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| author | Ranke Johannes <johannes.ranke@agroscope.admin.ch> | 2023-10-30 17:09:21 +0100 |
|---|---|---|
| committer | Ranke Johannes <johannes.ranke@agroscope.admin.ch> | 2023-10-30 17:09:21 +0100 |
| commit | b7901aac76df753ec1213cb02bebea055965ee87 (patch) | |
| tree | e907e87d81aa07f19e8387acca612026337add75 /docs/articles | |
| parent | 193b46af027c7b30abf7cf215d77517370e5fb2c (diff) | |
Update static docs
Diffstat (limited to 'docs/articles')
72 files changed, 642 insertions, 716 deletions
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 19367c68..303ddb6f 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -74,6 +74,9 @@ <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> + <a href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -135,7 +138,7 @@ D</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change 31 January 2019 -(rebuilt 2023-05-19)</h4> +(rebuilt 2023-10-30)</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> @@ -237,10 +240,10 @@ the <code>mkinparplot</code> function.</p> <code>summary</code> method for <code>mkinfit</code> objects.</p> <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.4 </span></span> -<span><span class="co">## R version used for fitting: 4.3.0 </span></span> -<span><span class="co">## Date of fit: Fri May 19 09:20:23 2023 </span></span> -<span><span class="co">## Date of summary: Fri May 19 09:20:23 2023 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.6 </span></span> +<span><span class="co">## R version used for fitting: 4.3.1 </span></span> +<span><span class="co">## Date of fit: Mon Oct 30 09:40:58 2023 </span></span> +<span><span class="co">## Date of summary: Mon Oct 30 09:40:58 2023 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - k_parent * parent</span></span> @@ -248,7 +251,7 @@ the <code>mkinparplot</code> function.</p> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 401 model solutions performed in 0.048 s</span></span> +<span><span class="co">## Fitted using 401 model solutions performed in 0.123 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> diff --git a/docs/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/articles/FOCUS_D_files/figure-html/plot-1.png Binary files differindex c0832a1a..f0b51c1f 100644 --- a/docs/articles/FOCUS_D_files/figure-html/plot-1.png +++ b/docs/articles/FOCUS_D_files/figure-html/plot-1.png diff --git a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png Binary files differindex 02cfcfb4..f6180470 100644 --- a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png +++ b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png diff --git a/docs/articles/prebuilt/2022_cyan_pathway.html b/docs/articles/prebuilt/2022_cyan_pathway.html index c22c6735..c22b07e4 100644 --- a/docs/articles/prebuilt/2022_cyan_pathway.html +++ b/docs/articles/prebuilt/2022_cyan_pathway.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -74,6 +74,9 @@ <a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> + <a href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -135,7 +138,7 @@ residue data on cyantraniliprole</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change on 20 April 2023, -last compiled on 19 Mai 2023</h4> +last compiled on 30 October 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_cyan_pathway.rmd" class="external-link"><code>vignettes/prebuilt/2022_cyan_pathway.rmd</code></a></small> <div class="hidden name"><code>2022_cyan_pathway.rmd</code></div> @@ -155,7 +158,7 @@ be fitted with the mkin package.</p> 173340 (Application of nonlinear hierarchical models to the kinetic evaluation of chemical degradation data) of the German Environment Agency carried out in 2022 and 2023.</p> -<p>The mkin package is used in version 1.2.4 which is currently under +<p>The mkin package is used in version 1.2.6 which is currently under development. The newly introduced functionality that is used here is a simplification of excluding random effects for a set of fits based on a related set of fits with a reduced model, and the documentation of the @@ -2205,10 +2208,10 @@ Hierarchical SFO path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:27:54 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 10:03:13 2023 +Date of summary: Mon Oct 30 11:18:26 2023 Equations: d_cyan/dt = - k_cyan * cyan @@ -2221,7 +2224,7 @@ Data: Model predictions using solution type deSolve -Fitted in 422.743 s +Fitted in 1273.632 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2333,10 +2336,10 @@ Hierarchical SFO path 1 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:27:49 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 09:58:51 2023 +Date of summary: Mon Oct 30 11:18:26 2023 Equations: d_cyan/dt = - k_cyan * cyan @@ -2349,7 +2352,7 @@ Data: Model predictions using solution type deSolve -Fitted in 417.436 s +Fitted in 1011.299 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -2463,10 +2466,10 @@ Hierarchical FOMC path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:28:29 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 10:04:48 2023 +Date of summary: Mon Oct 30 11:18:26 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -2481,7 +2484,7 @@ Data: Model predictions using solution type deSolve -Fitted in 457.122 s +Fitted in 1368.338 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2608,10 +2611,10 @@ Hierarchical FOMC path 1 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:28:21 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 10:00:40 2023 +Date of summary: Mon Oct 30 11:18:26 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -2626,7 +2629,7 @@ Data: Model predictions using solution type deSolve -Fitted in 449.531 s +Fitted in 1120.168 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -2746,10 +2749,10 @@ Hierarchical DFOP path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:29:15 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 10:02:52 2023 +Date of summary: Mon Oct 30 11:18:26 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -2768,7 +2771,7 @@ Data: Model predictions using solution type deSolve -Fitted in 503.737 s +Fitted in 1252.502 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2892,10 +2895,10 @@ Hierarchical DFOP path 1 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:31:24 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 10:12:10 2023 +Date of summary: Mon Oct 30 11:18:26 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -2914,7 +2917,7 @@ Data: Model predictions using solution type deSolve -Fitted in 632.55 s +Fitted in 1809.832 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3038,10 +3041,10 @@ Hierarchical SFORB path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:29:23 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 10:02:30 2023 +Date of summary: Mon Oct 30 11:18:26 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3059,7 +3062,7 @@ Data: Model predictions using solution type deSolve -Fitted in 511.715 s +Fitted in 1230.946 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -3203,10 +3206,10 @@ Hierarchical SFORB path 1 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:31:23 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 10:09:13 2023 +Date of summary: Mon Oct 30 11:18:26 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3224,7 +3227,7 @@ Data: Model predictions using solution type deSolve -Fitted in 630.627 s +Fitted in 1633.433 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3368,143 +3371,15 @@ Hierarchical HS path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:28:57 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 10:02:52 2023 +Date of summary: Mon Oct 30 11:18:27 2023 Equations: -d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan -d_JCZ38/dt = + f_cyan_to_JCZ38 * ifelse(time <= tb, k1, k2) * cyan - - k_JCZ38 * JCZ38 -d_J9Z38/dt = + f_cyan_to_J9Z38 * ifelse(time <= tb, k1, k2) * cyan - - k_J9Z38 * J9Z38 -d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 - -Data: -433 observations of 4 variable(s) grouped in 5 datasets - -Model predictions using solution type deSolve - -Fitted in 485.304 s -Using 300, 100 iterations and 10 chains - -Variance model: Constant variance - -Starting values for degradation parameters: - cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 - 102.8845 -3.4495 -4.9355 -5.6040 0.6468 - f_cyan_ilr_2 f_JCZ38_qlogis log_k1 log_k2 log_tb - 1.2396 9.7220 -2.9079 -4.1810 1.7813 - -Fixed degradation parameter values: -None - -Starting values for random effects (square root of initial entries in omega): - cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 -cyan_0 5.406 0.00 0.00 0.000 0.0000 -log_k_JCZ38 0.000 2.33 0.00 0.000 0.0000 -log_k_J9Z38 0.000 0.00 1.59 0.000 0.0000 -log_k_JSE76 0.000 0.00 0.00 1.013 0.0000 -f_cyan_ilr_1 0.000 0.00 0.00 0.000 0.6367 -f_cyan_ilr_2 0.000 0.00 0.00 0.000 0.0000 -f_JCZ38_qlogis 0.000 0.00 0.00 0.000 0.0000 -log_k1 0.000 0.00 0.00 0.000 0.0000 -log_k2 0.000 0.00 0.00 0.000 0.0000 -log_tb 0.000 0.00 0.00 0.000 0.0000 - f_cyan_ilr_2 f_JCZ38_qlogis log_k1 log_k2 log_tb -cyan_0 0.000 0.00 0.0000 0.0000 0.0000 -log_k_JCZ38 0.000 0.00 0.0000 0.0000 0.0000 -log_k_J9Z38 0.000 0.00 0.0000 0.0000 0.0000 -log_k_JSE76 0.000 0.00 0.0000 0.0000 0.0000 -f_cyan_ilr_1 0.000 0.00 0.0000 0.0000 0.0000 -f_cyan_ilr_2 2.038 0.00 0.0000 0.0000 0.0000 -f_JCZ38_qlogis 0.000 10.33 0.0000 0.0000 0.0000 -log_k1 0.000 0.00 0.7006 0.0000 0.0000 -log_k2 0.000 0.00 0.0000 0.8928 0.0000 -log_tb 0.000 0.00 0.0000 0.0000 0.6773 - -Starting values for error model parameters: -a.1 - 1 - -Results: - -Likelihood computed by importance sampling - AIC BIC logLik - 2427 2419 -1194 - -Optimised parameters: - est. lower upper -cyan_0 101.9660 1.005e+02 1.035e+02 -log_k_JCZ38 -3.4698 -4.716e+00 -2.224e+00 -log_k_J9Z38 -5.0947 -5.740e+00 -4.450e+00 -log_k_JSE76 -5.5977 -6.321e+00 -4.875e+00 -f_cyan_ilr_1 0.6595 3.734e-01 9.456e-01 -f_cyan_ilr_2 0.5905 1.664e-01 1.015e+00 -f_JCZ38_qlogis 25.8627 -4.224e+05 4.225e+05 -log_k1 -3.0884 -3.453e+00 -2.723e+00 -log_k2 -4.3877 -4.778e+00 -3.998e+00 -log_tb 2.3057 1.715e+00 2.896e+00 -a.1 3.3228 NA NA -SD.log_k_JCZ38 1.4071 NA NA -SD.log_k_J9Z38 0.5774 NA NA -SD.log_k_JSE76 0.6214 NA NA -SD.f_cyan_ilr_1 0.3058 NA NA -SD.f_cyan_ilr_2 0.3470 NA NA -SD.f_JCZ38_qlogis 0.0644 NA NA -SD.log_k1 0.3994 NA NA -SD.log_k2 0.4373 NA NA -SD.log_tb 0.6419 NA NA - -Correlation is not available - -Random effects: - est. lower upper -SD.log_k_JCZ38 1.4071 NA NA -SD.log_k_J9Z38 0.5774 NA NA -SD.log_k_JSE76 0.6214 NA NA -SD.f_cyan_ilr_1 0.3058 NA NA -SD.f_cyan_ilr_2 0.3470 NA NA -SD.f_JCZ38_qlogis 0.0644 NA NA -SD.log_k1 0.3994 NA NA -SD.log_k2 0.4373 NA NA -SD.log_tb 0.6419 NA NA - -Variance model: - est. lower upper -a.1 3.323 NA NA - -Backtransformed parameters: - est. lower upper -cyan_0 1.020e+02 1.005e+02 1.035e+02 -k_JCZ38 3.112e-02 8.951e-03 1.082e-01 -k_J9Z38 6.129e-03 3.216e-03 1.168e-02 -k_JSE76 3.706e-03 1.798e-03 7.639e-03 -f_cyan_to_JCZ38 5.890e-01 NA NA -f_cyan_to_J9Z38 2.318e-01 NA NA -f_JCZ38_to_JSE76 1.000e+00 0.000e+00 1.000e+00 -k1 4.558e-02 3.164e-02 6.565e-02 -k2 1.243e-02 8.417e-03 1.835e-02 -tb 1.003e+01 5.557e+00 1.811e+01 - -Resulting formation fractions: - ff -cyan_JCZ38 5.890e-01 -cyan_J9Z38 2.318e-01 -cyan_sink 1.793e-01 -JCZ38_JSE76 1.000e+00 -JCZ38_sink 5.861e-12 - -Estimated disappearance times: - DT50 DT90 DT50back DT50_k1 DT50_k2 -cyan 29.02 158.51 47.72 15.21 55.77 -JCZ38 22.27 73.98 NA NA NA -J9Z38 113.09 375.69 NA NA NA -JSE76 187.01 621.23 NA NA NA - -</code></pre> -<p></p> +d_cyan/dt = - ifelse(time +<p></p></code> +</pre> </div> <div class="section level4"> <h4 id="pathway-2">Pathway 2<a class="anchor" aria-label="anchor" href="#pathway-2"></a> @@ -3514,10 +3389,10 @@ Hierarchical FOMC path 2 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:39:30 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 10:32:26 2023 +Date of summary: Mon Oct 30 11:18:27 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -3532,7 +3407,7 @@ Data: Model predictions using solution type deSolve -Fitted in 474.942 s +Fitted in 1185.728 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3680,10 +3555,10 @@ Hierarchical DFOP path 2 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:40:29 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 10:34:49 2023 +Date of summary: Mon Oct 30 11:18:27 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -3703,7 +3578,7 @@ Data: Model predictions using solution type deSolve -Fitted in 533.901 s +Fitted in 1329.843 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -3871,10 +3746,10 @@ Hierarchical DFOP path 2 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:43:04 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 10:41:05 2023 +Date of summary: Mon Oct 30 11:18:27 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -3894,7 +3769,7 @@ Data: Model predictions using solution type deSolve -Fitted in 688.913 s +Fitted in 1705.043 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4062,10 +3937,10 @@ Hierarchical SFORB path 2 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:40:32 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 10:35:39 2023 +Date of summary: Mon Oct 30 11:18:27 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4083,7 +3958,7 @@ Data: Model predictions using solution type deSolve -Fitted in 536.94 s +Fitted in 1379.466 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -4258,10 +4133,10 @@ Hierarchical SFORB path 2 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:42:47 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 10:41:39 2023 +Date of summary: Mon Oct 30 11:18:27 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4279,7 +4154,7 @@ Data: Model predictions using solution type deSolve -Fitted in 671.849 s +Fitted in 1739.402 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4459,10 +4334,10 @@ error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:55:35 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 11:12:56 2023 +Date of summary: Mon Oct 30 11:18:27 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -4477,7 +4352,7 @@ Data: Model predictions using solution type deSolve -Fitted in 748.54 s +Fitted in 1872.856 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4602,10 +4477,10 @@ variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:57:10 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 11:17:06 2023 +Date of summary: Mon Oct 30 11:18:27 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4625,7 +4500,7 @@ Data: Model predictions using solution type deSolve -Fitted in 843.793 s +Fitted in 2122.961 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -4702,12 +4577,12 @@ f_JSE76_qlogis 1.9658 NA NA log_k1 -1.9503 NA NA log_k2 -4.4745 NA NA g_qlogis -0.4967 NA NA -a.1 2.7461 2.59274 2.8994 +a.1 2.7461 2.59886 2.8932 SD.log_k_JCZ38 1.3178 0.47602 2.1596 SD.log_k_J9Z38 0.7022 0.15061 1.2538 -SD.log_k_JSE76 0.6566 0.15613 1.1570 +SD.log_k_JSE76 0.6566 0.15614 1.1570 SD.f_cyan_ilr_1 0.3409 0.11666 0.5652 -SD.f_cyan_ilr_2 0.4385 0.09482 0.7821 +SD.f_cyan_ilr_2 0.4385 0.09483 0.7821 SD.log_k1 0.7381 0.25599 1.2202 SD.log_k2 0.5133 0.18152 0.8450 SD.g_qlogis 0.9866 0.35681 1.6164 @@ -4718,16 +4593,16 @@ Random effects: est. lower upper SD.log_k_JCZ38 1.3178 0.47602 2.1596 SD.log_k_J9Z38 0.7022 0.15061 1.2538 -SD.log_k_JSE76 0.6566 0.15613 1.1570 +SD.log_k_JSE76 0.6566 0.15614 1.1570 SD.f_cyan_ilr_1 0.3409 0.11666 0.5652 -SD.f_cyan_ilr_2 0.4385 0.09482 0.7821 +SD.f_cyan_ilr_2 0.4385 0.09483 0.7821 SD.log_k1 0.7381 0.25599 1.2202 SD.log_k2 0.5133 0.18152 0.8450 SD.g_qlogis 0.9866 0.35681 1.6164 Variance model: est. lower upper -a.1 2.746 2.593 2.899 +a.1 2.746 2.599 2.893 Backtransformed parameters: est. lower upper @@ -4768,10 +4643,10 @@ error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:57:32 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 11:17:59 2023 +Date of summary: Mon Oct 30 11:18:27 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4791,7 +4666,7 @@ Data: Model predictions using solution type deSolve -Fitted in 865.636 s +Fitted in 2175.807 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4934,10 +4809,10 @@ variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:57:01 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 11:17:04 2023 +Date of summary: Mon Oct 30 11:18:27 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4955,7 +4830,7 @@ Data: Model predictions using solution type deSolve -Fitted in 834.906 s +Fitted in 2121.218 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -5105,10 +4980,10 @@ error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.3.0 -Date of fit: Fri May 19 09:57:17 2023 -Date of summary: Fri May 19 09:57:33 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 11:18:24 2023 +Date of summary: Mon Oct 30 11:18:27 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -5126,7 +5001,7 @@ Data: Model predictions using solution type deSolve -Fitted in 850.751 s +Fitted in 2200.603 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -5275,23 +5150,23 @@ JSE76 25.44 84.51 NA NA NA <div class="section level3"> <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h3> -<pre><code>R version 4.3.0 Patched (2023-05-18 r84448) +<pre><code>R version 4.3.1 (2023-06-16) Platform: x86_64-pc-linux-gnu (64-bit) -Running under: Debian GNU/Linux 12 (bookworm) +Running under: Ubuntu 22.04.3 LTS Matrix products: default -BLAS: /home/jranke/svn/R/r-patched/build/lib/libRblas.so -LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/liblapack.so.3; LAPACK version 3.11.0 +BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 +LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 locale: - [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C - [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 - [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 - [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C + [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C + [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 + [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 + [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C -[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C +[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C -time zone: Europe/Berlin +time zone: Europe/Zurich tzcode source: system (glibc) attached base packages: @@ -5299,32 +5174,32 @@ attached base packages: [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.4 +[1] saemix_3.2 npde_3.3 knitr_1.44 mkin_1.2.6 loaded via a namespace (and not attached): - [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 - [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 - [9] grid_4.3.0 fastmap_1.1.1 cellranger_1.1.0 rprojroot_2.0.3 -[13] jsonlite_1.8.4 processx_3.8.1 pkgbuild_1.4.0 deSolve_1.35 -[17] DBI_1.1.3 mclust_6.0.0 ps_1.7.5 gridExtra_2.3 -[21] purrr_1.0.1 fansi_1.0.4 scales_1.2.1 codetools_0.2-19 -[25] textshaping_0.3.6 jquerylib_0.1.4 cli_3.6.1 crayon_1.5.2 -[29] rlang_1.1.1 munsell_0.5.0 cachem_1.0.8 yaml_2.3.7 -[33] inline_0.3.19 tools_4.3.0 memoise_2.0.1 dplyr_1.1.2 -[37] colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.2 R6_2.5.1 -[41] zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 fs_1.6.2 + [1] sass_0.4.7 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 + [5] lattice_0.21-9 digest_0.6.33 magrittr_2.0.3 evaluate_0.22 + [9] grid_4.3.1 fastmap_1.1.1 cellranger_1.1.0 rprojroot_2.0.3 +[13] jsonlite_1.8.7 processx_3.8.2 pkgbuild_1.4.2 deSolve_1.35 +[17] mclust_6.0.0 ps_1.7.5 gridExtra_2.3 purrr_1.0.1 +[21] fansi_1.0.4 scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 +[25] jquerylib_0.1.4 cli_3.6.1 crayon_1.5.2 rlang_1.1.1 +[29] munsell_0.5.0 cachem_1.0.8 yaml_2.3.7 inline_0.3.19 +[33] tools_4.3.1 memoise_2.0.1 dplyr_1.1.2 colorspace_2.1-0 +[37] ggplot2_3.4.2 vctrs_0.6.3 R6_2.5.1 zoo_1.8-12 +[41] lifecycle_1.0.3 stringr_1.5.0 fs_1.6.3 MASS_7.3-60 [45] ragg_1.2.5 callr_3.7.3 pkgconfig_2.0.3 desc_1.4.2 -[49] pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 gtable_0.3.3 -[53] glue_1.6.2 systemfonts_1.0.4 highr_0.10 xfun_0.39 -[57] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5 -[61] nlme_3.1-162 rmarkdown_2.21 compiler_4.3.0 prettyunits_1.1.1 +[49] pkgdown_2.0.7 bslib_0.5.1 pillar_1.9.0 gtable_0.3.3 +[53] glue_1.6.2 systemfonts_1.0.4 xfun_0.40 tibble_3.2.1 +[57] lmtest_0.9-40 tidyselect_1.2.0 rstudioapi_0.15.0 htmltools_0.5.6.1 +[61] nlme_3.1-163 rmarkdown_2.23 compiler_4.3.1 prettyunits_1.2.0 [65] readxl_1.4.2 </code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> </h3> -<pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> -<pre><code>MemTotal: 64925476 kB</code></pre> +<pre><code>CPU model: Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</code></pre> +<pre><code>MemTotal: 247605564 kB</code></pre> </div> </div> </div> diff --git a/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-13-1.png b/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-13-1.png Binary files differindex b3d6066b..50f17cf4 100644 --- a/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-13-1.png +++ b/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-13-1.png diff --git 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2da41981..9fdf75f7 100644 --- a/docs/articles/prebuilt/2022_dmta_parent.html +++ b/docs/articles/prebuilt/2022_dmta_parent.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -74,6 +74,9 @@ <a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> + <a href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -135,7 +138,7 @@ with residue data on dimethenamid and dimethenamid-P</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change on 5 January -2023, last compiled on 19 Mai 2023</h4> +2023, last compiled on 30 October 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_dmta_parent.rmd" class="external-link"><code>vignettes/prebuilt/2022_dmta_parent.rmd</code></a></small> <div class="hidden name"><code>2022_dmta_parent.rmd</code></div> @@ -154,7 +157,7 @@ FOMC, DFOP and HS can be fitted with the mkin package.</p> 173340 (Application of nonlinear hierarchical models to the kinetic evaluation of chemical degradation data) of the German Environment Agency carried out in 2022 and 2023.</p> -<p>The mkin package is used in version 1.2.4. It contains the test data +<p>The mkin package is used in version 1.2.6. It contains the test data and the functions used in the evaluations. The <code>saemix</code> package is used as a backend for fitting the NLHM, but is also loaded to make the convergence plot function available.</p> @@ -1005,7 +1008,7 @@ updated assuming two-component error.</p> <td align="left">DFOP</td> <td align="left">OK</td> <td align="left">OK</td> -<td align="left">C</td> +<td align="left">OK</td> <td align="left">OK</td> <td align="left">C</td> <td align="left">OK</td> @@ -1013,7 +1016,7 @@ updated assuming two-component error.</p> <tr class="even"> <td align="left">HS</td> <td align="left">OK</td> -<td align="left">C</td> +<td align="left">OK</td> <td align="left">OK</td> <td align="left">OK</td> <td align="left">OK</td> @@ -1111,9 +1114,9 @@ the best fits.</p> <tr class="even"> <td align="left">FOMC tc</td> <td align="right">8</td> -<td align="right">720.4</td> -<td align="right">718.8</td> -<td align="right">-352.2</td> +<td align="right">720.7</td> +<td align="right">719.1</td> +<td align="right">-352.4</td> </tr> <tr class="odd"> <td align="left">DFOP const</td> @@ -1132,9 +1135,9 @@ the best fits.</p> <tr class="odd"> <td align="left">DFOP tc</td> <td align="right">10</td> -<td align="right">665.5</td> -<td align="right">663.4</td> -<td align="right">-322.8</td> +<td align="right">665.7</td> +<td align="right">663.6</td> +<td align="right">-322.9</td> </tr> <tr class="even"> <td align="left">HS tc</td> @@ -1215,12 +1218,12 @@ achieved with the argument <code>test = TRUE</code> to the <span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>format.args <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>digits <span class="op">=</span> <span class="fl">4</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <table class="table"> <colgroup> -<col width="37%"> -<col width="6%"> +<col width="38%"> +<col width="7%"> <col width="8%"> <col width="8%"> <col width="9%"> -<col width="9%"> +<col width="8%"> <col width="4%"> <col width="15%"> </colgroup> @@ -1238,8 +1241,8 @@ achieved with the argument <code>test = TRUE</code> to the <tr class="odd"> <td align="left">f_saem_dfop_tc_no_ranef_k2</td> <td align="right">9</td> -<td align="right">663.8</td> -<td align="right">661.9</td> +<td align="right">663.7</td> +<td align="right">661.8</td> <td align="right">-322.9</td> <td align="right">NA</td> <td align="right">NA</td> @@ -1248,12 +1251,12 @@ achieved with the argument <code>test = TRUE</code> to the <tr class="even"> <td align="left">f_saem[[“DFOP”, “tc”]]</td> <td align="right">10</td> -<td align="right">665.5</td> -<td align="right">663.4</td> -<td align="right">-322.8</td> -<td align="right">0.2809</td> +<td align="right">665.7</td> +<td align="right">663.6</td> +<td align="right">-322.9</td> +<td align="right">0</td> +<td align="right">1</td> <td align="right">1</td> -<td align="right">0.5961</td> </tr> </tbody> </table> @@ -1286,10 +1289,10 @@ Plot of the final NLHM DFOP fit <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_tc_no_ranef_k2</span><span class="op">)</span></span></code></pre></div> <pre><code>saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 14:07:09 2023 -Date of summary: Thu Apr 20 14:07:10 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 11:19:13 2023 +Date of summary: Mon Oct 30 11:19:14 2023 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -1301,21 +1304,21 @@ Data: Model predictions using solution type analytical -Fitted in 4.175 s +Fitted in 8.975 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function Starting values for degradation parameters: - DMTA_0 k1 k2 g -98.759266 0.087034 0.009933 0.930827 + DMTA_0 k1 k2 g +98.71186 0.08675 0.01374 0.93491 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): DMTA_0 k1 k2 g -DMTA_0 98.76 0 0 0 +DMTA_0 98.71 0 0 0 k1 0.00 1 0 0 k2 0.00 0 1 0 g 0.00 0 0 1 @@ -1328,40 +1331,40 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 663.8 661.9 -322.9 + 663.7 661.8 -322.9 Optimised parameters: est. lower upper -DMTA_0 98.228939 96.285869 100.17201 -k1 0.064063 0.033477 0.09465 -k2 0.008297 0.005824 0.01077 -g 0.953821 0.914328 0.99331 -a.1 1.068479 0.869538 1.26742 -b.1 0.029424 0.022406 0.03644 -SD.DMTA_0 2.030437 0.404824 3.65605 -SD.k1 0.594692 0.256660 0.93272 -SD.g 1.006754 0.361327 1.65218 +DMTA_0 98.256267 96.286112 100.22642 +k1 0.064037 0.033281 0.09479 +k2 0.008469 0.006002 0.01094 +g 0.954167 0.914460 0.99387 +a.1 1.061795 0.863943 1.25965 +b.1 0.029550 0.022529 0.03657 +SD.DMTA_0 2.068581 0.427706 3.70946 +SD.k1 0.598285 0.258235 0.93833 +SD.g 1.016689 0.360057 1.67332 Correlation: DMTA_0 k1 k2 -k1 0.0218 -k2 0.0556 0.0355 -g -0.0516 -0.0284 -0.2800 +k1 0.0213 +k2 0.0541 0.0344 +g -0.0521 -0.0286 -0.2744 Random effects: est. lower upper -SD.DMTA_0 2.0304 0.4048 3.6560 -SD.k1 0.5947 0.2567 0.9327 -SD.g 1.0068 0.3613 1.6522 +SD.DMTA_0 2.0686 0.4277 3.7095 +SD.k1 0.5983 0.2582 0.9383 +SD.g 1.0167 0.3601 1.6733 Variance model: est. lower upper -a.1 1.06848 0.86954 1.26742 -b.1 0.02942 0.02241 0.03644 +a.1 1.06180 0.86394 1.25965 +b.1 0.02955 0.02253 0.03657 Estimated disappearance times: - DT50 DT90 DT50back DT50_k1 DT50_k2 -DMTA 11.45 41.4 12.46 10.82 83.54</code></pre> + DT50 DT90 DT50back DT50_k1 DT50_k2 +DMTA 11.45 41.32 12.44 10.82 81.85</code></pre> </div> <div class="section level3"> <h3 id="alternative-check-of-parameter-identifiability">Alternative check of parameter identifiability<a class="anchor" aria-label="anchor" href="#alternative-check-of-parameter-identifiability"></a> @@ -1462,10 +1465,10 @@ Hierarchical mkin fit of the SFO model with error model const </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 14:07:02 2023 -Date of summary: Thu Apr 20 14:08:16 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 11:18:56 2023 +Date of summary: Mon Oct 30 11:21:30 2023 Equations: d_DMTA/dt = - k_DMTA * DMTA @@ -1475,7 +1478,7 @@ Data: Model predictions using solution type analytical -Fitted in 0.982 s +Fitted in 1.899 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1534,10 +1537,10 @@ Hierarchical mkin fit of the SFO model with error model tc </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 14:07:03 2023 -Date of summary: Thu Apr 20 14:08:16 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 11:19:00 2023 +Date of summary: Mon Oct 30 11:21:30 2023 Equations: d_DMTA/dt = - k_DMTA * DMTA @@ -1547,7 +1550,7 @@ Data: Model predictions using solution type analytical -Fitted in 2.398 s +Fitted in 5.364 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1608,10 +1611,10 @@ Hierarchical mkin fit of the FOMC model with error model const </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 14:07:02 2023 -Date of summary: Thu Apr 20 14:08:16 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 11:18:57 2023 +Date of summary: Mon Oct 30 11:21:30 2023 Equations: d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA @@ -1621,7 +1624,7 @@ Data: Model predictions using solution type analytical -Fitted in 1.398 s +Fitted in 2.944 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1653,7 +1656,7 @@ Optimised parameters: est. lower upper DMTA_0 98.3435 96.9033 99.784 alpha 7.2007 2.5889 11.812 -beta 112.8746 34.8816 190.868 +beta 112.8745 34.8816 190.867 a.1 2.0459 1.8054 2.286 SD.DMTA_0 1.4795 0.2717 2.687 SD.alpha 0.6396 0.1509 1.128 @@ -1685,10 +1688,10 @@ Hierarchical mkin fit of the FOMC model with error model tc </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 14:07:04 2023 -Date of summary: Thu Apr 20 14:08:16 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 11:19:01 2023 +Date of summary: Mon Oct 30 11:21:30 2023 Equations: d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA @@ -1698,7 +1701,7 @@ Data: Model predictions using solution type analytical -Fitted in 3.044 s +Fitted in 6.228 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1724,38 +1727,38 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 720.4 718.8 -352.2 + 720.7 719.1 -352.4 Optimised parameters: est. lower upper -DMTA_0 98.99136 97.26011 100.72261 -alpha 5.86312 2.57485 9.15138 -beta 88.55571 29.20889 147.90254 -a.1 1.51063 1.24384 1.77741 -b.1 0.02824 0.02040 0.03609 -SD.DMTA_0 1.57436 -0.04867 3.19739 -SD.alpha 0.59871 0.17132 1.02611 -SD.beta 0.72994 0.22849 1.23139 +DMTA_0 99.10577 97.33296 100.87859 +alpha 5.46260 2.52199 8.40321 +beta 81.66080 30.46664 132.85497 +a.1 1.50219 1.23601 1.76836 +b.1 0.02893 0.02099 0.03687 +SD.DMTA_0 1.61887 -0.03636 3.27411 +SD.alpha 0.58145 0.17364 0.98925 +SD.beta 0.68205 0.21108 1.15303 Correlation: DMTA_0 alpha -alpha -0.1363 -beta -0.1414 0.2542 +alpha -0.1321 +beta -0.1430 0.2467 Random effects: - est. lower upper -SD.DMTA_0 1.5744 -0.04867 3.197 -SD.alpha 0.5987 0.17132 1.026 -SD.beta 0.7299 0.22849 1.231 + est. lower upper +SD.DMTA_0 1.6189 -0.03636 3.2741 +SD.alpha 0.5814 0.17364 0.9892 +SD.beta 0.6821 0.21108 1.1530 Variance model: - est. lower upper -a.1 1.51063 1.2438 1.77741 -b.1 0.02824 0.0204 0.03609 + est. lower upper +a.1 1.50219 1.23601 1.76836 +b.1 0.02893 0.02099 0.03687 Estimated disappearance times: - DT50 DT90 DT50back -DMTA 11.11 42.6 12.82 + DT50 DT90 DT50back +DMTA 11.05 42.81 12.89 </code></pre> <p></p> @@ -1764,10 +1767,10 @@ Hierarchical mkin fit of the DFOP model with error model const </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 14:07:02 2023 -Date of summary: Thu Apr 20 14:08:16 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 11:18:57 2023 +Date of summary: Mon Oct 30 11:21:30 2023 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -1779,7 +1782,7 @@ Data: Model predictions using solution type analytical -Fitted in 1.838 s +Fitted in 3.231 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1810,10 +1813,10 @@ Likelihood computed by importance sampling Optimised parameters: est. lower upper -DMTA_0 98.092481 96.573898 99.61106 +DMTA_0 98.092481 96.573899 99.61106 k1 0.062499 0.030336 0.09466 k2 0.009065 -0.005133 0.02326 -g 0.948967 0.862079 1.03586 +g 0.948967 0.862080 1.03586 a.1 1.821671 1.604774 2.03857 SD.DMTA_0 1.677785 0.472066 2.88350 SD.k1 0.634962 0.270788 0.99914 @@ -1848,10 +1851,10 @@ Hierarchical mkin fit of the DFOP model with error model tc </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 14:07:04 2023 -Date of summary: Thu Apr 20 14:08:16 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 11:19:01 2023 +Date of summary: Mon Oct 30 11:21:30 2023 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -1863,21 +1866,21 @@ Data: Model predictions using solution type analytical -Fitted in 3.297 s +Fitted in 6.71 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function Starting values for degradation parameters: - DMTA_0 k1 k2 g -98.759266 0.087034 0.009933 0.930827 + DMTA_0 k1 k2 g +98.71186 0.08675 0.01374 0.93491 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): DMTA_0 k1 k2 g -DMTA_0 98.76 0 0 0 +DMTA_0 98.71 0 0 0 k1 0.00 1 0 0 k2 0.00 0 1 0 g 0.00 0 0 1 @@ -1890,42 +1893,42 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 665.5 663.4 -322.8 + 665.7 663.6 -322.9 Optimised parameters: est. lower upper -DMTA_0 98.377019 96.447952 100.30609 -k1 0.064843 0.034607 0.09508 -k2 0.008895 0.006368 0.01142 -g 0.949696 0.903815 0.99558 -a.1 1.065241 0.865754 1.26473 -b.1 0.029340 0.022336 0.03634 -SD.DMTA_0 2.007754 0.387982 3.62753 -SD.k1 0.580473 0.250286 0.91066 -SD.k2 0.006105 -4.920337 4.93255 -SD.g 1.097149 0.412779 1.78152 +DMTA_0 98.347470 96.380815 100.31413 +k1 0.064524 0.034279 0.09477 +k2 0.008304 0.005843 0.01076 +g 0.952128 0.909578 0.99468 +a.1 1.068907 0.868694 1.26912 +b.1 0.029265 0.022262 0.03627 +SD.DMTA_0 2.065796 0.428485 3.70311 +SD.k1 0.583703 0.251796 0.91561 +SD.k2 0.004167 -7.832168 7.84050 +SD.g 1.064450 0.397476 1.73142 Correlation: DMTA_0 k1 k2 -k1 0.0235 -k2 0.0595 0.0424 -g -0.0470 -0.0278 -0.2731 +k1 0.0223 +k2 0.0568 0.0394 +g -0.0464 -0.0269 -0.2713 Random effects: est. lower upper -SD.DMTA_0 2.007754 0.3880 3.6275 -SD.k1 0.580473 0.2503 0.9107 -SD.k2 0.006105 -4.9203 4.9325 -SD.g 1.097149 0.4128 1.7815 +SD.DMTA_0 2.065796 0.4285 3.7031 +SD.k1 0.583703 0.2518 0.9156 +SD.k2 0.004167 -7.8322 7.8405 +SD.g 1.064450 0.3975 1.7314 Variance model: est. lower upper -a.1 1.06524 0.86575 1.26473 -b.1 0.02934 0.02234 0.03634 +a.1 1.06891 0.86869 1.26912 +b.1 0.02927 0.02226 0.03627 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 -DMTA 11.36 41.32 12.44 10.69 77.92 +DMTA 11.39 41.36 12.45 10.74 83.48 </code></pre> <p></p> @@ -1934,167 +1937,28 @@ Hierarchical mkin fit of the HS model with error model const </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 14:07:03 2023 -Date of summary: Thu Apr 20 14:08:16 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 11:18:59 2023 +Date of summary: Mon Oct 30 11:21:30 2023 Equations: -d_DMTA/dt = - ifelse(time <= tb, k1, k2) * DMTA - -Data: -155 observations of 1 variable(s) grouped in 6 datasets - -Model predictions using solution type analytical - -Fitted in 1.972 s -Using 300, 100 iterations and 9 chains - -Variance model: Constant variance - -Starting values for degradation parameters: - DMTA_0 k1 k2 tb -97.82176 0.06931 0.02997 11.13945 - -Fixed degradation parameter values: -None - -Starting values for random effects (square root of initial entries in omega): - DMTA_0 k1 k2 tb -DMTA_0 97.82 0 0 0 -k1 0.00 1 0 0 -k2 0.00 0 1 0 -tb 0.00 0 0 1 - -Starting values for error model parameters: -a.1 - 1 - -Results: - -Likelihood computed by importance sampling - AIC BIC logLik - 714 712.1 -348 - -Optimised parameters: - est. lower upper -DMTA_0 98.16102 96.47747 99.84456 -k1 0.07876 0.05261 0.10491 -k2 0.02227 0.01706 0.02747 -tb 13.99089 -7.40049 35.38228 -a.1 1.82305 1.60700 2.03910 -SD.DMTA_0 1.88413 0.56204 3.20622 -SD.k1 0.34292 0.10482 0.58102 -SD.k2 0.19851 0.01718 0.37985 -SD.tb 1.68168 0.58064 2.78272 - -Correlation: - DMTA_0 k1 k2 -k1 0.0142 -k2 0.0001 -0.0025 -tb 0.0165 -0.1256 -0.0301 - -Random effects: - est. lower upper -SD.DMTA_0 1.8841 0.56204 3.2062 -SD.k1 0.3429 0.10482 0.5810 -SD.k2 0.1985 0.01718 0.3798 -SD.tb 1.6817 0.58064 2.7827 - -Variance model: - est. lower upper -a.1 1.823 1.607 2.039 - -Estimated disappearance times: - DT50 DT90 DT50back DT50_k1 DT50_k2 -DMTA 8.801 67.91 20.44 8.801 31.13 - -</code></pre> -<p></p> +d_DMTA/dt = - ifelse(time +<p></p></code> <caption> Hierarchical mkin fit of the HS model with error model tc </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.3 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 14:07:04 2023 -Date of summary: Thu Apr 20 14:08:16 2023 +mkin version used for pre-fitting: 1.2.6 +R version used for fitting: 4.3.1 +Date of fit: Mon Oct 30 11:19:02 2023 +Date of summary: Mon Oct 30 11:21:30 2023 Equations: -d_DMTA/dt = - ifelse(time <= tb, k1, k2) * DMTA - -Data: -155 observations of 1 variable(s) grouped in 6 datasets - -Model predictions using solution type analytical - -Fitted in 3.378 s -Using 300, 100 iterations and 9 chains - -Variance model: Two-component variance function - -Starting values for degradation parameters: - DMTA_0 k1 k2 tb -98.45190 0.07525 0.02576 19.19375 - -Fixed degradation parameter values: -None - -Starting values for random effects (square root of initial entries in omega): - DMTA_0 k1 k2 tb -DMTA_0 98.45 0 0 0 -k1 0.00 1 0 0 -k2 0.00 0 1 0 -tb 0.00 0 0 1 - -Starting values for error model parameters: -a.1 b.1 - 1 1 - -Results: - -Likelihood computed by importance sampling - AIC BIC logLik - 667.1 665 -323.6 - -Optimised parameters: - est. lower upper -DMTA_0 97.76570 95.81350 99.71791 -k1 0.05855 0.03080 0.08630 -k2 0.02337 0.01664 0.03010 -tb 31.09638 29.38289 32.80987 -a.1 1.08835 0.88590 1.29080 -b.1 0.02964 0.02257 0.03671 -SD.DMTA_0 2.04877 0.42607 3.67147 -SD.k1 0.59166 0.25621 0.92711 -SD.k2 0.30698 0.09561 0.51835 -SD.tb 0.01274 -0.10914 0.13462 - -Correlation: - DMTA_0 k1 k2 -k1 0.0160 -k2 -0.0070 -0.0024 -tb -0.0668 -0.0103 -0.2013 - -Random effects: - est. lower upper -SD.DMTA_0 2.04877 0.42607 3.6715 -SD.k1 0.59166 0.25621 0.9271 -SD.k2 0.30698 0.09561 0.5183 -SD.tb 0.01274 -0.10914 0.1346 - -Variance model: - est. lower upper -a.1 1.08835 0.88590 1.29080 -b.1 0.02964 0.02257 0.03671 - -Estimated disappearance times: - DT50 DT90 DT50back DT50_k1 DT50_k2 -DMTA 11.84 51.71 15.57 11.84 29.66 - -</code></pre> -<p></p> +d_DMTA/dt = - ifelse(time +<p></p></code> +</pre></pre> </div> <div class="section level3"> <h3 id="hierarchical-model-convergence-plots">Hierarchical model convergence plots<a class="anchor" aria-label="anchor" href="#hierarchical-model-convergence-plots"></a> @@ -2143,50 +2007,53 @@ Convergence plot for the NLHM HS fit with two-component error <div class="section level3"> <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h3> -<pre><code>R version 4.2.3 (2023-03-15) +<pre><code>R version 4.3.1 (2023-06-16) Platform: x86_64-pc-linux-gnu (64-bit) -Running under: Debian GNU/Linux 12 (bookworm) +Running under: Ubuntu 22.04.3 LTS Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 -LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so +BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 +LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 locale: - [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C - [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 - [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 - [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C + [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C + [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 + [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 + [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C -[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C +[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C + +time zone: Europe/Zurich +tzcode source: system (glibc) attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.3 +[1] saemix_3.2 npde_3.3 knitr_1.44 mkin_1.2.6 loaded via a namespace (and not attached): - [1] highr_0.10 pillar_1.9.0 bslib_0.4.2 compiler_4.2.3 - [5] jquerylib_0.1.4 tools_4.2.3 mclust_6.0.0 digest_0.6.31 - [9] tibble_3.2.1 jsonlite_1.8.4 evaluate_0.20 memoise_2.0.1 -[13] lifecycle_1.0.3 nlme_3.1-162 gtable_0.3.3 lattice_0.21-8 -[17] pkgconfig_2.0.3 rlang_1.1.0 DBI_1.1.3 cli_3.6.1 -[21] yaml_2.3.7 pkgdown_2.0.7 xfun_0.38 fastmap_1.1.1 -[25] gridExtra_2.3 dplyr_1.1.1 stringr_1.5.0 generics_0.1.3 -[29] desc_1.4.2 fs_1.6.1 vctrs_0.6.1 sass_0.4.5 -[33] systemfonts_1.0.4 tidyselect_1.2.0 rprojroot_2.0.3 lmtest_0.9-40 -[37] grid_4.2.3 glue_1.6.2 R6_2.5.1 textshaping_0.3.6 -[41] fansi_1.0.4 rmarkdown_2.21 purrr_1.0.1 ggplot2_3.4.2 -[45] magrittr_2.0.3 codetools_0.2-19 scales_1.2.1 htmltools_0.5.5 -[49] colorspace_2.1-0 ragg_1.2.5 utf8_1.2.3 stringi_1.7.12 -[53] munsell_0.5.0 cachem_1.0.7 zoo_1.8-12 </code></pre> + [1] sass_0.4.7 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 + [5] lattice_0.21-9 digest_0.6.33 magrittr_2.0.3 evaluate_0.22 + [9] grid_4.3.1 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.7 +[13] mclust_6.0.0 gridExtra_2.3 purrr_1.0.1 fansi_1.0.4 +[17] scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 jquerylib_0.1.4 +[21] cli_3.6.1 rlang_1.1.1 munsell_0.5.0 cachem_1.0.8 +[25] yaml_2.3.7 tools_4.3.1 memoise_2.0.1 dplyr_1.1.2 +[29] colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.3 R6_2.5.1 +[33] zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 fs_1.6.3 +[37] MASS_7.3-60 ragg_1.2.5 pkgconfig_2.0.3 desc_1.4.2 +[41] pkgdown_2.0.7 bslib_0.5.1 pillar_1.9.0 gtable_0.3.3 +[45] glue_1.6.2 systemfonts_1.0.4 xfun_0.40 tibble_3.2.1 +[49] lmtest_0.9-40 tidyselect_1.2.0 rstudioapi_0.15.0 htmltools_0.5.6.1 +[53] nlme_3.1-163 rmarkdown_2.23 compiler_4.3.1 </code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> </h3> -<pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> -<pre><code>MemTotal: 64936316 kB</code></pre> +<pre><code>CPU model: Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</code></pre> +<pre><code>MemTotal: 247605564 kB</code></pre> </div> </div> </div> diff --git a/docs/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-dfop-const-1.png b/docs/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-dfop-const-1.png Binary files differindex 3f145074..4c74de78 100644 --- a/docs/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-dfop-const-1.png +++ b/docs/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-dfop-const-1.png diff --git a/docs/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-dfop-tc-1.png b/docs/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-dfop-tc-1.png Binary files differindex 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dimethenamid and dimethenamid-P</a> </li> <li> + <a href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -135,7 +138,7 @@ residue data on dimethenamid and dimethenamid-P</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change on 20 April 2023, -last compiled on 19 Mai 2023</h4> +last compiled on 30 October 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_dmta_pathway.rmd" class="external-link"><code>vignettes/prebuilt/2022_dmta_pathway.rmd</code></a></small> <div class="hidden name"><code>2022_dmta_pathway.rmd</code></div> @@ -155,7 +158,7 @@ can be fitted with the mkin package.</p> 173340 (Application of nonlinear hierarchical models to the kinetic evaluation of chemical degradation data) of the German Environment Agency carried out in 2022 and 2023.</p> -<p>The mkin package is used in version 1.2.4, which is currently under +<p>The mkin package is used in version 1.2.6, which is currently under development. It contains the test data, and the functions used in the evaluations. The <code>saemix</code> package is used as a backend for fitting the NLHM, but is also loaded to make the convergence plot @@ -1976,23 +1979,23 @@ error<a class="anchor" aria-label="anchor" href="#improved-fit-of-the-sforb-path <div class="section level3"> <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h3> -<pre><code>R version 4.3.0 Patched (2023-05-18 r84448) +<pre><code>R version 4.3.1 (2023-06-16) Platform: x86_64-pc-linux-gnu (64-bit) -Running under: Debian GNU/Linux 12 (bookworm) +Running under: Ubuntu 22.04.3 LTS Matrix products: default -BLAS: /home/jranke/svn/R/r-patched/build/lib/libRblas.so -LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/liblapack.so.3; LAPACK version 3.11.0 +BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 +LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 locale: - [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C - [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 - [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 - [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C + [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C + [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 + [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 + [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C -[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C +[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C -time zone: Europe/Berlin +time zone: Europe/Zurich tzcode source: system (glibc) attached base packages: @@ -2000,31 +2003,31 @@ attached base packages: [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.4 +[1] saemix_3.2 npde_3.3 knitr_1.44 mkin_1.2.6 loaded via a namespace (and not attached): - [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 - [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 - [9] grid_4.3.0 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.4 -[13] processx_3.8.1 pkgbuild_1.4.0 deSolve_1.35 DBI_1.1.3 -[17] mclust_6.0.0 ps_1.7.5 gridExtra_2.3 purrr_1.0.1 -[21] fansi_1.0.4 scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 -[25] jquerylib_0.1.4 cli_3.6.1 crayon_1.5.2 rlang_1.1.1 -[29] munsell_0.5.0 cachem_1.0.8 yaml_2.3.7 inline_0.3.19 -[33] tools_4.3.0 memoise_2.0.1 dplyr_1.1.2 colorspace_2.1-0 -[37] ggplot2_3.4.2 vctrs_0.6.2 R6_2.5.1 zoo_1.8-12 -[41] lifecycle_1.0.3 stringr_1.5.0 fs_1.6.2 ragg_1.2.5 + [1] sass_0.4.7 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 + [5] lattice_0.21-9 digest_0.6.33 magrittr_2.0.3 evaluate_0.22 + [9] grid_4.3.1 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.7 +[13] processx_3.8.2 pkgbuild_1.4.2 deSolve_1.35 mclust_6.0.0 +[17] ps_1.7.5 gridExtra_2.3 purrr_1.0.1 fansi_1.0.4 +[21] scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 jquerylib_0.1.4 +[25] cli_3.6.1 crayon_1.5.2 rlang_1.1.1 munsell_0.5.0 +[29] cachem_1.0.8 yaml_2.3.7 inline_0.3.19 tools_4.3.1 +[33] memoise_2.0.1 dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 +[37] vctrs_0.6.3 R6_2.5.1 zoo_1.8-12 lifecycle_1.0.3 +[41] stringr_1.5.0 fs_1.6.3 MASS_7.3-60 ragg_1.2.5 [45] callr_3.7.3 pkgconfig_2.0.3 desc_1.4.2 pkgdown_2.0.7 -[49] bslib_0.4.2 pillar_1.9.0 gtable_0.3.3 glue_1.6.2 -[53] systemfonts_1.0.4 highr_0.10 xfun_0.39 tibble_3.2.1 -[57] lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5 nlme_3.1-162 -[61] rmarkdown_2.21 compiler_4.3.0 prettyunits_1.1.1</code></pre> +[49] bslib_0.5.1 pillar_1.9.0 gtable_0.3.3 glue_1.6.2 +[53] systemfonts_1.0.4 xfun_0.40 tibble_3.2.1 lmtest_0.9-40 +[57] tidyselect_1.2.0 rstudioapi_0.15.0 htmltools_0.5.6.1 nlme_3.1-163 +[61] rmarkdown_2.23 compiler_4.3.1 prettyunits_1.2.0</code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> </h3> -<pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> -<pre><code>MemTotal: 64925476 kB</code></pre> +<pre><code>CPU model: Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</code></pre> +<pre><code>MemTotal: 247605564 kB</code></pre> </div> </div> </div> diff --git 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a/docs/articles/twa.html b/docs/articles/twa.html index 4b48437e..4b3e11a3 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -74,6 +74,9 @@ <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> + <a href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -135,7 +138,7 @@ concentrations with mkin</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change 18 September 2019 -(rebuilt 2023-05-19)</h4> +(rebuilt 2023-10-30)</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> diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 4cda45e3..f19f59ad 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -74,6 +74,9 @@ <a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> + <a href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -134,7 +137,7 @@ Ranke</h4> <h4 data-toc-skip class="date">Last change 16 January 2018 -(rebuilt 2023-05-19)</h4> +(rebuilt 2023-10-30)</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> diff --git 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<a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> + <a href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -135,7 +138,7 @@ to the US EPA SOP for the NAFTA guidance</h1> Ranke</h4> <h4 data-toc-skip class="date">26 February 2019 (rebuilt -2023-05-19)</h4> +2023-10-30)</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> diff --git 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- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -74,6 +74,9 @@ <a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> + <a href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -134,7 +137,7 @@ Ranke</h4> <h4 data-toc-skip class="date">Last change 17 February 2023 -(rebuilt 2023-05-19)</h4> +(rebuilt 2023-10-30)</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> @@ -231,7 +234,15 @@ systems. All trademarks belong to their respective owners.</p> </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="8%"> +<col width="54%"> +<col width="8%"> +<col width="12%"> +<col width="8%"> +<col width="9%"> +</colgroup> <thead><tr class="header"> <th align="left">OS</th> <th align="left">CPU</th> @@ -433,6 +444,22 @@ models fitted to two datasets, i.e. eight fits for each test.</p> <td align="right">1.386</td> <td align="right">1.960</td> </tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">4.3.1</td> +<td align="left">1.2.5</td> +<td align="right">2.369</td> +<td align="right">3.632</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">4.3.1</td> +<td align="left">1.2.6</td> +<td align="right">2.856</td> +<td align="right">4.960</td> +</tr> </tbody> </table> </div> @@ -443,6 +470,15 @@ models fitted to two datasets, i.e. eight fits for each test.</p> by variable (t5) for three models fitted to one dataset, i.e. three fits for each test.</p> <table class="table"> +<colgroup> +<col width="7%"> +<col width="50%"> +<col width="7%"> +<col width="11%"> +<col width="7%"> +<col width="8%"> +<col width="7%"> +</colgroup> <thead><tr class="header"> <th align="left">OS</th> <th align="left">CPU</th> @@ -669,6 +705,24 @@ for each test.</p> <td align="right">2.080</td> <td align="right">1.106</td> </tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">4.3.1</td> +<td align="left">1.2.5</td> +<td align="right">1.823</td> +<td align="right">5.555</td> +<td align="right">2.404</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">4.3.1</td> +<td align="left">1.2.6</td> +<td align="right">1.761</td> +<td align="right">5.405</td> +<td align="right">2.462</td> +</tr> </tbody> </table> </div> @@ -678,18 +732,18 @@ for each test.</p> <p>Constant variance (t6 and t7), two-component error model (t8 and t9), and variance by variable (t10 and t11) for one model fitted to one dataset, i.e. one fit for each test.</p> -<table class="table"> +<table style="width:100%;" class="table"> <colgroup> +<col width="5%"> +<col width="40%"> +<col width="5%"> <col width="8%"> -<col width="19%"> -<col width="8%"> -<col width="12%"> -<col width="8%"> -<col width="8%"> -<col width="8%"> -<col width="9%"> -<col width="8%"> -<col width="9%"> +<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">OS</th> @@ -992,6 +1046,30 @@ dataset, i.e. one fit for each test.</p> <td align="right">0.712</td> <td align="right">0.948</td> </tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">4.3.1</td> +<td align="left">1.2.5</td> +<td align="right">0.798</td> +<td align="right">1.096</td> +<td align="right">1.217</td> +<td align="right">3.173</td> +<td align="right">1.634</td> +<td align="right">2.271</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">4.3.1</td> +<td align="left">1.2.6</td> +<td align="right">0.813</td> +<td align="right">1.136</td> +<td align="right">1.220</td> +<td align="right">3.114</td> +<td align="right">1.598</td> +<td align="right">2.255</td> +</tr> </tbody> </table> </div> diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 3c53b40a..1aa88e05 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -74,6 +74,9 @@ <a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> + <a href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -134,7 +137,7 @@ definitions in mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">2023-05-19</h4> + <h4 data-toc-skip class="date">2023-10-30</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> @@ -152,7 +155,7 @@ compiled from autogenerated C code when defining a model using mkinmod. Starting from version 0.9.49.9, the <code><a href="../../reference/mkinmod.html">mkinmod()</a></code> function checks for presence of a compiler using</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu">pkgbuild</span><span class="fu">::</span><span class="fu"><a href="https://r-lib.github.io/pkgbuild/reference/has_compiler.html" class="external-link">has_compiler</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu">pkgbuild</span><span class="fu">::</span><span class="fu"><a href="https://pkgbuild.r-lib.org/reference/has_compiler.html" class="external-link">has_compiler</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> <p>In previous versions, it used <code>Sys.which("gcc")</code> for this check.</p> <p>On Linux, you need to have the essential build tools like make and @@ -213,10 +216,10 @@ solution is also implemented, which is included in the tests below.</p> <span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="st">"R package rbenchmark is not available"</span><span class="op">)</span></span> <span><span class="op">}</span></span></code></pre></div> <pre><code><span><span class="co">## test replications relative elapsed</span></span> -<span><span class="co">## 4 analytical 1 1.000 0.099</span></span> -<span><span class="co">## 3 deSolve, compiled 1 1.303 0.129</span></span> -<span><span class="co">## 2 Eigenvalue based 1 1.697 0.168</span></span> -<span><span class="co">## 1 deSolve, not compiled 1 21.475 2.126</span></span></code></pre> +<span><span class="co">## 4 analytical 1 1.000 0.213</span></span> +<span><span class="co">## 3 deSolve, compiled 1 1.418 0.302</span></span> +<span><span class="co">## 2 Eigenvalue based 1 2.000 0.426</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 23.535 5.013</span></span></code></pre> <p>We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.</p> </div> @@ -247,15 +250,15 @@ compiled code is available.</p> <span><span class="op">}</span></span></code></pre></div> <pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <pre><code><span><span class="co">## test replications relative elapsed</span></span> -<span><span class="co">## 2 deSolve, compiled 1 1.000 0.165</span></span> -<span><span class="co">## 1 deSolve, not compiled 1 22.673 3.741</span></span></code></pre> -<p>Here we get a performance benefit of a factor of 23 using the version +<span><span class="co">## 2 deSolve, compiled 1 1.000 0.492</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 20.398 10.036</span></span></code></pre> +<p>Here we get a performance benefit of a factor of 20 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 1.2.4 on</p> -<pre><code><span><span class="co">## R version 4.3.0 Patched (2023-05-18 r84448)</span></span> +<p>This vignette was built with mkin 1.2.6 on</p> +<pre><code><span><span class="co">## R version 4.3.1 (2023-06-16)</span></span> <span><span class="co">## Platform: x86_64-pc-linux-gnu (64-bit)</span></span> -<span><span class="co">## Running under: Debian GNU/Linux 12 (bookworm)</span></span></code></pre> -<pre><code><span><span class="co">## CPU model: AMD Ryzen 9 7950X 16-Core Processor</span></span></code></pre> +<span><span class="co">## Running under: Ubuntu 22.04.3 LTS</span></span></code></pre> +<pre><code><span><span class="co">## CPU model: Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</span></span></code></pre> </div> </div> diff --git a/docs/articles/web_only/dimethenamid_2018.html b/docs/articles/web_only/dimethenamid_2018.html index a89631a2..1cffd561 100644 --- a/docs/articles/web_only/dimethenamid_2018.html +++ b/docs/articles/web_only/dimethenamid_2018.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -74,6 +74,9 @@ <a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> + <a href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -135,7 +138,7 @@ from 2018</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change 1 July 2022, -built on 19 May 2023</h4> +built on 30 Oct 2023</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> @@ -222,12 +225,12 @@ least in some datasets the degradation slows down towards later time points, and that the scatter of the residuals error is smaller for smaller values (panel to the right):</p> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_sfo_const-1.png" width="700"></p> <p>Using biexponential decline (DFOP) results in a slightly more random scatter of the residuals:</p> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_const-1.png" width="700"></p> <p>The population curve (bold line) in the above plot results from taking the mean of the individual transformed parameters, i.e. of log k1 @@ -239,7 +242,7 @@ dominates the average. This is alleviated if only rate constants that pass the t-test for significant difference from zero (on the untransformed scale) are considered in the averaging:</p> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_const_test-1.png" width="700"></p> <p>While this is visually much more satisfactory, such an average procedure could introduce a bias, as not all results from the individual @@ -251,7 +254,7 @@ degradation model and the error model (see below).</p> predicted residues is reduced by using the two-component error model:</p> <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_tc_test-1.png" width="700"></p> <p>However, note that in the case of using this error model, the fits to the Flaach and BBA 2.3 datasets appear to be ill-defined, indicated by @@ -263,7 +266,7 @@ 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 C: Optimisation did not converge: iteration limit reached without convergence (10) @@ -319,7 +322,7 @@ indicates that this difference is significant as the p-value is below <pre><code> Model df AIC BIC logLik Test L.Ratio p-value f_parent_nlme_sfo_const 1 5 796.60 811.82 -393.30 f_parent_nlme_sfo_tc 2 6 798.60 816.86 -393.30 1 vs 2 0.00 0.998 -f_parent_nlme_dfop_tc 3 10 671.91 702.34 -325.96 2 vs 3 134.69 <.0001</code></pre> +f_parent_nlme_dfop_tc 3 10 671.91 702.34 -325.95 2 vs 3 134.69 <.0001</code></pre> <p>In addition to these fits, attempts were also made to include correlations between random effects by using the log Cholesky parameterisation of the matrix specifying them. The code used for these @@ -341,7 +344,7 @@ effects does not improve the fits.</p> <p>The selected model (DFOP with two-component error) fitted to the data assuming no correlations between random effects is shown below.</p> <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_nlme_dfop_tc</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_nlme_dfop_tc</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/plot_parent_nlme-1.png" width="700"></p> </div> <div class="section level4"> @@ -358,8 +361,17 @@ implemented in the saemix package, the convergence plots need to be manually checked for every fit. We define control settings that work well for all the parent data fits shown in this vignette.</p> <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></span> -<span><span class="va">saemix_control</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">800</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></span></code></pre></div> +<pre><code>Loading required package: npde</code></pre> +<pre><code>Package saemix, version 3.2 + please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</code></pre> +<pre><code> +Attaching package: 'saemix'</code></pre> +<pre><code>The following objects are masked from 'package:npde': + + kurtosis, skewness</code></pre> +<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">saemix_control</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">800</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span> <span> print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> <span><span class="va">saemix_control_moreiter</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1600</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span> <span> print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> @@ -367,7 +379,7 @@ well for all the parent data fits shown in this vignette.</p> <span> print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> <p>The convergence plot for the SFO model using constant variance is shown below.</p> -<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_sfo_const</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> @@ -375,19 +387,19 @@ shown below.</p> <p>Obviously the selected number of iterations is sufficient to reach convergence. This can also be said for the SFO fit using the two-component error model.</p> -<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_sfo_tc</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_sfo_tc-1.png" width="700"></p> <p>When fitting the DFOP model with constant variance (see below), parameter convergence is not as unambiguous.</p> -<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_const</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_const</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_dfop_const-1.png" width="700"></p> -<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_const</span><span class="op">)</span></span></code></pre></div> <pre><code>Kinetic nonlinear mixed-effects model fit by SAEM Structural model: @@ -408,11 +420,11 @@ 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 1.65122 1.9916 -SD.DMTA_0 1.64787 0.45772 2.8380 +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 -2.50195 2.5679 -SD.g 1.10266 0.32369 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 @@ -423,14 +435,14 @@ this model.</p> 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><span class="va">f_parent_saemix_dfop_tc</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> <span><span class="va">f_parent_saemix_dfop_tc_moreiter</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> control <span class="op">=</span> <span class="va">saemix_control_moreiter</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_dfop_tc-1.png" width="700"></p> -<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">)</span></span></code></pre></div> <pre><code>Kinetic nonlinear mixed-effects model fit by SAEM Structural model: @@ -446,17 +458,17 @@ 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 98.24165 96.29190 100.1914 +k1 0.06421 0.03352 0.0949 +k2 0.00866 0.00617 0.0111 +g 0.95340 0.91218 0.9946 +a.1 1.06463 0.86503 1.2642 +b.1 0.02964 0.02259 0.0367 +SD.DMTA_0 2.03611 0.40416 3.6681 +SD.k1 0.59534 0.25692 0.9338 +SD.k2 0.00042 -73.01372 73.0146 +SD.g 1.04234 0.37189 1.7128</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 @@ -472,7 +484,7 @@ 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="cb28"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">AIC_parent_saemix</span> <span class="op"><-</span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span></span> <span> <span class="va">f_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>,</span> <span> <span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>,</span> @@ -480,7 +492,7 @@ comparison function of the saemix package:</p> <span> <span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>,</span> <span> <span class="va">f_parent_saemix_dfop_tc_moreiter</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span></code></pre></div> <pre><code>Likelihoods calculated by importance sampling</code></pre> -<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">AIC_parent_saemix</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span> <span> <span class="st">"SFO const"</span>, <span class="st">"SFO tc"</span>, <span class="st">"DFOP const"</span>, <span class="st">"DFOP tc"</span>, <span class="st">"DFOP tc more iterations"</span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix</span><span class="op">)</span></span></code></pre></div> @@ -488,13 +500,13 @@ comparison function of the saemix package:</p> 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 665.67 663.59 +DFOP tc more iterations 665.85 663.76</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="cb32"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span> <span class="op"><-</span></span> <span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/llgq.saemix.html" class="external-link">llgq.saemix</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span> <span><span class="va">AIC_parent_saemix_methods</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span> @@ -504,7 +516,7 @@ the three methods are compared.</p> <span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix_methods</span><span class="op">)</span></span></code></pre></div> <pre><code> is gq lin -665.65 665.68 665.11 </code></pre> +665.67 665.74 665.13 </code></pre> <p>The AIC values based on importance sampling and Gaussian quadrature are very similar. Using linearisation is known to be less accurate, but still gives a similar value.</p> @@ -518,7 +530,7 @@ iterations makes a lot of difference. When using the LAPACK version coming with Debian Bullseye, the AIC based on Gaussian quadrature is almost the same as the one obtained with the other methods, also when using defaults for the fit.</p> -<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_tc_defaults</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span> <span><span class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span> <span class="op"><-</span></span> <span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/llgq.saemix.html" class="external-link">llgq.saemix</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span> @@ -529,7 +541,7 @@ using defaults for the fit.</p> <span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix_methods_defaults</span><span class="op">)</span></span></code></pre></div> <pre><code> is gq lin -669.77 669.36 670.95 </code></pre> +670.09 669.37 671.29 </code></pre> </div> </div> <div class="section level3"> @@ -538,7 +550,7 @@ using defaults for the fit.</p> <p>The following table gives the AIC values obtained with both backend packages using the same control parameters (800 iterations burn-in, 300 iterations second phase, 15 chains).</p> -<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">AIC_all</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> <span> check.names <span class="op">=</span> <span class="cn">FALSE</span>,</span> <span> <span class="st">"Degradation model"</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"SFO"</span>, <span class="st">"DFOP"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span> @@ -549,7 +561,7 @@ iterations second phase, 15 chains).</p> <span> saemix_is <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</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>,</span> <span> <span class="va">f_parent_saemix_dfop_const</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span>, <span class="va">AIC</span>, method <span class="op">=</span> <span class="st">"is"</span><span class="op">)</span></span> <span><span class="op">)</span></span> -<span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="va">AIC_all</span><span class="op">)</span></span></code></pre></div> +<span><span class="fu">kable</span><span class="op">(</span><span class="va">AIC_all</span><span class="op">)</span></span></code></pre></div> <table class="table"> <thead><tr class="header"> <th align="left">Degradation model</th> @@ -577,15 +589,15 @@ iterations second phase, 15 chains).</p> <td align="left">DFOP</td> <td align="left">const</td> <td align="right">NA</td> -<td align="right">709.26</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">665.13</td> +<td align="right">665.67</td> </tr> </tbody> </table> @@ -612,48 +624,48 @@ satisfactory precision.</p> <div class="section level2"> <h2 id="session-info">Session Info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h2> -<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> -<pre><code>R version 4.3.0 Patched (2023-05-18 r84448) +<pre><code>R version 4.3.1 (2023-06-16) Platform: x86_64-pc-linux-gnu (64-bit) -Running under: Debian GNU/Linux 12 (bookworm) +Running under: Ubuntu 22.04.3 LTS Matrix products: default -BLAS: /home/jranke/svn/R/r-patched/build/lib/libRblas.so -LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/liblapack.so.3; LAPACK version 3.11.0 +BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 +LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 locale: - [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C - [3] LC_TIME=C LC_COLLATE=de_DE.UTF-8 - [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 - [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C + [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C + [3] LC_TIME=C LC_COLLATE=en_US.UTF-8 + [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 + [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C -[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C +[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C -time zone: Europe/Berlin +time zone: Europe/Zurich tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: -[1] nlme_3.1-162 mkin_1.2.4 knitr_1.42 +[1] saemix_3.2 npde_3.3 nlme_3.1-163 mkin_1.2.6 knitr_1.44 loaded via a namespace (and not attached): - [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 saemix_3.2 - [5] stringi_1.7.12 lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 - [9] evaluate_0.21 grid_4.3.0 fastmap_1.1.1 rprojroot_2.0.3 -[13] jsonlite_1.8.4 DBI_1.1.3 mclust_6.0.0 gridExtra_2.3 -[17] purrr_1.0.1 fansi_1.0.4 scales_1.2.1 textshaping_0.3.6 -[21] jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1 munsell_0.5.0 -[25] cachem_1.0.8 yaml_2.3.7 tools_4.3.0 parallel_4.3.0 -[29] memoise_2.0.1 dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 -[33] vctrs_0.6.2 R6_2.5.1 zoo_1.8-12 lifecycle_1.0.3 -[37] stringr_1.5.0 fs_1.6.2 ragg_1.2.5 pkgconfig_2.0.3 -[41] desc_1.4.2 pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 -[45] gtable_0.3.3 glue_1.6.2 systemfonts_1.0.4 xfun_0.39 -[49] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 npde_3.3 -[53] htmltools_0.5.5 rmarkdown_2.21 compiler_4.3.0 </code></pre> + [1] sass_0.4.7 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 + [5] lattice_0.21-9 digest_0.6.33 magrittr_2.0.3 evaluate_0.22 + [9] grid_4.3.1 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.7 +[13] mclust_6.0.0 gridExtra_2.3 purrr_1.0.1 fansi_1.0.4 +[17] scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 jquerylib_0.1.4 +[21] cli_3.6.1 rlang_1.1.1 munsell_0.5.0 cachem_1.0.8 +[25] yaml_2.3.7 tools_4.3.1 parallel_4.3.1 memoise_2.0.1 +[29] dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.3 +[33] R6_2.5.1 zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 +[37] fs_1.6.3 MASS_7.3-60 ragg_1.2.5 pkgconfig_2.0.3 +[41] desc_1.4.2 pkgdown_2.0.7 bslib_0.5.1 pillar_1.9.0 +[45] gtable_0.3.3 glue_1.6.2 systemfonts_1.0.4 xfun_0.40 +[49] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 rstudioapi_0.15.0 +[53] htmltools_0.5.6.1 rmarkdown_2.23 compiler_4.3.1 </code></pre> </div> <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> diff --git a/docs/articles/web_only/multistart.html b/docs/articles/web_only/multistart.html index b9224bb0..dff087e4 100644 --- a/docs/articles/web_only/multistart.html +++ b/docs/articles/web_only/multistart.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -74,6 +74,9 @@ <a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> + <a href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -134,7 +137,7 @@ Ranke</h4> <h4 data-toc-skip class="date">Last change 20 April 2023 -(rebuilt 2023-05-19)</h4> +(rebuilt 2023-10-30)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/multistart.rmd" class="external-link"><code>vignettes/web_only/multistart.rmd</code></a></small> <div class="hidden name"><code>multistart.rmd</code></div> diff --git a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png Binary files differindex f41dc889..8be6ba61 100644 --- a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png +++ b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png diff --git a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png Binary files differindex 9e206791..bc518c0c 100644 --- a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png +++ b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png diff --git a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png Binary files differindex c8e918cd..9ecdf4c9 100644 --- a/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png +++ b/docs/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png diff --git a/docs/articles/web_only/saem_benchmarks.html b/docs/articles/web_only/saem_benchmarks.html index a9637876..095a37e2 100644 --- a/docs/articles/web_only/saem_benchmarks.html +++ b/docs/articles/web_only/saem_benchmarks.html @@ -33,7 +33,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -74,6 +74,9 @@ <a href="../../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> + <a href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -134,7 +137,7 @@ Ranke</h4> <h4 data-toc-skip class="date">Last change 17 February 2023 -(rebuilt 2023-05-19)</h4> +(rebuilt 2023-10-30)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/saem_benchmarks.rmd" class="external-link"><code>vignettes/web_only/saem_benchmarks.rmd</code></a></small> <div class="hidden name"><code>saem_benchmarks.rmd</code></div> @@ -190,7 +193,7 @@ explanation of the following preprocessing.</p> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span></span> <span> <span class="va">sfo_const</span>, <span class="va">dfop_const</span>, <span class="va">sforb_const</span>, <span class="va">hs_const</span>,</span> -<span> <span class="va">sfo_tc</span>, <span class="va">dfop_tc</span>, <span class="va">sforb_tc</span>, <span class="va">hs_tc</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>, digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> +<span> <span class="va">sfo_tc</span>, <span class="va">dfop_tc</span>, <span class="va">sforb_tc</span>, <span class="va">hs_tc</span><span class="op">)</span> <span class="op">|></span> <span class="fu">kable</span><span class="op">(</span>, digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> <table class="table"> <thead><tr class="header"> <th align="left"></th> @@ -330,7 +333,17 @@ systems. All trademarks belong to their respective owners.</p> <h3 id="parent-only-1">Parent only<a class="anchor" aria-label="anchor" href="#parent-only-1"></a> </h3> <p>Constant variance for SFO, DFOP, SFORB and HS.</p> -<table class="table"> +<table style="width:100%;" class="table"> +<colgroup> +<col width="48%"> +<col width="7%"> +<col width="7%"> +<col width="8%"> +<col width="7%"> +<col width="7%"> +<col width="7%"> +<col width="7%"> +</colgroup> <thead><tr class="header"> <th align="left">CPU</th> <th align="left">OS</th> @@ -412,10 +425,30 @@ systems. All trademarks belong to their respective owners.</p> <td align="right">1.987</td> <td align="right">2.055</td> </tr> +<tr class="even"> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">Linux</td> +<td align="left">1.2.6</td> +<td align="left">3.2</td> +<td align="right">2.998</td> +<td align="right">6.523</td> +<td align="right">6.126</td> +<td align="right">4.721</td> +</tr> </tbody> </table> <p>Two-component error fits for SFO, DFOP, SFORB and HS.</p> -<table class="table"> +<table style="width:100%;" class="table"> +<colgroup> +<col width="48%"> +<col width="7%"> +<col width="7%"> +<col width="8%"> +<col width="7%"> +<col width="7%"> +<col width="7%"> +<col width="7%"> +</colgroup> <thead><tr class="header"> <th align="left">CPU</th> <th align="left">OS</th> @@ -497,6 +530,16 @@ systems. All trademarks belong to their respective owners.</p> <td align="right">3.433</td> <td align="right">3.595</td> </tr> +<tr class="even"> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">Linux</td> +<td align="left">1.2.6</td> +<td align="left">3.2</td> +<td align="right">5.070</td> +<td align="right">8.464</td> +<td align="right">8.525</td> +<td align="right">7.599</td> +</tr> </tbody> </table> </div> @@ -505,6 +548,14 @@ systems. All trademarks belong to their respective owners.</p> </h3> <p>Two-component error for DFOP-SFO and SFORB-SFO.</p> <table class="table"> +<colgroup> +<col width="54%"> +<col width="8%"> +<col width="8%"> +<col width="9%"> +<col width="9%"> +<col width="10%"> +</colgroup> <thead><tr class="header"> <th align="left">CPU</th> <th align="left">OS</th> @@ -570,6 +621,14 @@ systems. All trademarks belong to their respective owners.</p> <td align="right">12.160</td> <td align="right">265.934</td> </tr> +<tr class="even"> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">Linux</td> +<td align="left">1.2.6</td> +<td align="left">3.2</td> +<td align="right">30.168</td> +<td align="right">748.675</td> +</tr> </tbody> </table> </div> @@ -577,7 +636,14 @@ systems. All trademarks belong to their respective owners.</p> <h3 id="three-metabolites-1">Three metabolites<a class="anchor" aria-label="anchor" href="#three-metabolites-1"></a> </h3> <p>Two-component error for SFORB-SFO3-plus</p> -<table class="table"> +<table style="width:100%;" class="table"> +<colgroup> +<col width="59%"> +<col width="8%"> +<col width="8%"> +<col width="10%"> +<col width="13%"> +</colgroup> <thead><tr class="header"> <th align="left">CPU</th> <th align="left">OS</th> @@ -635,6 +701,13 @@ systems. All trademarks belong to their respective owners.</p> <td align="left">3.2</td> <td align="right">456.252</td> </tr> +<tr class="even"> +<td align="left">Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</td> +<td align="left">Linux</td> +<td align="left">1.2.6</td> +<td align="left">3.2</td> +<td align="right">1235.028</td> +</tr> </tbody> </table> </div> |
