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Diffstat (limited to 'docs')
231 files changed, 1055 insertions, 870 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> diff --git a/docs/index.html b/docs/index.html index 79dadd3b..eb3fe7f9 100644 --- a/docs/index.html +++ b/docs/index.html @@ -242,6 +242,7 @@ </ul> <p>Thanks to everyone involved for collaboration and support!</p> <p>Thanks are due also to Emmanuelle Comets, maintainer of the saemix package, for her interest and support for using the SAEM algorithm and its implementation in saemix for the evaluation of chemical degradation data.</p> +<p>Regarding the application of nonlinear mixed-effects models to degradation data, von Götz et al (1999) have already proposed to use this technique in the context of environmental risk assessments of pesticides. However, this work was apparently not followed up, which is why we had to independently arrive at the idea and missed to cite this previous work on the topic in our first publications.</p> </div> <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> @@ -249,6 +250,11 @@ <table class="table"> <tr> <td> +Ranke J (2023) Application of nonlinear hierarchical models to the kinetic evaluation of chemical degradation data - Guidance for the use of an R markdown template file. <a href="https://www.umweltbundesamt.de/publikationen/application-of-nonlinear-hierarchical-models-to-the" class="external-link">Umweltbundesamt TEXTE 151/2023</a> +</td> +</tr> +<tr> +<td> Ranke J, Wöltjen J, Schmidt J, and Comets E (2021) Taking kinetic evaluations of degradation data to the next level with nonlinear mixed-effects models. <i>Environments</i> <b>8</b> (8) 71 <a href="https://doi.org/10.3390/environments8080071" class="external-link">doi:10.3390/environments8080071</a> </td> </tr> @@ -262,6 +268,11 @@ Ranke J, Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical D Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic evaluation of chemical degradation data <i>Environmental Sciences Europe</i> <b>30</b> 17 <a href="https://doi.org/10.1186/s12302-018-0145-1" class="external-link">doi:10.1186/s12302-018-0145-1</a> </td> </tr> +<tr> +<td> +Von Götz N, Nörtersheuser P, Richter O (1999) Population based analysis of pesticide kinetics <i>Chemosphere</i> <b>38</b> 7 <a href="https://doi.org/10.1016/S0045-6535(98)00388-9" class="external-link">doi:10.1016/S0045-6535(98)00388-9</a> +</td> +</tr> </table> </div> <div class="section level2"> diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index e4473e98..bf37df68 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 2.17.1.1 +pandoc: 3.1.1 pkgdown: 2.0.7 pkgdown_sha: ~ articles: @@ -17,7 +17,7 @@ articles: dimethenamid_2018: web_only/dimethenamid_2018.html multistart: web_only/multistart.html saem_benchmarks: web_only/saem_benchmarks.html -last_built: 2023-10-13T14:33Z +last_built: 2023-10-30T14:07Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index 15df31b6..78296f28 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -18,7 +18,7 @@ same dataset."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li </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> @@ -55,6 +55,9 @@ same dataset."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li <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> diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index 50f4599f..92cb2755 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -18,7 +18,7 @@ specified as well."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/aj </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> @@ -55,6 +55,9 @@ specified as well."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/aj <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> diff --git a/docs/reference/DFOP.solution-1.png b/docs/reference/DFOP.solution-1.png Binary files differindex 6b78836f..5ebba336 100644 --- a/docs/reference/DFOP.solution-1.png +++ b/docs/reference/DFOP.solution-1.png diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index ee7f7888..b526ac9e 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -18,7 +18,7 @@ two exponential decline functions."><!-- mathjax --><script src="https://cdnjs.c </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> @@ -55,6 +55,9 @@ two exponential decline functions."><!-- mathjax --><script src="https://cdnjs.c <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> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 81995a34..76a2cda8 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -17,7 +17,7 @@ </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> @@ -54,6 +54,9 @@ <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> diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index b9d4e4cf..2483a632 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -21,7 +21,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib </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> @@ -58,6 +58,9 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib <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> diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index 0f62dc27..d3ee5aba 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -21,7 +21,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib </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> @@ -58,6 +58,9 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib <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> diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index 4339fd5d..cb563cdf 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -21,7 +21,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib </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> @@ -58,6 +58,9 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib <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> diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index eb7162a1..93fc9030 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -21,7 +21,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib </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> @@ -58,6 +58,9 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib <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> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 51e699a1..f1343c5c 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -17,7 +17,7 @@ </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> @@ -54,6 +54,9 @@ <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> diff --git a/docs/reference/FOMC.solution-1.png b/docs/reference/FOMC.solution-1.png Binary files differindex 18a4b586..9d222d42 100644 --- a/docs/reference/FOMC.solution-1.png +++ b/docs/reference/FOMC.solution-1.png diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 4ae477f8..e5087117 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -18,7 +18,7 @@ a decreasing rate constant."><!-- mathjax --><script src="https://cdnjs.cloudfla </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> @@ -55,6 +55,9 @@ a decreasing rate constant."><!-- mathjax --><script src="https://cdnjs.cloudfla <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> diff --git a/docs/reference/HS.solution-1.png b/docs/reference/HS.solution-1.png Binary files differindex 61d89dbc..dd7a76c8 100644 --- a/docs/reference/HS.solution-1.png +++ b/docs/reference/HS.solution-1.png diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 61fbc41c..d24015a0 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -18,7 +18,7 @@ between them."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li </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> @@ -55,6 +55,9 @@ between them."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li <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> diff --git a/docs/reference/IORE.solution-1.png b/docs/reference/IORE.solution-1.png Binary files differindex 54c9dcae..9b6ab58f 100644 --- a/docs/reference/IORE.solution-1.png +++ b/docs/reference/IORE.solution-1.png diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 942c86ca..0ab484cd 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -18,7 +18,7 @@ a concentration dependent rate constant."><!-- mathjax --><script src="https://c </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> @@ -55,6 +55,9 @@ a concentration dependent rate constant."><!-- mathjax --><script src="https://c <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> diff --git a/docs/reference/NAFTA_SOP_2015-1.png b/docs/reference/NAFTA_SOP_2015-1.png Binary files differindex 98d4246c..5d2d434b 100644 --- a/docs/reference/NAFTA_SOP_2015-1.png +++ b/docs/reference/NAFTA_SOP_2015-1.png diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 86610f6e..9a4f668e 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -17,7 +17,7 @@ </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> @@ -54,6 +54,9 @@ <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> diff --git a/docs/reference/NAFTA_SOP_Attachment-1.png b/docs/reference/NAFTA_SOP_Attachment-1.png Binary files differindex a6066441..d8951fc3 100644 --- a/docs/reference/NAFTA_SOP_Attachment-1.png +++ b/docs/reference/NAFTA_SOP_Attachment-1.png diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index 7f72e172..02b33e7d 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -17,7 +17,7 @@ </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> @@ -54,6 +54,9 @@ <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> diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png Binary files differindex fa2316b9..ca982688 100644 --- a/docs/reference/Rplot001.png +++ b/docs/reference/Rplot001.png diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png Binary files differindex fa2316b9..de2d61aa 100644 --- a/docs/reference/Rplot002.png +++ b/docs/reference/Rplot002.png diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png Binary files differindex fa2316b9..8fd02b8e 100644 --- a/docs/reference/Rplot003.png +++ b/docs/reference/Rplot003.png diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png Binary files differindex d5fef0f0..2c12ceb1 100644 --- a/docs/reference/Rplot004.png +++ b/docs/reference/Rplot004.png diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png Binary files differindex 7274c79d..1d28b587 100644 --- a/docs/reference/Rplot005.png +++ b/docs/reference/Rplot005.png diff --git a/docs/reference/Rplot006.png b/docs/reference/Rplot006.png Binary files differindex f646fa66..48f5bbd8 100644 --- a/docs/reference/Rplot006.png +++ b/docs/reference/Rplot006.png diff --git a/docs/reference/Rplot007.png b/docs/reference/Rplot007.png Binary files differindex d3b6ddd4..21a6ea76 100644 --- a/docs/reference/Rplot007.png +++ b/docs/reference/Rplot007.png diff --git a/docs/reference/SFO.solution-1.png b/docs/reference/SFO.solution-1.png Binary files differindex 34fdd460..a00499cb 100644 --- a/docs/reference/SFO.solution-1.png +++ b/docs/reference/SFO.solution-1.png diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index b5aff531..67c7abc7 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -17,7 +17,7 @@ </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> @@ -54,6 +54,9 @@ <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> diff --git a/docs/reference/SFORB.solution-1.png b/docs/reference/SFORB.solution-1.png Binary files differindex 08d25616..7bea3b78 100644 --- a/docs/reference/SFORB.solution-1.png +++ b/docs/reference/SFORB.solution-1.png diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 490fbbb5..a99deac7 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -21,7 +21,7 @@ and no substance in the bound fraction."><!-- mathjax --><script src="https://cd </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> @@ -58,6 +58,9 @@ and no substance in the bound fraction."><!-- mathjax --><script src="https://cd <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> diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png Binary files differindex 68cfb344..4a3b4062 100644 --- a/docs/reference/add_err-1.png +++ b/docs/reference/add_err-1.png diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png Binary files differindex d2f0cf08..5aec1744 100644 --- a/docs/reference/add_err-2.png +++ b/docs/reference/add_err-2.png diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png Binary files differindex 17b5416a..2e71f02f 100644 --- a/docs/reference/add_err-3.png +++ b/docs/reference/add_err-3.png diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 09a92fba..4db51d10 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -19,7 +19,7 @@ may depend on the predicted value and is specified as a standard deviation."><!- </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> @@ -56,6 +56,9 @@ may depend on the predicted value and is specified as a standard deviation."><!- <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> diff --git a/docs/reference/anova.saem.mmkin.html b/docs/reference/anova.saem.mmkin.html index df85fc6f..03ca588d 100644 --- a/docs/reference/anova.saem.mmkin.html +++ b/docs/reference/anova.saem.mmkin.html @@ -20,7 +20,7 @@ the model on the previous line."><!-- mathjax --><script src="https://cdnjs.clou </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> @@ -57,6 +57,9 @@ the model on the previous line."><!-- mathjax --><script src="https://cdnjs.clou <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> diff --git a/docs/reference/aw.html b/docs/reference/aw.html index ffb9dd82..5740d67d 100644 --- a/docs/reference/aw.html +++ b/docs/reference/aw.html @@ -19,7 +19,7 @@ by Burnham and Anderson (2004)."><!-- mathjax --><script src="https://cdnjs.clou </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> @@ -56,6 +56,9 @@ by Burnham and Anderson (2004)."><!-- mathjax --><script src="https://cdnjs.clou <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> diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 33c4a939..48240abc 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -24,7 +24,7 @@ method of Venzon and Moolgavkar (1988)."><!-- mathjax --><script src="https://cd </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> @@ -61,6 +61,9 @@ method of Venzon and Moolgavkar (1988)."><!-- mathjax --><script src="https://cd <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> @@ -254,7 +257,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span><span class="va">f_d_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">ci_profile</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"profile"</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.086 0.000 1.086 </span> +<span class="r-out co"><span class="r-pr">#></span> 2.578 0.005 2.599 </span> <span class="r-in"><span><span class="co"># Using more cores does not save much time here, as parent_0 takes up most of the time</span></span></span> <span class="r-in"><span><span class="co"># If we additionally exclude parent_0 (the confidence of which is often of</span></span></span> <span class="r-in"><span><span class="co"># minor interest), we get a nice performance improvement if we use at least 4 cores</span></span></span> @@ -262,7 +265,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><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">"k_parent_sink"</span>, <span class="st">"k_parent_m1"</span>, <span class="st">"k_m1_sink"</span>, <span class="st">"sigma"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 0.396 0.065 0.263 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.963 0.255 0.636 </span> <span class="r-in"><span><span class="va">ci_profile</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 96.456003640 1.027703e+02</span> diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html index 4735f334..bf02afe3 100644 --- a/docs/reference/create_deg_func.html +++ b/docs/reference/create_deg_func.html @@ -17,7 +17,7 @@ </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> @@ -54,6 +54,9 @@ <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> @@ -148,8 +151,8 @@ <span class="r-in"><span> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.218 1.000 0.217 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.273 1.252 0.274 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.421 1.000 0.412 0.000 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.601 1.428 0.566 0.024 0</span> <span class="r-out co"><span class="r-pr">#></span> sys.child</span> <span class="r-out co"><span class="r-pr">#></span> 1 0</span> <span class="r-out co"><span class="r-pr">#></span> 2 0</span> @@ -162,8 +165,8 @@ <span class="r-in"><span> deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> <span class="r-in"><span> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.352 1.000 0.352 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.486 1.381 0.485 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.762 1.000 0.758 0.004 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 1.194 1.567 1.140 0.052 0</span> <span class="r-out co"><span class="r-pr">#></span> sys.child</span> <span class="r-out co"><span class="r-pr">#></span> 1 0</span> <span class="r-out co"><span class="r-pr">#></span> 2 0</span> diff --git a/docs/reference/ds_mixed-1.png b/docs/reference/ds_mixed-1.png Binary files differindex 7b73613a..053a7253 100644 --- a/docs/reference/ds_mixed-1.png +++ b/docs/reference/ds_mixed-1.png diff --git a/docs/reference/ds_mixed.html b/docs/reference/ds_mixed.html index 9618edae..fdf72593 100644 --- a/docs/reference/ds_mixed.html +++ b/docs/reference/ds_mixed.html @@ -18,7 +18,7 @@ the 'dataset_generation' directory."><!-- mathjax --><script src="https://cdnjs. </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> @@ -55,6 +55,9 @@ the 'dataset_generation' directory."><!-- mathjax --><script src="https://cdnjs. <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> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index b8ccdb2e..4ce6a8ca 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -23,7 +23,7 @@ advantage that the SFORB model can also be used for metabolites."><!-- mathjax - </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> @@ -60,6 +60,9 @@ advantage that the SFORB model can also be used for metabolites."><!-- mathjax - <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> diff --git a/docs/reference/experimental_data_for_UBA-1.png b/docs/reference/experimental_data_for_UBA-1.png Binary files differindex f0dfab85..4de80e3a 100644 --- a/docs/reference/experimental_data_for_UBA-1.png +++ b/docs/reference/experimental_data_for_UBA-1.png diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index bad2ad49..6a02f430 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -45,7 +45,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </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> @@ -82,6 +82,9 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <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> diff --git a/docs/reference/f_time_norm_focus.html b/docs/reference/f_time_norm_focus.html index 17a63ce2..ace7c028 100644 --- a/docs/reference/f_time_norm_focus.html +++ b/docs/reference/f_time_norm_focus.html @@ -18,7 +18,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)."><!-- mathjax </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> @@ -55,6 +55,9 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)."><!-- mathjax <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> diff --git a/docs/reference/focus_soil_moisture.html b/docs/reference/focus_soil_moisture.html index 0d460160..4cb95b77 100644 --- a/docs/reference/focus_soil_moisture.html +++ b/docs/reference/focus_soil_moisture.html @@ -18,7 +18,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5."><!-- mathjax --><script </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> @@ -55,6 +55,9 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5."><!-- mathjax --><script <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> diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html index 4963ad94..79c88c54 100644 --- a/docs/reference/get_deg_func.html +++ b/docs/reference/get_deg_func.html @@ -17,7 +17,7 @@ </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> @@ -54,6 +54,9 @@ <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> diff --git a/docs/reference/hierarchical_kinetics.html b/docs/reference/hierarchical_kinetics.html index 35edf6b3..ab0b3d04 100644 --- a/docs/reference/hierarchical_kinetics.html +++ b/docs/reference/hierarchical_kinetics.html @@ -24,7 +24,7 @@ includes them.'><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/l </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> @@ -61,6 +61,9 @@ includes them.'><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/l <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> diff --git a/docs/reference/illparms.html b/docs/reference/illparms.html index 2dc8f503..bd90c0ed 100644 --- a/docs/reference/illparms.html +++ b/docs/reference/illparms.html @@ -21,7 +21,7 @@ without parameter transformations is used."><!-- mathjax --><script src="https:/ </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> @@ -58,6 +58,9 @@ without parameter transformations is used."><!-- mathjax --><script src="https:/ <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> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 68041671..7937d770 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -18,7 +18,7 @@ transformations."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax </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> @@ -55,6 +55,9 @@ transformations."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax <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> diff --git a/docs/reference/intervals.saem.mmkin.html b/docs/reference/intervals.saem.mmkin.html index d148140e..d52d8501 100644 --- a/docs/reference/intervals.saem.mmkin.html +++ b/docs/reference/intervals.saem.mmkin.html @@ -17,7 +17,7 @@ </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> @@ -54,6 +54,9 @@ <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> diff --git a/docs/reference/llhist.html b/docs/reference/llhist.html index c54796fc..d53d6319 100644 --- a/docs/reference/llhist.html +++ b/docs/reference/llhist.html @@ -18,7 +18,7 @@ original fit is shown as a red vertical line."><!-- mathjax --><script src="http </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> @@ -55,6 +55,9 @@ original fit is shown as a red vertical line."><!-- mathjax --><script src="http <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> diff --git a/docs/reference/loftest-1.png b/docs/reference/loftest-1.png Binary files differindex 750a2acf..f1dc5fa7 100644 --- a/docs/reference/loftest-1.png +++ b/docs/reference/loftest-1.png diff --git a/docs/reference/loftest-2.png b/docs/reference/loftest-2.png Binary files differindex d12c26e7..3f1015a9 100644 --- a/docs/reference/loftest-2.png +++ b/docs/reference/loftest-2.png diff --git a/docs/reference/loftest-3.png b/docs/reference/loftest-3.png Binary files differindex 1b2fd838..e876cbab 100644 --- a/docs/reference/loftest-3.png +++ b/docs/reference/loftest-3.png diff --git a/docs/reference/loftest-4.png b/docs/reference/loftest-4.png Binary files differindex 3beb9d1a..ac44c162 100644 --- a/docs/reference/loftest-4.png +++ b/docs/reference/loftest-4.png diff --git a/docs/reference/loftest-5.png b/docs/reference/loftest-5.png Binary files differindex f60f5ff7..14537feb 100644 --- a/docs/reference/loftest-5.png +++ b/docs/reference/loftest-5.png diff --git a/docs/reference/loftest.html b/docs/reference/loftest.html index a5c5e198..b474ad20 100644 --- a/docs/reference/loftest.html +++ b/docs/reference/loftest.html @@ -20,7 +20,7 @@ lrtest.default from the lmtest package."><!-- mathjax --><script src="https://cd </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> @@ -57,6 +57,9 @@ lrtest.default from the lmtest package."><!-- mathjax --><script src="https://cd <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> diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 1dd40d48..07884f26 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -21,7 +21,7 @@ the error model."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax </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> @@ -58,6 +58,9 @@ the error model."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax <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> diff --git a/docs/reference/logLik.saem.mmkin.html b/docs/reference/logLik.saem.mmkin.html index 2dd52ebd..92d14aed 100644 --- a/docs/reference/logLik.saem.mmkin.html +++ b/docs/reference/logLik.saem.mmkin.html @@ -17,7 +17,7 @@ </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> @@ -54,6 +54,9 @@ <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> diff --git a/docs/reference/logistic.solution-1.png b/docs/reference/logistic.solution-1.png Binary files differindex 23c031de..73dad0a4 100644 --- a/docs/reference/logistic.solution-1.png +++ b/docs/reference/logistic.solution-1.png diff --git a/docs/reference/logistic.solution-2.png b/docs/reference/logistic.solution-2.png Binary files differindex b56db0cb..8d2514a3 100644 --- a/docs/reference/logistic.solution-2.png +++ b/docs/reference/logistic.solution-2.png diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index c936637b..412a981c 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -18,7 +18,7 @@ an increasing rate constant, supposedly caused by microbial growth"><!-- mathjax </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> @@ -55,6 +55,9 @@ an increasing rate constant, supposedly caused by microbial growth"><!-- mathjax <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> diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html index aac564fa..45466262 100644 --- a/docs/reference/lrtest.mkinfit.html +++ b/docs/reference/lrtest.mkinfit.html @@ -21,7 +21,7 @@ and can be expressed by fixing the parameters of the other."><!-- mathjax --><sc </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> @@ -58,6 +58,9 @@ and can be expressed by fixing the parameters of the other."><!-- mathjax --><sc <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> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 40995e83..892aa4e1 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -23,7 +23,7 @@ soil section of the FOCUS guidance."><!-- mathjax --><script src="https://cdnjs. </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> @@ -60,6 +60,9 @@ soil section of the FOCUS guidance."><!-- mathjax --><script src="https://cdnjs. <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> diff --git a/docs/reference/mccall81_245T-1.png b/docs/reference/mccall81_245T-1.png Binary files differindex 5e4ea6ef..79c45fe6 100644 --- a/docs/reference/mccall81_245T-1.png +++ b/docs/reference/mccall81_245T-1.png diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 0c5cb21a..6b057c9d 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -19,7 +19,7 @@ </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> @@ -56,6 +56,9 @@ <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> diff --git a/docs/reference/mean_degparms.html b/docs/reference/mean_degparms.html index 20f539cf..6e17045a 100644 --- a/docs/reference/mean_degparms.html +++ b/docs/reference/mean_degparms.html @@ -17,7 +17,7 @@ </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> @@ -54,6 +54,9 @@ <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> diff --git a/docs/reference/mhmkin-1.png b/docs/reference/mhmkin-1.png Binary files differindex 1c99aead..2ecb6759 100644 --- a/docs/reference/mhmkin-1.png +++ b/docs/reference/mhmkin-1.png diff --git a/docs/reference/mhmkin-2.png b/docs/reference/mhmkin-2.png Binary files differindex 3051bddc..70cd7723 100644 --- a/docs/reference/mhmkin-2.png +++ b/docs/reference/mhmkin-2.png diff --git a/docs/reference/mhmkin.html b/docs/reference/mhmkin.html index 08726dfc..7fcb98fb 100644 --- a/docs/reference/mhmkin.html +++ b/docs/reference/mhmkin.html @@ -22,7 +22,7 @@ mixed-effects model fitting functions."><!-- mathjax --><script src="https://cdn </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> @@ -59,6 +59,9 @@ mixed-effects model fitting functions."><!-- mathjax --><script src="https://cdn <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> diff --git a/docs/reference/mixed-1.png b/docs/reference/mixed-1.png Binary files differindex 846ca6a1..3992b681 100644 --- a/docs/reference/mixed-1.png +++ b/docs/reference/mixed-1.png diff --git a/docs/reference/mixed.html b/docs/reference/mixed.html index 91bb26ce..b0cce30b 100644 --- a/docs/reference/mixed.html +++ b/docs/reference/mixed.html @@ -17,7 +17,7 @@ </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> @@ -54,6 +54,9 @@ <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> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index ab80a18e..9e1487bd 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -19,7 +19,7 @@ variable and several dependent variables as columns."><!-- mathjax --><script sr </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> @@ -56,6 +56,9 @@ variable and several dependent variables as columns."><!-- mathjax --><script sr <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> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 0fb06a94..8bf04bdf 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -19,7 +19,7 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma </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> @@ -56,6 +56,9 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma <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> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index b3c0e5d5..dda44620 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -20,7 +20,7 @@ provided by this package come as mkinds objects nevertheless."><!-- mathjax -->< </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> @@ -57,6 +57,9 @@ provided by this package come as mkinds objects nevertheless."><!-- mathjax -->< <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> diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html index 118f7650..ac6a2471 100644 --- a/docs/reference/mkindsg.html +++ b/docs/reference/mkindsg.html @@ -20,7 +20,7 @@ dataset if no data are supplied."><!-- mathjax --><script src="https://cdnjs.clo </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> @@ -57,6 +57,9 @@ dataset if no data are supplied."><!-- mathjax --><script src="https://cdnjs.clo <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> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 517af738..11837e63 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -18,7 +18,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006."><!-- ma </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> @@ -55,6 +55,9 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006."><!-- ma <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> diff --git a/docs/reference/mkinerrplot-1.png b/docs/reference/mkinerrplot-1.png Binary files differindex 078614fc..49bb1c0e 100644 --- a/docs/reference/mkinerrplot-1.png +++ b/docs/reference/mkinerrplot-1.png diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 136cddcc..6996eb86 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -21,7 +21,7 @@ using the argument show_errplot = TRUE."><!-- mathjax --><script src="https://cd </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> @@ -58,6 +58,9 @@ using the argument show_errplot = TRUE."><!-- mathjax --><script src="https://cd <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> diff --git a/docs/reference/mkinfit-1.png b/docs/reference/mkinfit-1.png Binary files differindex 578f64a5..7c51deb6 100644 --- a/docs/reference/mkinfit-1.png +++ b/docs/reference/mkinfit-1.png diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 88848768..865bdc28 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -25,7 +25,7 @@ likelihood function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ </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> @@ -62,6 +62,9 @@ likelihood function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ <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> @@ -401,17 +404,17 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span><span class="co"># Use shorthand notation for parent only degradation</span></span></span> <span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.4 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:15:57 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:15:57 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.6 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:30:09 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:30:09 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.013 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.031 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -552,9 +555,9 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.226</span> -<span class="r-out co"><span class="r-pr">#></span> 2 eigen 1.845 0.417</span> -<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 2.354 0.532</span> +<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.465</span> +<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.260 1.051</span> +<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 2.282 1.061</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span></span> @@ -581,10 +584,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>diag(.) had 0 or NA entries; non-finite result is doubtful</span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.4 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:16:01 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:16:01 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.6 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:30:19 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:30:19 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> @@ -593,7 +596,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 4062 model solutions performed in 0.718 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 4062 model solutions performed in 1.981 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index e4761e73..11a87acc 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -21,7 +21,7 @@ components."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs </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> @@ -58,6 +58,9 @@ components."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs <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> @@ -266,7 +269,7 @@ in the FOCUS and NAFTA guidance documents are used.</p> <p>For kinetic models with more than one observed variable, a symbolic solution of the system of differential equations is included in the resulting mkinmod object in some cases, speeding up the solution.</p> -<p>If a C compiler is found by <code><a href="https://r-lib.github.io/pkgbuild/reference/has_compiler.html" class="external-link">pkgbuild::has_compiler()</a></code> and there +<p>If a C compiler is found by <code><a href="https://pkgbuild.r-lib.org/reference/has_compiler.html" class="external-link">pkgbuild::has_compiler()</a></code> and there is more than one observed variable in the specification, C code is generated for evaluating the differential equations, compiled using <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code> and added to the resulting mkinmod object.</p> @@ -330,7 +333,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpUEfrXw/file723a02cdd855b.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> +<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpkUSV6I/file244bcd2ba24b1a.so to /home/agsad.admin.ch/f80868656/.local/share/mkin/SFO_SFO.so</span> <span class="r-in"><span><span class="co"># Now we can save the model and restore it in a new session</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="co"># Terminate the R session here if you would like to check, and then do</span></span></span> @@ -383,7 +386,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-out co"><span class="r-pr">#></span> })</span> <span class="r-out co"><span class="r-pr">#></span> return(predicted)</span> <span class="r-out co"><span class="r-pr">#></span> }</span> -<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55555f4ce060></span> +<span class="r-out co"><span class="r-pr">#></span> <environment: 0x560630960080></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># If we have several parallel metabolites</span></span></span> <span class="r-in"><span><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span></span> diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png Binary files differindex 8d34b451..5d6fde87 100644 --- a/docs/reference/mkinparplot-1.png +++ b/docs/reference/mkinparplot-1.png diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 0e7985d8..71957650 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -18,7 +18,7 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma </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> @@ -55,6 +55,9 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma <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> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 8a35bae9..da047bf7 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -18,7 +18,7 @@ plot.mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li </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> @@ -55,6 +55,9 @@ plot.mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li <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> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 5e016527..d52e57cc 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -19,7 +19,7 @@ kinetic parameters and initial values for the state variables."><!-- mathjax --> </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> @@ -56,6 +56,9 @@ kinetic parameters and initial values for the state variables."><!-- mathjax --> <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> @@ -395,10 +398,10 @@ as these always return mapped output.</p></dd> <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.0 0.002</span> -<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.0 0.002</span> -<span class="r-out co"><span class="r-pr">#></span> 1 eigen 3.5 0.007</span> -<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 29.0 0.058</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.0 0.005</span> +<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.0 0.005</span> +<span class="r-out co"><span class="r-pr">#></span> 1 eigen 3.2 0.016</span> +<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 24.4 0.122</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span> <span class="co"># Predict from a fitted model</span></span></span> diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png Binary files differindex 7c64d0f0..97ccd762 100644 --- a/docs/reference/mkinresplot-1.png +++ b/docs/reference/mkinresplot-1.png diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 8cdb55d0..4bfd033e 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -20,7 +20,7 @@ argument show_residuals = TRUE."><!-- mathjax --><script src="https://cdnjs.clou </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> @@ -57,6 +57,9 @@ argument show_residuals = TRUE."><!-- mathjax --><script src="https://cdnjs.clou <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> diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png Binary files differindex 9642db70..2361d3dc 100644 --- a/docs/reference/mmkin-1.png +++ b/docs/reference/mmkin-1.png diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png Binary files differindex d9aa755d..6ce2010f 100644 --- a/docs/reference/mmkin-2.png +++ b/docs/reference/mmkin-2.png diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png Binary files differindex ed8e87e6..5d56da86 100644 --- a/docs/reference/mmkin-3.png +++ b/docs/reference/mmkin-3.png diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png Binary files differindex 11eae1f9..132380a8 100644 --- a/docs/reference/mmkin-4.png +++ b/docs/reference/mmkin-4.png diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png Binary files differindex e88bd59f..4bfcc55e 100644 --- a/docs/reference/mmkin-5.png +++ b/docs/reference/mmkin-5.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index e09dc469..57039604 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -20,7 +20,7 @@ datasets specified in its first two arguments."><!-- mathjax --><script src="htt </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> @@ -57,6 +57,9 @@ datasets specified in its first two arguments."><!-- mathjax --><script src="htt <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> @@ -206,10 +209,10 @@ plotting.</p></div> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">time_default</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.502 0.665 0.624 </span> +<span class="r-out co"><span class="r-pr">#></span> 3.540 1.287 1.429 </span> <span class="r-in"><span><span class="va">time_1</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.824 0.028 1.852 </span> +<span class="r-out co"><span class="r-pr">#></span> 4.074 0.037 4.142 </span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="st">"SFO_lin"</span>, <span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> diff --git a/docs/reference/multistart-1.png b/docs/reference/multistart-1.png Binary files differindex 8133170b..cf3cdca3 100644 --- a/docs/reference/multistart-1.png +++ b/docs/reference/multistart-1.png diff --git a/docs/reference/multistart-2.png b/docs/reference/multistart-2.png Binary files differindex 5cfdbd63..05a160d0 100644 --- a/docs/reference/multistart-2.png +++ b/docs/reference/multistart-2.png diff --git a/docs/reference/multistart.html b/docs/reference/multistart.html index 4da88d48..840f0e01 100644 --- a/docs/reference/multistart.html +++ b/docs/reference/multistart.html @@ -22,7 +22,7 @@ mixed-effects models by Duchesne et al (2021)."><!-- mathjax --><script src="htt </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> @@ -59,6 +59,9 @@ mixed-effects models by Duchesne et al (2021)."><!-- mathjax --><script src="htt <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> diff --git a/docs/reference/nafta-1.png b/docs/reference/nafta-1.png Binary files differindex 98d4246c..5d2d434b 100644 --- a/docs/reference/nafta-1.png +++ b/docs/reference/nafta-1.png diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index 5e733f99..011b766a 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -21,7 +21,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP."><! </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> @@ -58,6 +58,9 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP."><! <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> diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png Binary files differindex 9583da2a..0134107f 100644 --- a/docs/reference/nlme-1.png +++ b/docs/reference/nlme-1.png diff --git a/docs/reference/nlme-2.png b/docs/reference/nlme-2.png Binary files differindex 02aa0573..95739890 100644 --- a/docs/reference/nlme-2.png +++ b/docs/reference/nlme-2.png diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index 60095af6..26c56e54 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -20,7 +20,7 @@ datasets. They are used internally by the nlme.mmkin() method."><!-- mathjax --> </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> @@ -57,6 +57,9 @@ datasets. They are used internally by the nlme.mmkin() method."><!-- mathjax --> <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> diff --git a/docs/reference/nlme.mmkin-1.png b/docs/reference/nlme.mmkin-1.png Binary files differindex 762d5412..7cabb086 100644 --- a/docs/reference/nlme.mmkin-1.png +++ b/docs/reference/nlme.mmkin-1.png diff --git a/docs/reference/nlme.mmkin-2.png b/docs/reference/nlme.mmkin-2.png Binary files differindex 779adbdb..b9a68e92 100644 --- a/docs/reference/nlme.mmkin-2.png +++ b/docs/reference/nlme.mmkin-2.png diff --git a/docs/reference/nlme.mmkin-3.png b/docs/reference/nlme.mmkin-3.png Binary files differindex 046d0238..ce7999bd 100644 --- a/docs/reference/nlme.mmkin-3.png +++ b/docs/reference/nlme.mmkin-3.png diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index d41f9abd..05fbac5c 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -19,7 +19,7 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja </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> @@ -56,6 +56,9 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja <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> diff --git a/docs/reference/nobs.mkinfit.html b/docs/reference/nobs.mkinfit.html index 5781c4dc..c3e24a08 100644 --- a/docs/reference/nobs.mkinfit.html +++ b/docs/reference/nobs.mkinfit.html @@ -17,7 +17,7 @@ </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> @@ -54,6 +54,9 @@ <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> diff --git a/docs/reference/parms.html b/docs/reference/parms.html index 345bb1bc..89831adb 100644 --- a/docs/reference/parms.html +++ b/docs/reference/parms.html @@ -19,7 +19,7 @@ without considering the error structure that was assumed for the fit."><!-- math </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> @@ -56,6 +56,9 @@ without considering the error structure that was assumed for the fit."><!-- math <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> diff --git a/docs/reference/parplot.html b/docs/reference/parplot.html index edefb059..2ae8d39f 100644 --- a/docs/reference/parplot.html +++ b/docs/reference/parplot.html @@ -19,7 +19,7 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><!-- ma </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> @@ -56,6 +56,9 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><!-- ma <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> diff --git a/docs/reference/plot.mixed.mmkin-1.png b/docs/reference/plot.mixed.mmkin-1.png Binary files differindex 2e145bb7..8a09a167 100644 --- a/docs/reference/plot.mixed.mmkin-1.png +++ b/docs/reference/plot.mixed.mmkin-1.png diff --git a/docs/reference/plot.mixed.mmkin-2.png b/docs/reference/plot.mixed.mmkin-2.png Binary files differindex 65f5593b..68a76b47 100644 --- a/docs/reference/plot.mixed.mmkin-2.png +++ b/docs/reference/plot.mixed.mmkin-2.png diff --git a/docs/reference/plot.mixed.mmkin-3.png b/docs/reference/plot.mixed.mmkin-3.png Binary files differindex ef4fa3a7..e18a0da1 100644 --- a/docs/reference/plot.mixed.mmkin-3.png +++ b/docs/reference/plot.mixed.mmkin-3.png diff --git a/docs/reference/plot.mixed.mmkin-4.png b/docs/reference/plot.mixed.mmkin-4.png Binary files differindex d7030dea..f574fdd9 100644 --- a/docs/reference/plot.mixed.mmkin-4.png +++ b/docs/reference/plot.mixed.mmkin-4.png diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html index 507684a1..b0e0f159 100644 --- a/docs/reference/plot.mixed.mmkin.html +++ b/docs/reference/plot.mixed.mmkin.html @@ -17,7 +17,7 @@ </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> @@ -54,6 +54,9 @@ <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> diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png Binary files differindex a48ea72b..ea1032fb 100644 --- a/docs/reference/plot.mkinfit-1.png +++ b/docs/reference/plot.mkinfit-1.png diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png Binary files differindex 43184bcb..4a3ddf29 100644 --- a/docs/reference/plot.mkinfit-2.png +++ b/docs/reference/plot.mkinfit-2.png diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png Binary files differindex 8de1babc..8a9dbd13 100644 --- a/docs/reference/plot.mkinfit-3.png +++ b/docs/reference/plot.mkinfit-3.png diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png Binary files differindex 4b7a5f27..a7164caa 100644 --- a/docs/reference/plot.mkinfit-4.png +++ b/docs/reference/plot.mkinfit-4.png diff --git a/docs/reference/plot.mkinfit-5.png b/docs/reference/plot.mkinfit-5.png Binary files differindex 50c13686..3545b8d8 100644 --- a/docs/reference/plot.mkinfit-5.png +++ b/docs/reference/plot.mkinfit-5.png diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png Binary files differindex 878e3dd6..3d0fb25e 100644 --- a/docs/reference/plot.mkinfit-6.png +++ b/docs/reference/plot.mkinfit-6.png diff --git a/docs/reference/plot.mkinfit-7.png b/docs/reference/plot.mkinfit-7.png Binary files differindex e81d2737..85045bc3 100644 --- a/docs/reference/plot.mkinfit-7.png +++ b/docs/reference/plot.mkinfit-7.png diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 3cd677be..bc4c743f 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -19,7 +19,7 @@ observed data together with the solution of the fitted model."><!-- mathjax -->< </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> @@ -56,6 +56,9 @@ observed data together with the solution of the fitted model."><!-- mathjax -->< <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> diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png Binary files differindex c4fcb9ac..235e33a7 100644 --- a/docs/reference/plot.mmkin-1.png +++ b/docs/reference/plot.mmkin-1.png diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png Binary files differindex 8cc727c3..7af84edf 100644 --- a/docs/reference/plot.mmkin-2.png +++ b/docs/reference/plot.mmkin-2.png diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png Binary files differindex 066958c9..56bfac50 100644 --- a/docs/reference/plot.mmkin-3.png +++ b/docs/reference/plot.mmkin-3.png diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png Binary files differindex 09caa509..29439156 100644 --- a/docs/reference/plot.mmkin-4.png +++ b/docs/reference/plot.mmkin-4.png diff --git a/docs/reference/plot.mmkin-5.png b/docs/reference/plot.mmkin-5.png Binary files differindex c35f7c80..77aa611d 100644 --- a/docs/reference/plot.mmkin-5.png +++ b/docs/reference/plot.mmkin-5.png diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 455a67f3..f3d56cd2 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -21,7 +21,7 @@ the fit of at least one model to the same dataset is shown."><!-- mathjax --><sc </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> @@ -58,6 +58,9 @@ the fit of at least one model to the same dataset is shown."><!-- mathjax --><sc <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> diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html index 0d5a0940..81cfd7b2 100644 --- a/docs/reference/plot.nafta.html +++ b/docs/reference/plot.nafta.html @@ -18,7 +18,7 @@ function (SFO, then IORE, then DFOP)."><!-- mathjax --><script src="https://cdnj </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> @@ -55,6 +55,9 @@ function (SFO, then IORE, then DFOP)."><!-- mathjax --><script src="https://cdnj <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> diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index a50ee30f..847be2cb 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -28,7 +28,7 @@ intervals, nlme </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> @@ -65,6 +65,9 @@ intervals, nlme <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> diff --git a/docs/reference/residuals.mkinfit.html b/docs/reference/residuals.mkinfit.html index f4516026..0115cc3f 100644 --- a/docs/reference/residuals.mkinfit.html +++ b/docs/reference/residuals.mkinfit.html @@ -17,7 +17,7 @@ </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> @@ -54,6 +54,9 @@ <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> diff --git a/docs/reference/saem-1.png b/docs/reference/saem-1.png Binary files differindex 1fa206c4..9e310252 100644 --- a/docs/reference/saem-1.png +++ b/docs/reference/saem-1.png diff --git a/docs/reference/saem-2.png b/docs/reference/saem-2.png Binary files differindex e5c62c35..de1bcf57 100644 --- a/docs/reference/saem-2.png +++ b/docs/reference/saem-2.png diff --git a/docs/reference/saem-3.png b/docs/reference/saem-3.png Binary files differindex f191ad3a..8667ef06 100644 --- a/docs/reference/saem-3.png +++ b/docs/reference/saem-3.png diff --git a/docs/reference/saem-4.png b/docs/reference/saem-4.png Binary files differindex 36deeada..cd464533 100644 --- a/docs/reference/saem-4.png +++ b/docs/reference/saem-4.png diff --git a/docs/reference/saem.html b/docs/reference/saem.html index 9c367984..527718ef 100644 --- a/docs/reference/saem.html +++ b/docs/reference/saem.html @@ -19,7 +19,7 @@ Expectation Maximisation algorithm (SAEM)."><!-- mathjax --><script src="https:/ </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> @@ -56,6 +56,9 @@ Expectation Maximisation algorithm (SAEM)."><!-- mathjax --><script src="https:/ <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> @@ -365,6 +368,8 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-in"><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_saem_fomc</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></span> <span class="r-plt img"><img src="saem-1.png" alt="" width="700" height="433"></span> <span class="r-in"><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_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"individual.fit"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Simulating data using nsim = 1000 simulated datasets</span> +<span class="r-out co"><span class="r-pr">#></span> Computing WRES and npde .</span> <span class="r-plt img"><img src="saem-2.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"npde"</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Simulating data using nsim = 1000 simulated datasets</span> @@ -439,10 +444,10 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span> <span class="r-in"><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_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.4 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:17:55 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:17:55 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.6 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:34:35 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:34:35 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -457,7 +462,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 4.02 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 8.745 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Constant variance </span> diff --git a/docs/reference/schaefer07_complex_case-1.png b/docs/reference/schaefer07_complex_case-1.png Binary files differindex 41665b13..a1d7d2f2 100644 --- a/docs/reference/schaefer07_complex_case-1.png +++ b/docs/reference/schaefer07_complex_case-1.png diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 075f22c0..abef385d 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -19,7 +19,7 @@ </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> @@ -56,6 +56,9 @@ <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> diff --git a/docs/reference/set_nd_nq.html b/docs/reference/set_nd_nq.html index 662779ca..249a7600 100644 --- a/docs/reference/set_nd_nq.html +++ b/docs/reference/set_nd_nq.html @@ -21,7 +21,7 @@ it automates the proposal of Boesten et al (2015)."><!-- mathjax --><script src= </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> @@ -58,6 +58,9 @@ it automates the proposal of Boesten et al (2015)."><!-- mathjax --><script src= <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> diff --git a/docs/reference/sigma_twocomp-1.png b/docs/reference/sigma_twocomp-1.png Binary files differindex 3671c658..0353b72c 100644 --- a/docs/reference/sigma_twocomp-1.png +++ b/docs/reference/sigma_twocomp-1.png diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 24593d2c..06bae61f 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -18,7 +18,7 @@ dependence of the measured value \(y\):"><!-- mathjax --><script src="https://cd </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> @@ -55,6 +55,9 @@ dependence of the measured value \(y\):"><!-- mathjax --><script src="https://cd <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> diff --git a/docs/reference/status.html b/docs/reference/status.html index 1acb7c2e..2ff35423 100644 --- a/docs/reference/status.html +++ b/docs/reference/status.html @@ -17,7 +17,7 @@ </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> @@ -54,6 +54,9 @@ <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> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 5bd1db76..fe24f3a4 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -21,7 +21,7 @@ values."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mat </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> @@ -58,6 +58,9 @@ values."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mat <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> @@ -231,17 +234,17 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <h2>Examples</h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><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="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.4 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:19:51 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:19:51 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.6 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:39:49 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:39:49 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 131 model solutions performed in 0.008 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 131 model solutions performed in 0.02 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/reference/summary.mmkin.html b/docs/reference/summary.mmkin.html index b5f17839..9b10a415 100644 --- a/docs/reference/summary.mmkin.html +++ b/docs/reference/summary.mmkin.html @@ -18,7 +18,7 @@ and gives an overview of ill-defined parameters calculated by illparms."><!-- ma </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> @@ -55,6 +55,9 @@ and gives an overview of ill-defined parameters calculated by illparms."><!-- ma <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> @@ -154,7 +157,7 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms. <span class="r-wrn co"><span class="r-pr">#></span> false convergence (8)</span> <span class="r-in"><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">fits</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.433 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.705 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Status:</span> <span class="r-out co"><span class="r-pr">#></span> dataset</span> diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html index 33d8c01d..58eb3e21 100644 --- a/docs/reference/summary.nlme.mmkin.html +++ b/docs/reference/summary.nlme.mmkin.html @@ -21,7 +21,7 @@ endpoints such as formation fractions and DT50 values. Optionally </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> @@ -58,6 +58,9 @@ endpoints such as formation fractions and DT50 values. Optionally <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> @@ -251,11 +254,11 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-wrn co"><span class="r-pr">#></span> iteration limit reached without convergence (10)</span> <span class="r-in"><span><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span></span> <span class="r-in"><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_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.162 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.4 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:19:53 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:19:53 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.163 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.6 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:39:53 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:39:53 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> @@ -265,7 +268,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.175 s using 4 iterations</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.451 s using 4 iterations</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/reference/summary.saem.mmkin.html b/docs/reference/summary.saem.mmkin.html index d9049ce5..54e5260b 100644 --- a/docs/reference/summary.saem.mmkin.html +++ b/docs/reference/summary.saem.mmkin.html @@ -21,7 +21,7 @@ endpoints such as formation fractions and DT50 values. Optionally </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> @@ -58,6 +58,9 @@ endpoints such as formation fractions and DT50 values. Optionally <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> @@ -330,10 +333,10 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> b.1 0.06401324 0.07920531 0.09439739</span> <span class="r-in"><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_sfo_2</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.4 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:20:09 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:20:09 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.6 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:40:27 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:40:27 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -348,7 +351,7 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.513 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 19.763 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> @@ -619,25 +622,25 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 98.32277831 101.40841461 104.49405092</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01510464 0.01667815 0.01841557</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.20195605 0.27597108 0.36471512</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.07321367 0.10121120 0.13991523</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.01466928 0.01766483 0.02127208</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.35098400 0.46314412 0.57916193</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 98.42519529 101.51623115 104.60726702</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01505059 0.01662123 0.01835577</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.20100222 0.27477835 0.36332008</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.07347479 0.10139028 0.13991179</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.01469861 0.01771120 0.02134125</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.35506898 0.46263682 0.57379888</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> sd(f_parent_qlogis) 0.3832326 0.4435601 0.5038876</span> -<span class="r-out co"><span class="r-pr">#></span> sd(log_k1) 0.1181772 0.2996192 0.4810613</span> -<span class="r-out co"><span class="r-pr">#></span> sd(log_k2) -0.6281964 0.1898692 1.0079349</span> -<span class="r-out co"><span class="r-pr">#></span> sd(g_qlogis) 0.1885523 0.4250717 0.6615911</span> -<span class="r-out co"><span class="r-pr">#></span> corr(log_k2,g_qlogis) -0.8453380 -0.5695240 -0.2937099</span> +<span class="r-out co"><span class="r-pr">#></span> sd(f_parent_qlogis) 0.3827416 0.4435866 0.5044315</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k1) 0.1226277 0.2981783 0.4737289</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k2) -0.5457764 0.1912531 0.9282825</span> +<span class="r-out co"><span class="r-pr">#></span> sd(g_qlogis) 0.1483976 0.3997298 0.6510619</span> +<span class="r-out co"><span class="r-pr">#></span> corr(log_k2,g_qlogis) -0.8537145 -0.5845703 -0.3154261</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.67302582 0.87410123 1.07517663</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.06403679 0.07925211 0.09446744</span> +<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.6732869 0.87421677 1.0751467</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.0640392 0.07925135 0.0944635</span> <span class="r-in"><span><span class="co"># The correlation does not improve the fit judged by AIC and BIC, although</span></span></span> <span class="r-in"><span><span class="co"># the likelihood is higher with the additional parameter</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, <span class="va">f_saem_dfop_sfo_2</span>, <span class="va">f_saem_dfop_sfo_3</span><span class="op">)</span></span></span> @@ -645,7 +648,7 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik</span> <span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo_2 12 806.91 802.23 -391.46</span> -<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo_3 13 807.91 802.83 -390.95</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo_3 13 807.96 802.88 -390.98</span> <span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo 14 810.83 805.36 -391.41</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> diff --git a/docs/reference/summary_listing.html b/docs/reference/summary_listing.html index 9869e2e6..315f7192 100644 --- a/docs/reference/summary_listing.html +++ b/docs/reference/summary_listing.html @@ -18,7 +18,7 @@ option results = "asis".'><!-- mathjax --><script src="https://cdnjs.cloudflare. </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> @@ -55,6 +55,9 @@ option results = "asis".'><!-- mathjax --><script src="https://cdnjs.cloudflare. <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> diff --git a/docs/reference/synthetic_data_for_UBA_2014-1.png b/docs/reference/synthetic_data_for_UBA_2014-1.png Binary files differindex 11eae1f9..132380a8 100644 --- a/docs/reference/synthetic_data_for_UBA_2014-1.png +++ b/docs/reference/synthetic_data_for_UBA_2014-1.png diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html index 91d7f6a6..ee71a4dd 100644 --- a/docs/reference/synthetic_data_for_UBA_2014.html +++ b/docs/reference/synthetic_data_for_UBA_2014.html @@ -32,7 +32,7 @@ Compare also the code in the example section to see the degradation models."><!- </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> @@ -69,6 +69,9 @@ Compare also the code in the example section to see the degradation models."><!- <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> @@ -269,10 +272,10 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="synthetic_data_for_UBA_2014-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.4 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:20:19 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:20:19 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.6 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:40:49 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:40:49 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> @@ -281,7 +284,7 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 848 model solutions performed in 0.154 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 848 model solutions performed in 0.408 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/reference/test_data_from_UBA_2014-1.png b/docs/reference/test_data_from_UBA_2014-1.png Binary files differindex a007a102..e4fc2a4c 100644 --- a/docs/reference/test_data_from_UBA_2014-1.png +++ b/docs/reference/test_data_from_UBA_2014-1.png diff --git a/docs/reference/test_data_from_UBA_2014-2.png b/docs/reference/test_data_from_UBA_2014-2.png Binary files differindex f460ac83..4ce36561 100644 --- a/docs/reference/test_data_from_UBA_2014-2.png +++ b/docs/reference/test_data_from_UBA_2014-2.png diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index b53b5de2..67acdb54 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -18,7 +18,7 @@ </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> @@ -55,6 +55,9 @@ <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> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 2cfe6df7..aade8415 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -22,7 +22,7 @@ the ilr transformation is used."><!-- mathjax --><script src="https://cdnjs.clou </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> @@ -59,6 +59,9 @@ the ilr transformation is used."><!-- mathjax --><script src="https://cdnjs.clou <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> diff --git a/docs/reference/update.mkinfit-1.png b/docs/reference/update.mkinfit-1.png Binary files differindex 9278aefd..12fe1f5b 100644 --- a/docs/reference/update.mkinfit-1.png +++ b/docs/reference/update.mkinfit-1.png diff --git a/docs/reference/update.mkinfit-2.png b/docs/reference/update.mkinfit-2.png Binary files differindex f73a6180..21817f94 100644 --- a/docs/reference/update.mkinfit-2.png +++ b/docs/reference/update.mkinfit-2.png diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html index c1e5edfc..10f9e8a2 100644 --- a/docs/reference/update.mkinfit.html +++ b/docs/reference/update.mkinfit.html @@ -20,7 +20,7 @@ override these starting values."><!-- mathjax --><script src="https://cdnjs.clou </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> @@ -57,6 +57,9 @@ override these starting values."><!-- mathjax --><script src="https://cdnjs.clou <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> |
