diff options
Diffstat (limited to 'docs/articles/prebuilt')
31 files changed, 342 insertions, 597 deletions
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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differindex 1f8eb9f0..277b7c18 100644 --- a/docs/articles/prebuilt/2022_dmta_parent_files/figure-html/plot-saem-dfop-tc-no-ranef-k2-1.png +++ b/docs/articles/prebuilt/2022_dmta_parent_files/figure-html/plot-saem-dfop-tc-no-ranef-k2-1.png diff --git a/docs/articles/prebuilt/2022_dmta_pathway.html b/docs/articles/prebuilt/2022_dmta_pathway.html index ea4bd087..2c3f326a 100644 --- a/docs/articles/prebuilt/2022_dmta_pathway.html +++ b/docs/articles/prebuilt/2022_dmta_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 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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