindex 10d3f35b..e92d81b2 100644 --- a/docs/reference/mmkin-3.png +++ b/docs/reference/mmkin-3.png diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png Binary files differindex 132380a8..8d747ffe 100644 --- a/docs/reference/mmkin-4.png +++ b/docs/reference/mmkin-4.png diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png Binary files differindex 4bfcc55e..ffd7640d 100644 --- a/docs/reference/mmkin-5.png +++ b/docs/reference/mmkin-5.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 1ca0190a..cbb46ab0 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -167,10 +167,10 @@ plotting.</p></div> <span class="r-in"></span> <span class="r-in"><span class="va">time_default</span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 4.710 0.665 1.757 </span> +<span class="r-out co"><span class="r-pr">#></span> 35.152 1.185 8.439 </span> <span class="r-in"><span class="va">time_1</span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 5.644 0.001 5.645 </span> +<span class="r-out co"><span class="r-pr">#></span> 14.744 0.008 14.768 </span> <span class="r-in"></span> <span class="r-in"><span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="st">"SFO_lin"</span>, <span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> @@ -180,8 +180,8 @@ plotting.</p></div> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> <span class="r-out co"><span class="r-pr">#></span> parent 0.877769 2.915885</span> -<span class="r-out co"><span class="r-pr">#></span> M1 2.325744 7.725956</span> -<span class="r-out co"><span class="r-pr">#></span> M2 33.720100 112.015749</span> +<span class="r-out co"><span class="r-pr">#></span> M1 2.325744 7.725955</span> +<span class="r-out co"><span class="r-pr">#></span> M2 33.720111 112.015785</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"></span> <span class="r-in"><span class="co"># plot.mkinfit handles rows or columns of mmkin result objects</span></span> @@ -214,10 +214,12 @@ plotting.</p></div> <span class="r-out co"><span class="r-pr">#></span> dataset</span> <span class="r-out co"><span class="r-pr">#></span> model A B C D </span> <span class="r-out co"><span class="r-pr">#></span> SFO OK OK OK OK</span> -<span class="r-out co"><span class="r-pr">#></span> FOMC OK OK OK OK</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC C OK OK OK</span> <span class="r-out co"><span class="r-pr">#></span> DFOP OK OK OK OK</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> +<span class="r-out co"><span class="r-pr">#></span> C: Optimisation did not converge:</span> +<span class="r-out co"><span class="r-pr">#></span> false convergence (8)</span> <span class="r-in"><span class="co"># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span></span> <span class="r-in"><span class="co"># dataset is really SFO, and the FOMC fit is overparameterised</span></span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">stopCluster</a></span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span> @@ -237,7 +239,7 @@ plotting.</p></div> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index 0711886a..1d22b617 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -209,7 +209,7 @@ list element "data" contains the dataset used in the fits.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png Binary files differindex 67cc7f3c..0b6cb78d 100644 --- a/docs/reference/nlme-1.png +++ b/docs/reference/nlme-1.png diff --git a/docs/reference/nlme-2.png b/docs/reference/nlme-2.png Binary files differindex bb1e6f81..ef152270 100644 --- a/docs/reference/nlme-2.png +++ b/docs/reference/nlme-2.png diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index 746cc6aa..ff8de9f3 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -202,7 +202,7 @@ A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external- </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/nlme.mmkin-1.png b/docs/reference/nlme.mmkin-1.png Binary files differindex d93b0950..fe1ff61d 100644 --- a/docs/reference/nlme.mmkin-1.png +++ b/docs/reference/nlme.mmkin-1.png diff --git a/docs/reference/nlme.mmkin-2.png b/docs/reference/nlme.mmkin-2.png Binary files differindex 5afccfbb..b9a68e92 100644 --- a/docs/reference/nlme.mmkin-2.png +++ b/docs/reference/nlme.mmkin-2.png diff --git a/docs/reference/nlme.mmkin-3.png b/docs/reference/nlme.mmkin-3.png Binary files differindex bf3aac6c..2ab51f97 100644 --- a/docs/reference/nlme.mmkin-3.png +++ b/docs/reference/nlme.mmkin-3.png diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index 1f071ffa..c8bd28e9 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -97,7 +97,7 @@ have been obtained by fitting the same model to a list of datasets.</p> data <span class="op">=</span> <span class="st">"auto"</span>, fixed <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">as.list</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>, <span class="kw">function</span><span class="op">(</span><span class="va">el</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/eval.html" class="external-link">eval</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/parse.html" class="external-link">parse</a></span><span class="op">(</span>text <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="va">el</span>, <span class="fl">1</span>, sep <span class="op">=</span> <span class="st">"~"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>, - random <span class="op">=</span> <span class="fu">pdDiag</span><span class="op">(</span><span class="va">fixed</span><span class="op">)</span>, + random <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">pdDiag</a></span><span class="op">(</span><span class="va">fixed</span><span class="op">)</span>, <span class="va">groups</span>, start <span class="op">=</span> <span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, correlation <span class="op">=</span> <span class="cn">NULL</span>, @@ -196,7 +196,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_sfo</span>, <span class="va">f_nlme_dfop</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio p-value</span> <span class="r-out co"><span class="r-pr">#></span> f_nlme_sfo 1 5 625.0539 637.5529 -307.5269 </span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9269 <.0001</span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9268 <.0001</span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_nlme_dfop</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> Kinetic nonlinear mixed-effects model fit by maximum likelihood</span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -227,7 +227,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> -<span class="r-out co"><span class="r-pr">#></span> parent 10.79857 100.7937 30.34193 4.193938 43.85443</span> +<span class="r-out co"><span class="r-pr">#></span> parent 10.79857 100.7937 30.34192 4.193936 43.85441</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"></span> <span class="r-in"> <span class="va">ds_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span> @@ -278,12 +278,12 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-in"> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> <span class="r-out co"><span class="r-pr">#></span> parent_A1 parent_sink </span> -<span class="r-out co"><span class="r-pr">#></span> 0.2768574 0.7231426 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.2768575 0.7231425 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $distimes</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> <span class="r-out co"><span class="r-pr">#></span> parent 11.07091 104.6320 31.49737 4.462383 46.20825</span> -<span class="r-out co"><span class="r-pr">#></span> A1 162.30519 539.1662 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> A1 162.30524 539.1663 NA NA NA</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"></span> <span class="r-in"> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu">findFunction</span><span class="op">(</span><span class="st">"varConstProp"</span><span class="op">)</span><span class="op">)</span> <span class="op">></span> <span class="fl">0</span><span class="op">)</span> <span class="op">{</span> <span class="co"># tc error model for nlme available</span></span> @@ -311,7 +311,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> <span class="r-out co"><span class="r-pr">#></span> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) </span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k1 log_k2 g_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> 94.04774 -1.82340 -4.16716 0.05686 </span> +<span class="r-out co"><span class="r-pr">#></span> 94.04775 -1.82340 -4.16715 0.05685 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)</span> @@ -325,7 +325,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-out co"><span class="r-pr">#></span> Formula: ~fitted(.) </span> <span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> <span class="r-out co"><span class="r-pr">#></span> const prop </span> -<span class="r-out co"><span class="r-pr">#></span> 2.23223147 0.01262395 </span> +<span class="r-out co"><span class="r-pr">#></span> 2.23223513 0.01262371 </span> <span class="r-in"></span> <span class="r-in"> <span class="va">f_2_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_2</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span> <span class="r-in"> <span class="va">f_nlme_sfo_sfo_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2_obs</span><span class="op">[</span><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span> @@ -358,7 +358,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-out co"><span class="r-pr">#></span> Formula: ~1 | name </span> <span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> <span class="r-out co"><span class="r-pr">#></span> parent A1 </span> -<span class="r-out co"><span class="r-pr">#></span> 1.0000000 0.2049995 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.0000000 0.2049985 </span> <span class="r-in"> <span class="va">f_nlme_dfop_sfo_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2_obs</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span>,</span> <span class="r-in"> control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>pnlsMaxIter <span class="op">=</span> <span class="fl">120</span>, tolerance <span class="op">=</span> <span class="fl">5e-4</span><span class="op">)</span><span class="op">)</span></span> <span class="r-in"></span> @@ -370,7 +370,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span>, <span class="va">f_nlme_dfop_sfo_obs</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> Model df AIC BIC logLik Test L.Ratio</span> <span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 </span> -<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32091</span> +<span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32092</span> <span class="r-out co"><span class="r-pr">#></span> p-value</span> <span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo </span> <span class="r-out co"><span class="r-pr">#></span> f_nlme_dfop_sfo_obs <.0001</span> @@ -390,7 +390,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/nobs.mkinfit.html b/docs/reference/nobs.mkinfit.html index 34da24d9..e37fff64 100644 --- a/docs/reference/nobs.mkinfit.html +++ b/docs/reference/nobs.mkinfit.html @@ -115,7 +115,7 @@ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/parms.html b/docs/reference/parms.html index 1ddd3eb9..18f3566e 100644 --- a/docs/reference/parms.html +++ b/docs/reference/parms.html @@ -157,10 +157,10 @@ such matrices is returned.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $DFOP</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 7</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 91.058971589</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 91.058971599</span> <span class="r-out co"><span class="r-pr">#></span> k1 0.044946770</span> <span class="r-out co"><span class="r-pr">#></span> k2 0.002868336</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.526942415</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.526942414</span> <span class="r-out co"><span class="r-pr">#></span> sigma 2.221302196</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span> @@ -179,10 +179,10 @@ such matrices is returned.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> $DFOP</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 96.55213663 91.058971589 90.34509493 98.14858820 94.311323734</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.55213663 91.058971599 90.34509493 98.14858821 94.311323732</span> <span class="r-out co"><span class="r-pr">#></span> k1 0.21954588 0.044946770 0.41232288 0.31697588 0.080663857</span> <span class="r-out co"><span class="r-pr">#></span> k2 0.02957934 0.002868336 0.07581766 0.03260384 0.003425417</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.44845068 0.526942415 0.66091967 0.65322767 0.342652880</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.44845068 0.526942414 0.66091967 0.65322767 0.342652880</span> <span class="r-out co"><span class="r-pr">#></span> sigma 1.35690468 2.221302196 1.34169076 2.87159846 1.942067831</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-in"><span class="fu">parms</span><span class="op">(</span><span class="va">fits</span>, transformed <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> @@ -222,7 +222,7 @@ such matrices is returned.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/plot.mixed.mmkin-2.png b/docs/reference/plot.mixed.mmkin-2.png Binary files differindex 8678c166..b35f28d6 100644 --- a/docs/reference/plot.mixed.mmkin-2.png +++ b/docs/reference/plot.mixed.mmkin-2.png diff --git a/docs/reference/plot.mixed.mmkin-3.png b/docs/reference/plot.mixed.mmkin-3.png Binary files differindex 9bd01852..c981538f 100644 --- a/docs/reference/plot.mixed.mmkin-3.png +++ b/docs/reference/plot.mixed.mmkin-3.png diff --git a/docs/reference/plot.mixed.mmkin-4.png b/docs/reference/plot.mixed.mmkin-4.png Binary files differindex d2fa1ae1..ccbe5861 100644 --- a/docs/reference/plot.mixed.mmkin-4.png +++ b/docs/reference/plot.mixed.mmkin-4.png diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html index 52971427..2af2328d 100644 --- a/docs/reference/plot.mixed.mmkin.html +++ b/docs/reference/plot.mixed.mmkin.html @@ -232,7 +232,7 @@ corresponding model prediction lines for the different datasets.</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png Binary files differindex cef94cb8..39098648 100644 --- a/docs/reference/plot.mkinfit-2.png +++ b/docs/reference/plot.mkinfit-2.png diff --git a/docs/reference/plot.mkinfit-5.png b/docs/reference/plot.mkinfit-5.png Binary files differindex f90b3f54..3545b8d8 100644 --- a/docs/reference/plot.mkinfit-5.png +++ b/docs/reference/plot.mkinfit-5.png diff --git a/docs/reference/plot.mkinfit-7.png b/docs/reference/plot.mkinfit-7.png Binary files differindex 3e5d828e..daf43033 100644 --- a/docs/reference/plot.mkinfit-7.png +++ b/docs/reference/plot.mkinfit-7.png diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 4c2ff570..23cf27b5 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -155,7 +155,8 @@ variables in the model.</p></dd> <dt>xlim</dt> <dd><p>Plot range in x direction.</p></dd> <dt>ylim</dt> -<dd><p>Plot range in y direction.</p></dd> +<dd><p>Plot range in y direction. If given as a list, plot ranges +for the different plot rows can be given for row layout.</p></dd> <dt>col_obs</dt> <dd><p>Colors used for plotting the observed data and the corresponding model prediction lines.</p></dd> @@ -237,7 +238,9 @@ latex is being used for the formatting of the chi2 error level, if <span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, full <span class="op">=</span> <span class="st">"Metabolite M1"</span> <span class="op">)</span><span class="op">)</span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> <span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> <span class="r-plt img"><img src="plot.mkinfit-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span class="fu">plot_res</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> @@ -276,7 +279,7 @@ latex is being used for the formatting of the chi2 error level, if </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png Binary files differindex 7af84edf..f5768c40 100644 --- a/docs/reference/plot.mmkin-2.png +++ b/docs/reference/plot.mmkin-2.png diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png Binary files differindex 56bfac50..c3f77d3d 100644 --- a/docs/reference/plot.mmkin-3.png +++ b/docs/reference/plot.mmkin-3.png diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png Binary files differindex 5da05f40..29439156 100644 --- a/docs/reference/plot.mmkin-4.png +++ b/docs/reference/plot.mmkin-4.png diff --git a/docs/reference/plot.mmkin-5.png b/docs/reference/plot.mmkin-5.png Binary files differindex 3ec224f4..89a111b0 100644 --- a/docs/reference/plot.mmkin-5.png +++ b/docs/reference/plot.mmkin-5.png diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index d7ad89dc..3dd0203b 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -173,6 +173,8 @@ latex is being used for the formatting of the chi2 error level.</p> <span class="r-in"> <span class="va">fits</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"HS"</span><span class="op">)</span>,</span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS B"</span> <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>, <span class="co"># named list for titles</span></span> <span class="r-in"> cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> +<span class="r-wrn co"><span class="r-pr">#></span> iteration limit reached without convergence (10)</span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span> <span class="r-plt img"><img src="plot.mmkin-1.png" alt="" width="700" height="433"></span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span> @@ -205,7 +207,7 @@ latex is being used for the formatting of the chi2 error level.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html index a14ed303..af65d8eb 100644 --- a/docs/reference/plot.nafta.html +++ b/docs/reference/plot.nafta.html @@ -129,7 +129,7 @@ function (SFO, then IORE, then DFOP).</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 1367ccf5..4da7092a 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -120,7 +120,7 @@ below to see their documentation.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/residuals.mkinfit.html b/docs/reference/residuals.mkinfit.html index c27cea76..7d9e50de 100644 --- a/docs/reference/residuals.mkinfit.html +++ b/docs/reference/residuals.mkinfit.html @@ -125,7 +125,7 @@ standard deviation obtained from the fitted error model?</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/saem-4.png b/docs/reference/saem-4.png Binary files differindex 5f65ba2e..bb775c25 100644 --- a/docs/reference/saem-4.png +++ b/docs/reference/saem-4.png diff --git a/docs/reference/saem.html b/docs/reference/saem.html index cc597665..7e22e839 100644 --- a/docs/reference/saem.html +++ b/docs/reference/saem.html @@ -291,21 +291,21 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> log_k1 -2.5841 -3.6876 -1.4805</span> <span class="r-out co"><span class="r-pr">#></span> log_k2 -3.5228 -5.3254 -1.7203</span> <span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.1027 -0.8719 0.6665</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 1.8856 1.6676 2.1037</span> -<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.7682 0.7668 4.7695</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 1.8856 1.6770 2.0943</span> +<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.7682 0.7669 4.7695</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k_A1 1.7447 0.4047 3.0848</span> <span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4525 0.1620 0.7431</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k1 1.2423 0.4560 2.0285</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k2 2.0390 0.7601 3.3180</span> -<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4439 -0.3069 1.1947</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4439 -0.3068 1.1946</span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-ANY-method.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span> <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.0 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:15:26 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:15:26 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed May 18 20:41:57 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed May 18 20:41:57 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -320,7 +320,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 8.741 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.745 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Constant variance </span> @@ -359,16 +359,16 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.7682 0.7668 4.7695</span> +<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 2.7682 0.7669 4.7695</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k_A1 1.7447 0.4047 3.0848</span> <span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4525 0.1620 0.7431</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k1 1.2423 0.4560 2.0285</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k2 2.0390 0.7601 3.3180</span> -<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4439 -0.3069 1.1947</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.4439 -0.3068 1.1946</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 1.886 1.668 2.104</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 1.886 1.677 2.094</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> @@ -554,7 +554,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 21 6.4 7.59693 -1.19693 1.886 -0.634761</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 21 7.2 7.59693 -0.39693 1.886 -0.210502</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 41 9.1 9.86436 -0.76436 1.886 -0.405361</span> -<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 41 8.5 9.86436 -1.36436 1.886 -0.723555</span> +<span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 41 8.5 9.86436 -1.36436 1.886 -0.723556</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 63 11.7 10.99397 0.70603 1.886 0.374425</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 63 12.0 10.99397 1.00603 1.886 0.533522</span> <span class="r-out co"><span class="r-pr">#></span> Dataset 10 A1 91 13.3 11.91274 1.38726 1.886 0.735696</span> @@ -589,7 +589,7 @@ using <a href="mmkin.html">mmkin</a>.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 7fef34e4..23102f17 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -125,7 +125,7 @@ Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> <p>Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data. <em>Environments</em> 6(12) 124 -doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link">10.3390/environments6120124</a> +<a href="https://doi.org/10.3390/environments6120124" class="external-link">doi:10.3390/environments6120124</a> .</p> </div> @@ -172,7 +172,7 @@ doi: <a href="https://doi.org/10.3390/environments6120124" class="external-link" </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index f01d1048..6d816366 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -179,16 +179,16 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:15:30 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:15:30 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed May 18 20:42:00 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed May 18 20:42:00 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 131 model solutions performed in 0.028 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 131 model solutions performed in 0.027 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -220,9 +220,9 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Parameter correlation:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent sigma</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000e+00 5.428e-01 1.642e-07</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent 5.428e-01 1.000e+00 2.507e-07</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 1.642e-07 2.507e-07 1.000e+00</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000e+00 5.428e-01 1.648e-07</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent 5.428e-01 1.000e+00 2.514e-07</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.648e-07 2.514e-07 1.000e+00</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> Confidence intervals for internally transformed parameters are asymmetric.</span> @@ -267,7 +267,7 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html index 3f98bec7..8440e8c2 100644 --- a/docs/reference/summary.nlme.mmkin.html +++ b/docs/reference/summary.nlme.mmkin.html @@ -96,7 +96,7 @@ endpoints such as formation fractions and DT50 values. Optionally <div id="ref-usage"> <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for nlme.mmkin</span> -<span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span> +<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span> <span class="va">object</span>, data <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, @@ -197,16 +197,13 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-in"><span class="co"># Evaluate using mmkin and nlme</span></span> <span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span> <span class="r-in"><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds_sfo_syn</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> -<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> -<span class="r-wrn co"><span class="r-pr">#></span> iteration limit reached without convergence (10)</span> <span class="r-in"><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span> -<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.155 </span> +<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.157 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 14 08:58:29 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 14 08:58:29 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed May 18 20:42:02 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed May 18 20:42:02 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> @@ -216,13 +213,13 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.527 s using 4 iterations</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.516 s using 4 iterations</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Mean of starting values for individual parameters:</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent </span> -<span class="r-out co"><span class="r-pr">#></span> 101.569 -4.454 </span> +<span class="r-out co"><span class="r-pr">#></span> 101.612 -4.454 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fixed degradation parameter values:</span> <span class="r-out co"><span class="r-pr">#></span> None</span> @@ -246,18 +243,18 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> Level: ds</span> <span class="r-out co"><span class="r-pr">#></span> Structure: Diagonal</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent Residual</span> -<span class="r-out co"><span class="r-pr">#></span> StdDev: 6.924e-05 0.5863 1</span> +<span class="r-out co"><span class="r-pr">#></span> StdDev: 6.904e-05 0.5863 1</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance function:</span> <span class="r-out co"><span class="r-pr">#></span> Structure: Constant plus proportion of variance covariate</span> <span class="r-out co"><span class="r-pr">#></span> Formula: ~fitted(.) </span> <span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> -<span class="r-out co"><span class="r-pr">#></span> const prop </span> -<span class="r-out co"><span class="r-pr">#></span> 0.0001208853 0.0789968036 </span> +<span class="r-out co"><span class="r-pr">#></span> const prop </span> +<span class="r-out co"><span class="r-pr">#></span> 0.000121099 0.078996777 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters with asymmetric confidence intervals:</span> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 99.370882 101.59243 103.81398</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.370886 101.59243 103.81398</span> <span class="r-out co"><span class="r-pr">#></span> k_parent 0.006923 0.01168 0.01972</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> @@ -268,48 +265,48 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> ds name time observed predicted residual std standardized</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 104.1 101.592 2.50757 8.0255 0.312451</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 105.0 101.592 3.40757 8.0255 0.424594</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 98.5 100.796 -2.29571 7.9625 -0.288313</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 98.5 100.796 -2.29571 7.9625 -0.288314</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 96.1 100.796 -4.69571 7.9625 -0.589725</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 101.9 99.221 2.67904 7.8381 0.341796</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 85.2 99.221 -14.02096 7.8381 -1.788812</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 99.1 96.145 2.95512 7.5951 0.389081</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 85.2 99.221 -14.02096 7.8381 -1.788813</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 99.1 96.145 2.95512 7.5951 0.389080</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 93.0 96.145 -3.14488 7.5951 -0.414065</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 88.1 90.989 -2.88944 7.1879 -0.401987</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 84.1 90.989 -6.88944 7.1879 -0.958480</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 88.1 90.989 -2.88944 7.1879 -0.401988</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 84.1 90.989 -6.88944 7.1879 -0.958481</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 80.2 81.493 -1.29305 6.4377 -0.200857</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 91.3 81.493 9.80695 6.4377 1.523364</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 65.1 63.344 1.75642 5.0039 0.351008</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 65.8 63.344 2.45642 5.0039 0.490898</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 47.8 50.018 -2.21764 3.9512 -0.561252</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 47.8 50.018 -2.21764 3.9512 -0.561253</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 53.5 50.018 3.48236 3.9512 0.881335</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 37.6 39.495 -1.89515 3.1200 -0.607423</span> <span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 39.3 39.495 -0.19515 3.1200 -0.062549</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 107.9 101.592 6.30757 8.0255 0.785943</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 102.1 101.592 0.50757 8.0255 0.063245</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 102.1 101.592 0.50757 8.0255 0.063244</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 103.8 100.058 3.74159 7.9043 0.473361</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 108.6 100.058 8.54159 7.9043 1.080626</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 91.0 97.060 -6.05952 7.6674 -0.790297</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 84.9 97.060 -12.15952 7.6674 -1.585874</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 79.3 91.329 -12.02867 7.2147 -1.667251</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 84.9 97.060 -12.15952 7.6674 -1.585875</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 79.3 91.329 -12.02867 7.2147 -1.667252</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 100.9 91.329 9.57133 7.2147 1.326647</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 77.3 82.102 -4.80185 6.4858 -0.740366</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 83.5 82.102 1.39815 6.4858 0.215571</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 66.8 66.351 0.44945 5.2415 0.085748</span> <span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 63.3 66.351 -3.05055 5.2415 -0.582002</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 40.8 40.775 0.02474 3.2211 0.007679</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 44.8 40.775 4.02474 3.2211 1.249485</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 27.8 25.832 1.96762 2.0407 0.964198</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 27.0 25.832 1.16762 2.0407 0.572171</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 15.2 16.366 -1.16561 1.2928 -0.901595</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 15.5 16.366 -0.86561 1.2928 -0.669547</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 97.7 101.592 -3.89243 8.0255 -0.485009</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668739</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 109.9 99.218 10.68196 7.8379 1.362858</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 97.8 99.218 -1.41804 7.8379 -0.180921</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 40.8 40.775 0.02474 3.2211 0.007681</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 44.8 40.775 4.02474 3.2211 1.249487</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 27.8 25.832 1.96762 2.0407 0.964200</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 27.0 25.832 1.16762 2.0407 0.572173</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 15.2 16.366 -1.16561 1.2928 -0.901593</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 15.5 16.366 -0.86561 1.2928 -0.669544</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 97.7 101.592 -3.89243 8.0255 -0.485010</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668740</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 109.9 99.218 10.68195 7.8379 1.362858</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 97.8 99.218 -1.41805 7.8379 -0.180921</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 100.5 94.634 5.86555 7.4758 0.784603</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 77.4 94.634 -17.23445 7.4758 -2.305360</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 78.3 86.093 -7.79273 6.8011 -1.145813</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 90.3 86.093 4.20727 6.8011 0.618620</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 77.4 94.634 -17.23445 7.4758 -2.305361</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 78.3 86.093 -7.79273 6.8010 -1.145814</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 90.3 86.093 4.20727 6.8010 0.618620</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 76.0 72.958 3.04222 5.7634 0.527848</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 79.1 72.958 6.14222 5.7634 1.065722</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 46.0 52.394 -6.39404 4.1390 -1.544842</span> @@ -317,45 +314,45 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 25.1 24.582 0.51786 1.9419 0.266676</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 21.4 24.582 -3.18214 1.9419 -1.638664</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 11.0 12.092 -1.09202 0.9552 -1.143199</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206776</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206778</span> <span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 5.8 5.948 -0.14810 0.4699 -0.315178</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 6.1 5.948 0.15190 0.4699 0.323282</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 6.1 5.948 0.15190 0.4699 0.323283</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 95.3 101.592 -6.29243 8.0255 -0.784057</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 102.0 101.592 0.40757 8.0255 0.050784</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 104.4 101.125 3.27549 7.9885 0.410025</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 105.4 101.125 4.27549 7.9885 0.535205</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 105.4 101.125 4.27549 7.9885 0.535204</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 113.7 100.195 13.50487 7.9151 1.706218</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 82.3 100.195 -17.89513 7.9151 -2.260886</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 98.1 98.362 -0.26190 7.7703 -0.033706</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 87.8 98.362 -10.56190 7.7703 -1.359270</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 97.9 95.234 2.66590 7.5232 0.354357</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 104.8 95.234 9.56590 7.5232 1.271521</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 85.0 89.274 -4.27372 7.0523 -0.606001</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 77.2 89.274 -12.07372 7.0523 -1.712017</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 82.2 77.013 5.18661 6.0838 0.852526</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 86.1 77.013 9.08661 6.0838 1.493571</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 70.5 67.053 3.44692 5.2970 0.650733</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 61.7 67.053 -5.35308 5.2970 -1.010591</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 60.0 58.381 1.61905 4.6119 0.351058</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 56.4 58.381 -1.98095 4.6119 -0.429530</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 92.6 101.592 -8.99243 8.0255 -1.120485</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 82.3 100.195 -17.89513 7.9151 -2.260887</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 98.1 98.362 -0.26191 7.7703 -0.033706</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 87.8 98.362 -10.56191 7.7703 -1.359271</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 97.9 95.234 2.66589 7.5232 0.354356</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 104.8 95.234 9.56589 7.5232 1.271521</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 85.0 89.274 -4.27373 7.0523 -0.606002</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 77.2 89.274 -12.07373 7.0523 -1.712019</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 82.2 77.013 5.18659 6.0838 0.852523</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 86.1 77.013 9.08659 6.0838 1.493568</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 70.5 67.053 3.44690 5.2970 0.650729</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 61.7 67.053 -5.35310 5.2970 -1.010595</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 60.0 58.381 1.61902 4.6119 0.351052</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 56.4 58.381 -1.98098 4.6119 -0.429535</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 92.6 101.592 -8.99243 8.0255 -1.120486</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 116.5 101.592 14.90757 8.0255 1.857531</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 108.0 99.914 8.08560 7.8929 1.024413</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 108.0 99.914 8.08560 7.8929 1.024412</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 104.9 99.914 4.98560 7.8929 0.631655</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 100.5 96.641 3.85898 7.6343 0.505477</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935382</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935383</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 91.7 90.412 1.28752 7.1423 0.180267</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 95.1 90.412 4.68752 7.1423 0.656304</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 82.2 80.463 1.73715 6.3563 0.273295</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 82.2 80.463 1.73715 6.3563 0.273296</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 84.5 80.463 4.03715 6.3563 0.635141</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 60.5 63.728 -3.22788 5.0343 -0.641178</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 72.8 63.728 9.07212 5.0343 1.802062</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 38.3 37.399 0.90061 2.9544 0.304835</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 40.7 37.399 3.30061 2.9544 1.117174</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 22.5 22.692 -0.19165 1.7926 -0.106913</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 20.8 22.692 -1.89165 1.7926 -1.055273</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 13.4 13.768 -0.36790 1.0876 -0.338259</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 13.8 13.768 0.03210 1.0876 0.029517</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 72.8 63.728 9.07212 5.0343 1.802063</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 38.3 37.399 0.90062 2.9544 0.304836</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 40.7 37.399 3.30062 2.9544 1.117176</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 22.5 22.692 -0.19164 1.7926 -0.106910</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 20.8 22.692 -1.89164 1.7926 -1.055271</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 13.4 13.768 -0.36789 1.0876 -0.338255</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 13.8 13.768 0.03211 1.0876 0.029520</span> <span class="r-in"><span class="co"># }</span></span> <span class="r-in"></span> </code></pre></div> @@ -372,7 +369,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/summary.saem.mmkin.html b/docs/reference/summary.saem.mmkin.html index 26ece42d..c2f9490e 100644 --- a/docs/reference/summary.saem.mmkin.html +++ b/docs/reference/summary.saem.mmkin.html @@ -199,9 +199,9 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.0 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:15:47 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:15:47 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed May 18 20:42:18 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed May 18 20:42:18 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -216,7 +216,7 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 12.164 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 12.833 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> @@ -225,7 +225,7 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 </span> <span class="r-out co"><span class="r-pr">#></span> 101.65645 -4.05368 -0.94311 -2.35943 -4.07006 </span> <span class="r-out co"><span class="r-pr">#></span> g_qlogis </span> -<span class="r-out co"><span class="r-pr">#></span> -0.01132 </span> +<span class="r-out co"><span class="r-pr">#></span> -0.01133 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fixed degradation parameter values:</span> <span class="r-out co"><span class="r-pr">#></span> None</span> @@ -234,231 +234,231 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> <span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 828.1 822.7 -400.1</span> +<span class="r-out co"><span class="r-pr">#></span> 829.3 823.8 -400.6</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Optimised parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 100.74378 97.813 103.6747</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.06168 -4.171 -3.9523</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.92584 -1.313 -0.5389</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.81914 -3.602 -2.0362</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.63916 -4.327 -2.9516</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.02927 -1.152 1.0939</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.26516 98.412 104.1188</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.07510 -4.168 -3.9819</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.94320 -1.350 -0.5364</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.87697 -3.703 -2.0510</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.58133 -4.313 -2.8492</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.03174 -1.564 1.5008</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> parnt_0 lg_k_m1 f_prnt_ log_k1 log_k2 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.3571 </span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.2190 0.2189 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 0.1248 -0.1042 -0.0514 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 0.0130 0.0043 -0.0049 0.0883 </span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.0643 0.0437 0.0354 -0.3477 -0.2589</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.4167 </span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.2084 0.2383 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 0.1324 -0.1242 -0.0500 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 0.0173 0.0001 -0.0067 0.1137 </span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.0849 0.0691 0.0399 -0.3916 -0.3012</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 0.73313 -7.46512 8.9314</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_m1 0.06488 -0.06041 0.1902</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.41955 0.15206 0.6870</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.81750 0.29140 1.3436</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.75265 0.27939 1.2259</span> -<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.34411 -1.70964 2.3979</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 0.16032 -34.0484 34.3690</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_m1 0.01463 -0.3605 0.3898</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.44391 0.1646 0.7232</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.84861 0.3044 1.3928</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.79185 0.2944 1.2893</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.34997 -3.0572 3.7572</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.86164 0.67928 1.04400</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.07973 0.06437 0.09509</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.87200 0.69118 1.0528</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.07963 0.06435 0.0949</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 100.74378 97.81291 103.67465</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01722 0.01544 0.01921</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.28377 0.21203 0.36843</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.05966 0.02727 0.13052</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.02627 0.01321 0.05226</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.49268 0.24004 0.74912</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.26516 98.41151 104.11881</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01699 0.01548 0.01865</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.28025 0.20588 0.36902</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.05630 0.02465 0.12861</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.02784 0.01339 0.05789</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.49207 0.17303 0.81770</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Resulting formation fractions:</span> <span class="r-out co"><span class="r-pr">#></span> ff</span> -<span class="r-out co"><span class="r-pr">#></span> parent_m1 0.2838</span> -<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7162</span> +<span class="r-out co"><span class="r-pr">#></span> parent_m1 0.2803</span> +<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7197</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> -<span class="r-out co"><span class="r-pr">#></span> parent 17.17 65.72 19.78 11.62 26.38</span> -<span class="r-out co"><span class="r-pr">#></span> m1 40.25 133.71 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> parent 17.28 63.65 19.16 12.31 24.9</span> +<span class="r-out co"><span class="r-pr">#></span> m1 40.80 135.52 NA NA NA</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Data:</span> -<span class="r-out co"><span class="r-pr">#></span> ds name time observed predicted residual std standardized</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 89.8 1.005e+02 -1.069e+01 8.0584 -1.327e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 104.1 1.005e+02 3.607e+00 8.0584 4.476e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 88.7 9.580e+01 -7.103e+00 7.6867 -9.241e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 95.5 9.580e+01 -3.030e-01 7.6867 -3.942e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 81.8 8.722e+01 -5.418e+00 7.0070 -7.733e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 94.5 8.722e+01 7.282e+00 7.0070 1.039e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 71.5 7.278e+01 -1.282e+00 5.8665 -2.186e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 70.3 7.278e+01 -2.482e+00 5.8665 -4.231e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 54.2 5.418e+01 2.128e-02 4.4047 4.831e-03</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 49.6 5.418e+01 -4.579e+00 4.4047 -1.040e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 31.5 3.235e+01 -8.510e-01 2.7194 -3.129e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 28.8 3.235e+01 -3.551e+00 2.7194 -1.306e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 12.1 1.282e+01 -7.213e-01 1.3369 -5.395e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 13.6 1.282e+01 7.787e-01 1.3369 5.825e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 6.2 6.184e+00 1.593e-02 0.9927 1.605e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 8.3 6.184e+00 2.116e+00 0.9927 2.131e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.2 3.092e+00 -8.915e-01 0.8962 -9.948e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.4 3.092e+00 -6.915e-01 0.8962 -7.716e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.3 1.147e+00 -8.468e-01 0.8665 -9.773e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.2 1.147e+00 -9.468e-01 0.8665 -1.093e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 2.2 3.190e+00 -9.901e-01 0.8984 -1.102e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 3.0 3.190e+00 -1.901e-01 0.8984 -2.116e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 6.5 6.422e+00 7.828e-02 1.0023 7.811e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 5.0 6.422e+00 -1.422e+00 1.0023 -1.418e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 10.2 1.002e+01 1.782e-01 1.1751 1.517e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 9.5 1.002e+01 -5.218e-01 1.1751 -4.440e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 12.2 1.265e+01 -4.548e-01 1.3268 -3.428e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 13.4 1.265e+01 7.452e-01 1.3268 5.617e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 11.8 1.093e+01 8.735e-01 1.2253 7.129e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 13.2 1.093e+01 2.273e+00 1.2253 1.855e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 6.6 7.845e+00 -1.245e+00 1.0647 -1.170e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 9.3 7.845e+00 1.455e+00 1.0647 1.366e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 3.5 5.322e+00 -1.822e+00 0.9605 -1.897e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 5.4 5.322e+00 7.779e-02 0.9605 8.099e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 118.0 1.008e+02 1.724e+01 8.0794 2.134e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 99.8 1.008e+02 -9.578e-01 8.0794 -1.185e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 90.2 9.538e+01 -5.183e+00 7.6535 -6.773e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 94.6 9.538e+01 -7.834e-01 7.6535 -1.024e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 96.1 8.604e+01 1.006e+01 6.9134 1.456e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 78.4 8.604e+01 -7.635e+00 6.9134 -1.104e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.9 7.170e+01 6.196e+00 5.7814 1.072e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.7 7.170e+01 5.996e+00 5.7814 1.037e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 56.0 5.556e+01 4.370e-01 4.5130 9.683e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 54.7 5.556e+01 -8.630e-01 4.5130 -1.912e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.6 3.869e+01 -2.085e+00 3.2024 -6.512e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.8 3.869e+01 -1.885e+00 3.2024 -5.888e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 22.1 2.103e+01 1.072e+00 1.8850 5.688e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 24.7 2.103e+01 3.672e+00 1.8850 1.948e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 12.4 1.231e+01 8.760e-02 1.3062 6.707e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 10.8 1.231e+01 -1.512e+00 1.3062 -1.158e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 6.8 7.222e+00 -4.220e-01 1.0363 -4.072e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 7.9 7.222e+00 6.780e-01 1.0363 6.542e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 1 1.3 1.431e+00 -1.313e-01 0.8692 -1.510e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 3.7 3.849e+00 -1.486e-01 0.9146 -1.624e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 4.7 3.849e+00 8.514e-01 0.9146 9.309e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 8.1 7.298e+00 8.021e-01 1.0397 7.715e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 7.9 7.298e+00 6.021e-01 1.0397 5.791e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.1 1.051e+01 -4.109e-01 1.2020 -3.418e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.3 1.051e+01 -2.109e-01 1.2020 -1.755e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 10.7 1.218e+01 -1.476e+00 1.2980 -1.137e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 12.2 1.218e+01 2.421e-02 1.2980 1.865e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 10.7 1.043e+01 2.682e-01 1.1976 2.240e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 12.5 1.043e+01 2.068e+00 1.1976 1.727e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 9.1 7.931e+00 1.169e+00 1.0688 1.094e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 7.4 7.931e+00 -5.310e-01 1.0688 -4.969e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 6.1 5.717e+00 3.829e-01 0.9748 3.928e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 4.5 5.717e+00 -1.217e+00 0.9748 -1.249e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.2 1.010e+02 5.220e+00 8.0970 6.447e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.9 1.010e+02 5.920e+00 8.0970 7.312e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 107.4 9.352e+01 1.388e+01 7.5058 1.849e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 96.1 9.352e+01 2.581e+00 7.5058 3.439e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 79.4 8.127e+01 -1.866e+00 6.5363 -2.855e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 82.6 8.127e+01 1.334e+00 6.5363 2.041e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 63.9 6.441e+01 -5.112e-01 5.2072 -9.818e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 62.4 6.441e+01 -2.011e+00 5.2072 -3.862e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 51.0 4.843e+01 2.573e+00 3.9560 6.505e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 47.1 4.843e+01 -1.327e+00 3.9560 -3.353e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.1 3.447e+01 1.631e+00 2.8801 5.664e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.6 3.447e+01 2.131e+00 2.8801 7.400e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 20.1 1.974e+01 3.570e-01 1.7945 1.989e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 19.8 1.974e+01 5.700e-02 1.7945 3.176e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 11.3 1.193e+01 -6.276e-01 1.2833 -4.891e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 10.7 1.193e+01 -1.228e+00 1.2833 -9.567e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 8.2 7.208e+00 9.920e-01 1.0357 9.578e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 7.3 7.208e+00 9.200e-02 1.0357 8.883e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 0 0.8 -6.821e-13 8.000e-01 0.8616 9.285e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 1.8 1.796e+00 4.189e-03 0.8735 4.795e-03</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 2.3 1.796e+00 5.042e-01 0.8735 5.772e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.2 4.656e+00 -4.556e-01 0.9382 -4.856e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.1 4.656e+00 -5.556e-01 0.9382 -5.922e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 6.8 8.280e+00 -1.480e+00 1.0854 -1.363e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 10.1 8.280e+00 1.820e+00 1.0854 1.677e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 11.4 1.094e+01 4.571e-01 1.2262 3.728e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 12.8 1.094e+01 1.857e+00 1.2262 1.515e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 11.5 1.150e+01 1.650e-05 1.2582 1.311e-05</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 10.6 1.150e+01 -9.000e-01 1.2582 -7.153e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 7.5 9.187e+00 -1.687e+00 1.1309 -1.492e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 8.6 9.187e+00 -5.875e-01 1.1309 -5.194e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 7.3 6.854e+00 4.461e-01 1.0203 4.372e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 8.1 6.854e+00 1.246e+00 1.0203 1.221e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 5.3 4.908e+00 3.917e-01 0.9463 4.139e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 3.8 4.908e+00 -1.108e+00 0.9463 -1.171e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 104.7 1.006e+02 4.116e+00 8.0656 5.104e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 88.3 1.006e+02 -1.228e+01 8.0656 -1.523e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.2 9.733e+01 -3.133e+00 7.8079 -4.012e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.6 9.733e+01 -2.733e+00 7.8079 -3.500e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 78.1 9.122e+01 -1.312e+01 7.3237 -1.791e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 96.5 9.122e+01 5.280e+00 7.3237 7.209e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 76.2 8.039e+01 -4.193e+00 6.4673 -6.484e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 77.8 8.039e+01 -2.593e+00 6.4673 -4.010e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 70.8 6.513e+01 5.670e+00 5.2637 1.077e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 67.3 6.513e+01 2.170e+00 5.2637 4.123e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 43.1 4.437e+01 -1.272e+00 3.6411 -3.493e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 45.1 4.437e+01 7.281e-01 3.6411 2.000e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 21.3 2.129e+01 7.295e-03 1.9038 3.832e-03</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 23.5 2.129e+01 2.207e+00 1.9038 1.159e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 11.8 1.187e+01 -6.922e-02 1.2798 -5.409e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 12.1 1.187e+01 2.308e-01 1.2798 1.803e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 7.0 6.901e+00 9.863e-02 1.0223 9.648e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 6.2 6.901e+00 -7.014e-01 1.0223 -6.860e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 0 1.6 7.958e-13 1.600e+00 0.8616 1.857e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 1 0.9 6.965e-01 2.035e-01 0.8634 2.357e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 3.7 1.970e+00 1.730e+00 0.8758 1.976e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 2.0 1.970e+00 3.043e-02 0.8758 3.474e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.6 4.090e+00 -4.896e-01 0.9213 -5.315e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.8 4.090e+00 -2.896e-01 0.9213 -3.144e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 7.1 6.699e+00 4.006e-01 1.0138 3.952e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 6.6 6.699e+00 -9.938e-02 1.0138 -9.803e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.5 9.139e+00 3.609e-01 1.1284 3.198e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.3 9.139e+00 1.609e-01 1.1284 1.426e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 8.3 8.777e+00 -4.772e-01 1.1100 -4.299e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 9.0 8.777e+00 2.228e-01 1.1100 2.007e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 6.6 6.654e+00 -5.373e-02 1.0119 -5.310e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 7.7 6.654e+00 1.046e+00 1.0119 1.034e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.7 4.695e+00 -9.950e-01 0.9394 -1.059e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.5 4.695e+00 -1.195e+00 0.9394 -1.272e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 110.4 1.012e+02 9.182e+00 8.1159 1.131e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 112.1 1.012e+02 1.088e+01 8.1159 1.341e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 93.5 9.450e+01 -9.992e-01 7.5834 -1.318e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 91.0 9.450e+01 -3.499e+00 7.5834 -4.614e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 71.0 8.289e+01 -1.189e+01 6.6644 -1.784e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.7 8.289e+01 6.814e+00 6.6644 1.022e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 60.4 6.541e+01 -5.014e+00 5.2861 -9.486e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 59.1 6.541e+01 -6.314e+00 5.2861 -1.195e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 56.5 4.682e+01 9.684e+00 3.8308 2.528e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 47.0 4.682e+01 1.835e-01 3.8308 4.791e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 30.2 3.039e+01 -1.888e-01 2.5715 -7.343e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 23.9 3.039e+01 -6.489e+00 2.5715 -2.523e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 17.0 1.783e+01 -8.306e-01 1.6623 -4.996e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 18.7 1.783e+01 8.694e-01 1.6623 5.230e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.3 1.186e+01 -5.608e-01 1.2793 -4.383e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.9 1.186e+01 3.924e-02 1.2793 3.067e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 9.0 7.932e+00 1.068e+00 1.0688 9.997e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 8.1 7.932e+00 1.684e-01 1.0688 1.576e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 0 0.7 4.974e-14 7.000e-01 0.8616 8.124e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 3.0 3.106e+00 -1.063e-01 0.8965 -1.186e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 2.6 3.106e+00 -5.063e-01 0.8965 -5.648e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 5.1 8.331e+00 -3.231e+00 1.0879 -2.970e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 7.5 8.331e+00 -8.307e-01 1.0879 -7.636e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 16.5 1.568e+01 8.233e-01 1.5181 5.424e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 19.0 1.568e+01 3.323e+00 1.5181 2.189e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 22.9 2.214e+01 7.593e-01 1.9643 3.865e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 23.2 2.214e+01 1.059e+00 1.9643 5.393e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 22.2 2.436e+01 -2.163e+00 2.1250 -1.018e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 24.4 2.436e+01 3.673e-02 2.1250 1.728e-02</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 15.5 1.887e+01 -3.367e+00 1.7335 -1.942e+00</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 19.8 1.887e+01 9.335e-01 1.7335 5.385e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.9 1.376e+01 1.139e+00 1.3951 8.162e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.2 1.376e+01 4.387e-01 1.3951 3.144e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.9 9.886e+00 1.014e+00 1.1677 8.687e-01</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.4 9.886e+00 5.144e-01 1.1677 4.405e-01</span> +<span class="r-out co"><span class="r-pr">#></span> ds name time observed predicted residual std standardized</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 89.8 1.012e+02 -11.441861 8.1085 -1.411097</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 104.1 1.012e+02 2.858139 8.1085 0.352487</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 88.7 9.642e+01 -7.717294 7.7267 -0.998787</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 95.5 9.642e+01 -0.917294 7.7267 -0.118718</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 81.8 8.761e+01 -5.811045 7.0304 -0.826561</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 94.5 8.761e+01 6.888955 7.0304 0.979883</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 71.5 7.288e+01 -1.380912 5.8683 -0.235315</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 70.3 7.288e+01 -2.580912 5.8683 -0.439802</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 54.2 5.406e+01 0.139892 4.3920 0.031851</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 49.6 5.406e+01 -4.460108 4.3920 -1.015504</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 31.5 3.222e+01 -0.722286 2.7099 -0.266540</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 28.8 3.222e+01 -3.422286 2.7099 -1.262902</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 12.1 1.280e+01 -0.696320 1.3411 -0.519211</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 13.6 1.280e+01 0.803680 1.3411 0.599263</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 6.2 6.147e+00 0.052772 1.0000 0.052772</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 8.3 6.147e+00 2.152772 1.0000 2.152793</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.2 3.047e+00 -0.847292 0.9051 -0.936096</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.4 3.047e+00 -0.647292 0.9051 -0.715134</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.3 1.172e+00 -0.871912 0.8770 -0.994217</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.2 1.172e+00 -0.971912 0.8770 -1.108244</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 2.2 3.253e+00 -1.053335 0.9097 -1.157932</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 3.0 3.253e+00 -0.253335 0.9097 -0.278492</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 6.5 6.524e+00 -0.024120 1.0150 -0.023763</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 5.0 6.524e+00 -1.524120 1.0150 -1.501571</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 10.2 1.012e+01 0.076122 1.1875 0.064101</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 9.5 1.012e+01 -0.623878 1.1875 -0.525359</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 12.2 1.268e+01 -0.478789 1.3340 -0.358908</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 13.4 1.268e+01 0.721211 1.3340 0.540631</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 11.8 1.085e+01 0.954822 1.2272 0.778023</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 13.2 1.085e+01 2.354822 1.2272 1.918794</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 6.6 7.751e+00 -1.151363 1.0683 -1.077718</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 9.3 7.751e+00 1.548637 1.0683 1.449581</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 3.5 5.236e+00 -1.735804 0.9665 -1.795893</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 5.4 5.236e+00 0.164196 0.9665 0.169880</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 118.0 1.013e+02 16.726081 8.1110 2.062142</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 99.8 1.013e+02 -1.473919 8.1110 -0.181718</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 90.2 9.591e+01 -5.708953 7.6864 -0.742730</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 94.6 9.591e+01 -1.308953 7.6864 -0.170294</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 96.1 8.654e+01 9.564450 6.9454 1.377088</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 78.4 8.654e+01 -8.135550 6.9454 -1.171355</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.9 7.206e+01 5.840823 5.8037 1.006405</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.7 7.206e+01 5.640823 5.8037 0.971944</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 56.0 5.562e+01 0.376382 4.5141 0.083379</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 54.7 5.562e+01 -0.923618 4.5141 -0.204607</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.6 3.849e+01 -1.891356 3.1865 -0.593546</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.8 3.849e+01 -1.691356 3.1865 -0.530782</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 22.1 2.105e+01 1.052796 1.8892 0.557274</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 24.7 2.105e+01 3.652796 1.8892 1.933527</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 12.4 1.249e+01 -0.085726 1.3224 -0.064825</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 10.8 1.249e+01 -1.685726 1.3224 -1.274728</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 6.8 7.425e+00 -0.625179 1.0535 -0.593407</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 7.9 7.425e+00 0.474821 1.0535 0.450690</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 1 1.3 1.420e+00 -0.119671 0.8793 -0.136098</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 3.7 3.831e+00 -0.130721 0.9238 -0.141501</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 4.7 3.831e+00 0.869279 0.9238 0.940968</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 8.1 7.307e+00 0.793062 1.0483 0.756531</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 7.9 7.307e+00 0.593062 1.0483 0.565743</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.1 1.060e+01 -0.500946 1.2136 -0.412765</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.3 1.060e+01 -0.300946 1.2136 -0.247970</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 10.7 1.236e+01 -1.663249 1.3151 -1.264727</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 12.2 1.236e+01 -0.163249 1.3151 -0.124134</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 10.7 1.063e+01 0.065269 1.2155 0.053697</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 12.5 1.063e+01 1.865269 1.2155 1.534560</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 9.1 8.134e+00 0.965918 1.0862 0.889243</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 7.4 8.134e+00 -0.734082 1.0862 -0.675811</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 6.1 5.918e+00 0.181998 0.9912 0.183617</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 4.5 5.918e+00 -1.418002 0.9912 -1.430615</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.2 1.013e+02 4.927395 8.1109 0.607501</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.9 1.013e+02 5.627395 8.1109 0.693805</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 107.4 9.362e+01 13.778324 7.5055 1.835758</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 96.1 9.362e+01 2.478324 7.5055 0.330200</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 79.4 8.111e+01 -1.714426 6.5174 -0.263054</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 82.6 8.111e+01 1.485574 6.5174 0.227940</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 63.9 6.406e+01 -0.160919 5.1749 -0.031096</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 62.4 6.406e+01 -1.660919 5.1749 -0.320957</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 51.0 4.811e+01 2.894697 3.9284 0.736859</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 47.1 4.811e+01 -1.005303 3.9284 -0.255905</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.1 3.433e+01 1.766324 2.8695 0.615541</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.6 3.433e+01 2.266324 2.8695 0.789785</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 20.1 1.973e+01 0.371727 1.7967 0.206897</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 19.8 1.973e+01 0.071727 1.7967 0.039922</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 11.3 1.194e+01 -0.639567 1.2900 -0.495771</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 10.7 1.194e+01 -1.239567 1.2900 -0.960871</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 8.2 7.228e+00 0.972496 1.0448 0.930805</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 7.3 7.228e+00 0.072496 1.0448 0.069388</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 0 0.8 2.046e-12 0.800000 0.8720 0.917426</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 1.8 1.802e+00 -0.002337 0.8837 -0.002644</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 2.3 1.802e+00 0.497663 0.8837 0.563136</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.2 4.662e+00 -0.461759 0.9477 -0.487230</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.1 4.662e+00 -0.561759 0.9477 -0.592746</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 6.8 8.261e+00 -1.460846 1.0923 -1.337436</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 10.1 8.261e+00 1.839154 1.0923 1.683785</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 11.4 1.088e+01 0.520066 1.2292 0.423096</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 12.8 1.088e+01 1.920066 1.2292 1.562058</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 11.5 1.143e+01 0.066711 1.2606 0.052919</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 10.6 1.143e+01 -0.833289 1.2606 -0.661009</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 7.5 9.224e+00 -1.723819 1.1401 -1.511997</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 8.6 9.224e+00 -0.623819 1.1401 -0.547165</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 7.3 6.951e+00 0.348894 1.0328 0.337804</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 8.1 6.951e+00 1.148894 1.0328 1.112374</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 5.3 5.028e+00 0.272355 0.9595 0.283849</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 3.8 5.028e+00 -1.227645 0.9595 -1.279452</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 104.7 1.012e+02 3.450870 8.1091 0.425557</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 88.3 1.012e+02 -12.949130 8.1091 -1.596872</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.2 9.787e+01 -3.670543 7.8417 -0.468083</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.6 9.787e+01 -3.270543 7.8417 -0.417073</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 78.1 9.154e+01 -13.439273 7.3409 -1.830749</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 96.5 9.154e+01 4.960727 7.3409 0.675769</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 76.2 8.040e+01 -4.195825 6.4607 -0.649438</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 77.8 8.040e+01 -2.595825 6.4607 -0.401787</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 70.8 6.485e+01 5.950631 5.2368 1.136312</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 67.3 6.485e+01 2.450631 5.2368 0.467964</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 43.1 4.403e+01 -0.927716 3.6126 -0.256803</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 45.1 4.403e+01 1.072284 3.6126 0.296821</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 21.3 2.121e+01 0.085295 1.9010 0.044868</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 23.5 2.121e+01 2.285295 1.9010 1.202136</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 11.8 1.187e+01 -0.069302 1.2859 -0.053892</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 12.1 1.187e+01 0.230698 1.2859 0.179402</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 7.0 6.896e+00 0.104203 1.0305 0.101121</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 6.2 6.896e+00 -0.695797 1.0305 -0.675218</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 0 1.6 4.661e-12 1.600000 0.8720 1.834853</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 1 0.9 6.932e-01 0.206778 0.8737 0.236656</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 3.7 1.958e+00 1.742149 0.8858 1.966684</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 2.0 1.958e+00 0.042149 0.8858 0.047581</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.6 4.056e+00 -0.456030 0.9299 -0.490412</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.8 4.056e+00 -0.256030 0.9299 -0.275333</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 7.1 6.624e+00 0.475608 1.0191 0.466682</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 6.6 6.624e+00 -0.024392 1.0191 -0.023934</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.5 9.013e+00 0.487100 1.1293 0.431311</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.3 9.013e+00 0.287100 1.1293 0.254218</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 8.3 8.710e+00 -0.409941 1.1142 -0.367933</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 9.0 8.710e+00 0.290059 1.1142 0.260335</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 6.6 6.696e+00 -0.095953 1.0221 -0.093880</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 7.7 6.696e+00 1.004047 1.0221 0.982349</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.7 4.803e+00 -1.102994 0.9522 -1.158384</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.5 4.803e+00 -1.302994 0.9522 -1.368427</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 110.4 1.013e+02 9.136362 8.1102 1.126526</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 112.1 1.013e+02 10.836362 8.1102 1.336138</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 93.5 9.462e+01 -1.119415 7.5844 -0.147594</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 91.0 9.462e+01 -3.619415 7.5844 -0.477216</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 71.0 8.313e+01 -12.125525 6.6761 -1.816251</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.7 8.313e+01 6.574475 6.6761 0.984774</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 60.4 6.580e+01 -5.399792 5.3114 -1.016637</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 59.1 6.580e+01 -6.699792 5.3114 -1.261392</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 56.5 4.728e+01 9.217968 3.8645 2.385273</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 47.0 4.728e+01 -0.282032 3.8645 -0.072979</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 30.2 3.077e+01 -0.574817 2.6010 -0.220999</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 23.9 3.077e+01 -6.874817 2.6010 -2.643147</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 17.0 1.796e+01 -0.957722 1.6748 -0.571838</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 18.7 1.796e+01 0.742278 1.6748 0.443201</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.3 1.186e+01 -0.560382 1.2854 -0.435957</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.9 1.186e+01 0.039618 1.2854 0.030821</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 9.0 7.875e+00 1.125373 1.0740 1.047800</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 8.1 7.875e+00 0.225373 1.0740 0.209838</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 0 0.7 7.105e-15 0.700000 0.8720 0.802748</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 3.0 3.133e+00 -0.132776 0.9070 -0.146393</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 2.6 3.133e+00 -0.532776 0.9070 -0.587416</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 5.1 8.401e+00 -3.300544 1.0990 -3.003203</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 7.5 8.401e+00 -0.900544 1.0990 -0.819415</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 16.5 1.580e+01 0.697935 1.5309 0.455905</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 19.0 1.580e+01 3.197935 1.5309 2.088955</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 22.9 2.230e+01 0.604922 1.9779 0.305846</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 23.2 2.230e+01 0.904922 1.9779 0.457525</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 22.2 2.446e+01 -2.255019 2.1336 -1.056917</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 24.4 2.446e+01 -0.055019 2.1336 -0.025787</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 15.5 1.874e+01 -3.242459 1.7285 -1.875916</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 19.8 1.874e+01 1.057541 1.7285 0.611838</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.9 1.352e+01 1.376176 1.3856 0.993173</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.2 1.352e+01 0.676176 1.3856 0.487989</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.9 9.609e+00 1.291013 1.1601 1.112858</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.4 9.609e+00 0.791013 1.1601 0.681856</span> <span class="r-in"><span class="co"># }</span></span> <span class="r-in"></span> </code></pre></div> @@ -475,7 +475,7 @@ saemix authors for the parts inherited from saemix.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/synthetic_data_for_UBA_2014-1.png b/docs/reference/synthetic_data_for_UBA_2014-1.png Binary files differindex 132380a8..8d747ffe 100644 --- a/docs/reference/synthetic_data_for_UBA_2014-1.png +++ b/docs/reference/synthetic_data_for_UBA_2014-1.png diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html index 39a92dd1..e9251de3 100644 --- a/docs/reference/synthetic_data_for_UBA_2014.html +++ b/docs/reference/synthetic_data_for_UBA_2014.html @@ -247,9 +247,9 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-plt img"><img src="synthetic_data_for_UBA_2014-1.png" alt="" width="700" height="433"></span> <span class="r-in"> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.1.0 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Mar 7 13:15:49 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Mar 7 13:15:49 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed May 18 20:42:21 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed May 18 20:42:21 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> @@ -258,7 +258,7 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 833 model solutions performed in 0.624 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 830 model solutions performed in 1.716 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -310,15 +310,15 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> log_k_M2 2.819e-02 7.166e-02 -3.929e-01 1.000e+00 -2.658e-01</span> <span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -4.624e-01 -5.682e-01 7.478e-01 -2.658e-01 1.000e+00</span> <span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 1.614e-01 4.102e-01 -8.109e-01 5.419e-01 -8.605e-01</span> -<span class="r-out co"><span class="r-pr">#></span> sigma -2.900e-08 -8.030e-09 -2.741e-08 3.938e-08 -2.681e-08</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.063e-07 -1.980e-07 1.088e-07 1.041e-07 7.820e-09</span> <span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis sigma</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 1.614e-01 -2.900e-08</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent 4.102e-01 -8.030e-09</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M1 -8.109e-01 -2.741e-08</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M2 5.419e-01 3.938e-08</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -8.605e-01 -2.681e-08</span> -<span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 1.000e+00 4.971e-08</span> -<span class="r-out co"><span class="r-pr">#></span> sigma 4.971e-08 1.000e+00</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.614e-01 2.063e-07</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent 4.102e-01 -1.980e-07</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M1 -8.109e-01 1.088e-07</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M2 5.419e-01 1.041e-07</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -8.605e-01 7.820e-09</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 1.000e+00 -6.495e-08</span> +<span class="r-out co"><span class="r-pr">#></span> sigma -6.495e-08 1.000e+00</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> Confidence intervals for internally transformed parameters are asymmetric.</span> @@ -355,8 +355,8 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Data:</span> <span class="r-out co"><span class="r-pr">#></span> time variable observed predicted residual</span> -<span class="r-out co"><span class="r-pr">#></span> 0 parent 101.5 1.021e+02 -0.56248</span> -<span class="r-out co"><span class="r-pr">#></span> 0 parent 101.2 1.021e+02 -0.86248</span> +<span class="r-out co"><span class="r-pr">#></span> 0 parent 101.5 1.021e+02 -0.56249</span> +<span class="r-out co"><span class="r-pr">#></span> 0 parent 101.2 1.021e+02 -0.86249</span> <span class="r-out co"><span class="r-pr">#></span> 1 parent 53.9 4.873e+01 5.17118</span> <span class="r-out co"><span class="r-pr">#></span> 1 parent 47.5 4.873e+01 -1.22882</span> <span class="r-out co"><span class="r-pr">#></span> 3 parent 10.4 1.111e+01 -0.70773</span> @@ -365,8 +365,8 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> 7 parent 0.3 5.772e-01 -0.27717</span> <span class="r-out co"><span class="r-pr">#></span> 14 parent 3.5 3.264e-03 3.49674</span> <span class="r-out co"><span class="r-pr">#></span> 28 parent 3.2 1.045e-07 3.20000</span> -<span class="r-out co"><span class="r-pr">#></span> 90 parent 0.6 9.530e-10 0.60000</span> -<span class="r-out co"><span class="r-pr">#></span> 120 parent 3.5 -5.940e-10 3.50000</span> +<span class="r-out co"><span class="r-pr">#></span> 90 parent 0.6 9.534e-10 0.60000</span> +<span class="r-out co"><span class="r-pr">#></span> 120 parent 3.5 -5.941e-10 3.50000</span> <span class="r-out co"><span class="r-pr">#></span> 1 M1 36.4 3.479e+01 1.61088</span> <span class="r-out co"><span class="r-pr">#></span> 1 M1 37.4 3.479e+01 2.61088</span> <span class="r-out co"><span class="r-pr">#></span> 3 M1 34.3 3.937e+01 -5.07027</span> @@ -376,9 +376,9 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> 14 M1 5.8 1.995e+00 3.80469</span> <span class="r-out co"><span class="r-pr">#></span> 14 M1 1.2 1.995e+00 -0.79531</span> <span class="r-out co"><span class="r-pr">#></span> 60 M1 0.5 2.111e-06 0.50000</span> -<span class="r-out co"><span class="r-pr">#></span> 90 M1 3.2 -9.670e-10 3.20000</span> -<span class="r-out co"><span class="r-pr">#></span> 120 M1 1.5 7.670e-10 1.50000</span> -<span class="r-out co"><span class="r-pr">#></span> 120 M1 0.6 7.670e-10 0.60000</span> +<span class="r-out co"><span class="r-pr">#></span> 90 M1 3.2 -9.675e-10 3.20000</span> +<span class="r-out co"><span class="r-pr">#></span> 120 M1 1.5 7.671e-10 1.50000</span> +<span class="r-out co"><span class="r-pr">#></span> 120 M1 0.6 7.671e-10 0.60000</span> <span class="r-out co"><span class="r-pr">#></span> 1 M2 4.8 4.455e+00 0.34517</span> <span class="r-out co"><span class="r-pr">#></span> 3 M2 20.9 2.153e+01 -0.62527</span> <span class="r-out co"><span class="r-pr">#></span> 3 M2 19.3 2.153e+01 -2.22527</span> @@ -409,7 +409,7 @@ Compare also the code in the example section to see the degradation models."><!- </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 95e8c6b6..2da09efe 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -288,7 +288,7 @@ This is no problem for the internal use in <a href="mkinfit.html">mkinfit</a>.</ </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html index ff175937..48bf1d7f 100644 --- a/docs/reference/update.mkinfit.html +++ b/docs/reference/update.mkinfit.html @@ -115,7 +115,7 @@ remove arguments given in the original call</p></dd> <span class="r-in"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span class="r-in"><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> <span class="r-out co"><span class="r-pr">#></span> parent_0 k_parent sigma </span> -<span class="r-out co"><span class="r-pr">#></span> 99.44423885 0.09793574 3.39632469 </span> +<span class="r-out co"><span class="r-pr">#></span> 99.44423886 0.09793574 3.39632469 </span> <span class="r-in"><span class="fu"><a href="plot.mkinfit.html">plot_err</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span> <span class="r-plt img"><img src="update.mkinfit-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">fit</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> @@ -139,7 +139,7 @@ remove arguments given in the original call</p></dd> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> </div> </footer></div> |
