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| author | Johannes Ranke <jranke@uni-bremen.de> | 2023-11-16 06:02:05 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2023-11-16 06:02:05 +0100 |
| commit | 8b7edd4eaf0d196e674a085f744d1a69260a6c91 (patch) | |
| tree | 96d79f504b775d2626ab2a9f700732bd142d66d9 /docs/articles/prebuilt | |
| parent | 6ae6b5230efd2e3d25b68600bd988ded60d3db77 (diff) | |
Update pkgdown docs to bootstrap 5 with search
Diffstat (limited to 'docs/articles/prebuilt')
32 files changed, 785 insertions, 711 deletions
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data-toc-skip>Testing hierarchical pathway kinetics with -residue data on cyantraniliprole</h1> + +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Testing hierarchical pathway kinetics with residue data on cyantraniliprole</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change on 20 April 2023, -last compiled on 30 October 2023</h4> +last compiled on 16 November 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> - + <div class="d-none name"><code>2022_cyan_pathway.rmd</code></div> </div> @@ -2209,9 +2168,9 @@ Hierarchical SFO path 1 fit with constant variance <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:27:41 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - k_cyan * cyan @@ -2224,7 +2183,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1273.632 s +Fitted in 421.347 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2337,9 +2296,9 @@ Hierarchical SFO path 1 fit with two-component error <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:27:55 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - k_cyan * cyan @@ -2352,7 +2311,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1011.299 s +Fitted in 435.122 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -2467,9 +2426,9 @@ Hierarchical FOMC path 1 fit with constant variance <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:28:33 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -2484,7 +2443,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1368.338 s +Fitted in 473.357 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2612,9 +2571,9 @@ Hierarchical FOMC path 1 fit with two-component error <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:28:46 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -2629,7 +2588,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1120.168 s +Fitted in 486.031 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -2750,9 +2709,9 @@ Hierarchical DFOP path 1 fit with constant variance <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:29:15 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -2771,7 +2730,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1252.502 s +Fitted in 514.477 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2896,9 +2855,9 @@ Hierarchical DFOP path 1 fit with two-component error <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:31:58 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -2917,7 +2876,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1809.832 s +Fitted in 677.928 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3042,9 +3001,9 @@ Hierarchical SFORB path 1 fit with constant variance <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:29:33 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3062,7 +3021,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1230.946 s +Fitted in 532.937 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -3207,9 +3166,9 @@ Hierarchical SFORB path 1 fit with two-component error <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:31:58 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3227,7 +3186,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1633.433 s +Fitted in 677.936 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3372,14 +3331,142 @@ Hierarchical HS path 1 fit with constant variance <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:29:18 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: -d_cyan/dt = - ifelse(time -<p></p></code> -</pre> +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 518.128 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> </div> <div class="section level4"> <h4 id="pathway-2">Pathway 2<a class="anchor" aria-label="anchor" href="#pathway-2"></a> @@ -3390,9 +3477,9 @@ Hierarchical FOMC path 2 fit with two-component error <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:40:28 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -3407,7 +3494,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1185.728 s +Fitted in 499.317 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3556,9 +3643,9 @@ Hierarchical DFOP path 2 fit with constant variance <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:41:25 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -3578,7 +3665,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1329.843 s +Fitted in 555.724 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -3747,9 +3834,9 @@ Hierarchical DFOP path 2 fit with two-component error <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:44:08 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -3769,7 +3856,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1705.043 s +Fitted in 718.988 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3938,9 +4025,9 @@ Hierarchical SFORB path 2 fit with constant variance <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:41:22 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3958,7 +4045,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1379.466 s +Fitted in 553.276 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -4134,9 +4221,9 @@ Hierarchical SFORB path 2 fit with two-component error <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:44:02 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4154,7 +4241,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1739.402 s +Fitted in 713.14 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4335,9 +4422,9 @@ error <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:57:07 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -4352,7 +4439,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1872.856 s +Fitted in 776.732 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4478,9 +4565,9 @@ variance <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:58:51 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4500,7 +4587,7 @@ Data: Model predictions using solution type deSolve -Fitted in 2122.961 s +Fitted in 880.94 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -4577,12 +4664,12 @@ 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 2.59886 2.8932 +a.1 2.7461 2.59274 2.8994 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 0.15614 1.1570 +SD.log_k_JSE76 0.6566 0.15613 1.1570 SD.f_cyan_ilr_1 0.3409 0.11666 0.5652 -SD.f_cyan_ilr_2 0.4385 0.09483 0.7821 +SD.f_cyan_ilr_2 0.4385 0.09482 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 @@ -4593,16 +4680,16 @@ 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 0.15614 1.1570 +SD.log_k_JSE76 0.6566 0.15613 1.1570 SD.f_cyan_ilr_1 0.3409 0.11666 0.5652 -SD.f_cyan_ilr_2 0.4385 0.09483 0.7821 +SD.f_cyan_ilr_2 0.4385 0.09482 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 2.599 2.893 +a.1 2.746 2.593 2.899 Backtransformed parameters: est. lower upper @@ -4644,9 +4731,9 @@ error <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:58:58 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4666,7 +4753,7 @@ Data: Model predictions using solution type deSolve -Fitted in 2175.807 s +Fitted in 887.853 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4810,9 +4897,9 @@ variance <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:58:49 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4830,7 +4917,7 @@ Data: Model predictions using solution type deSolve -Fitted in 2121.218 s +Fitted in 878.878 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -4981,9 +5068,9 @@ error <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:10 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -5001,7 +5088,7 @@ Data: Model predictions using solution type deSolve -Fitted in 2200.603 s +Fitted in 899.539 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -5150,23 +5237,23 @@ 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 4.3.1 (2023-06-16) +<pre><code>R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) -Running under: Ubuntu 22.04.3 LTS +Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -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 +BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 +LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 locale: - [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 + [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 [9] LC_ADDRESS=C LC_TELEPHONE=C -[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C +[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C -time zone: Europe/Zurich +time zone: Europe/Berlin tzcode source: system (glibc) attached base packages: @@ -5174,62 +5261,55 @@ attached base packages: [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.44 mkin_1.2.6 +[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.6 loaded via a namespace (and not attached): - [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_0.5.1 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> + [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_4.3.2 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_4.3.2 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 +[45] MASS_7.3-60 ragg_1.2.5 callr_3.7.3 pkgconfig_2.0.3 +[49] desc_1.4.2 pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 +[53] gtable_0.3.3 glue_1.6.2 systemfonts_1.0.4 highr_0.10 +[57] xfun_0.39 tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 +[61] htmltools_0.5.5 nlme_3.1-163 rmarkdown_2.21 compiler_4.3.2 +[65] prettyunits_1.1.1 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: Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</code></pre> -<pre><code>MemTotal: 247605564 kB</code></pre> +<pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> +<pre><code>MemTotal: 64927712 kB</code></pre> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> -</div> - + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside> </div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p> <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p> <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> + </footer> </div> - </body> 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 50f17cf4..b3d6066b 100644 --- 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class="page-header toc-ignore"> - <h1 data-toc-skip>Testing hierarchical parent degradation kinetics -with residue data on dimethenamid and dimethenamid-P</h1> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change on 5 January -2023, last compiled on 30 October 2023</h4> +2023, last compiled on 16 November 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> - + <div class="d-none name"><code>2022_dmta_parent.rmd</code></div> </div> @@ -1290,9 +1249,9 @@ Plot of the final NLHM DFOP fit <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: 1.2.6 -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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:35 2023 +Date of summary: Thu Nov 16 04:59:35 2023 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -1304,7 +1263,7 @@ Data: Model predictions using solution type analytical -Fitted in 8.975 s +Fitted in 4.4 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1466,9 +1425,9 @@ Hierarchical mkin fit of the SFO model with error model const <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:26 2023 +Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - k_DMTA * DMTA @@ -1478,7 +1437,7 @@ Data: Model predictions using solution type analytical -Fitted in 1.899 s +Fitted in 0.788 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1538,9 +1497,9 @@ Hierarchical mkin fit of the SFO model with error model tc <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:28 2023 +Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - k_DMTA * DMTA @@ -1550,7 +1509,7 @@ Data: Model predictions using solution type analytical -Fitted in 5.364 s +Fitted in 2.428 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1612,9 +1571,9 @@ Hierarchical mkin fit of the FOMC model with error model const <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:27 2023 +Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA @@ -1624,7 +1583,7 @@ Data: Model predictions using solution type analytical -Fitted in 2.944 s +Fitted in 1.28 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1689,9 +1648,9 @@ Hierarchical mkin fit of the FOMC model with error model tc <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:28 2023 +Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA @@ -1701,7 +1660,7 @@ Data: Model predictions using solution type analytical -Fitted in 6.228 s +Fitted in 2.793 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1768,9 +1727,9 @@ Hierarchical mkin fit of the DFOP model with error model const <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:27 2023 +Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -1782,7 +1741,7 @@ Data: Model predictions using solution type analytical -Fitted in 3.231 s +Fitted in 1.752 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1852,9 +1811,9 @@ Hierarchical mkin fit of the DFOP model with error model tc <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:29 2023 +Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -1866,7 +1825,7 @@ Data: Model predictions using solution type analytical -Fitted in 6.71 s +Fitted in 3.186 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1938,27 +1897,166 @@ Hierarchical mkin fit of the HS model with error model const <pre><code> saemix version used for fitting: 3.2 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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:28 2023 +Date of summary: Thu Nov 16 05:00:43 2023 Equations: -d_DMTA/dt = - ifelse(time -<p></p></code> +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 2.28 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> <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: 1.2.6 -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 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:29 2023 +Date of summary: Thu Nov 16 05:00:43 2023 Equations: -d_DMTA/dt = - ifelse(time -<p></p></code> -</pre></pre> +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 3.658 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 97.76571 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> </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> @@ -2007,23 +2105,23 @@ 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 4.3.1 (2023-06-16) +<pre><code>R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) -Running under: Ubuntu 22.04.3 LTS +Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -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 +BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 +LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 locale: - [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 + [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 [9] LC_ADDRESS=C LC_TELEPHONE=C -[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C +[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C -time zone: Europe/Zurich +time zone: Europe/Berlin tzcode source: system (glibc) attached base packages: @@ -2031,59 +2129,52 @@ attached base packages: [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.44 mkin_1.2.6 +[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.6 loaded via a namespace (and not attached): - [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> + [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_4.3.2 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.4 +[13] DBI_1.1.3 mclust_6.0.0 gridExtra_2.3 purrr_1.0.1 +[17] fansi_1.0.4 scales_1.2.1 codetools_0.2-19 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_4.3.2 memoise_2.0.1 +[29] dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.2 +[33] R6_2.5.1 zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 +[37] fs_1.6.2 MASS_7.3-60 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 highr_0.10 +[49] xfun_0.39 tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 +[53] htmltools_0.5.5 nlme_3.1-163 rmarkdown_2.21 compiler_4.3.2 </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: Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</code></pre> -<pre><code>MemTotal: 247605564 kB</code></pre> +<pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> +<pre><code>MemTotal: 64927712 kB</code></pre> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> -</div> - + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside> </div> - <footer><div class="copyright"> + <footer><div 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class="fab fa fab fa-github fa-lg"></span> </a> </li> </ul> </div> -<!--/.nav-collapse --> + + </div> -<!--/.container --> -</div> -<!--/.navbar --> +</nav><div class="container template-article"> + - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1 data-toc-skip>Testing hierarchical pathway kinetics with -residue data on dimethenamid and dimethenamid-P</h1> + +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change on 20 April 2023, -last compiled on 30 October 2023</h4> +last compiled on 16 November 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> - + <div class="d-none name"><code>2022_dmta_pathway.rmd</code></div> </div> @@ -1979,23 +1938,23 @@ 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 4.3.1 (2023-06-16) +<pre><code>R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) -Running under: Ubuntu 22.04.3 LTS +Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -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 +BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 +LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 locale: - [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 + [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 [9] LC_ADDRESS=C LC_TELEPHONE=C -[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C +[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C -time zone: Europe/Zurich +time zone: Europe/Berlin tzcode source: system (glibc) attached base packages: @@ -2003,61 +1962,54 @@ attached base packages: [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.44 mkin_1.2.6 +[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.6 loaded via a namespace (and not attached): - [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_0.5.1 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> + [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_4.3.2 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_4.3.2 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 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_3.1-163 rmarkdown_2.21 compiler_4.3.2 prettyunits_1.1.1</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: Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</code></pre> -<pre><code>MemTotal: 247605564 kB</code></pre> +<pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> +<pre><code>MemTotal: 64927712 kB</code></pre> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside> </div> -</div> - - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p> <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p> <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> + </footer> </div> - </body> diff --git a/docs/articles/prebuilt/2022_dmta_pathway_files/figure-html/saem-sforb-path-1-tc-reduced-convergence-1.png b/docs/articles/prebuilt/2022_dmta_pathway_files/figure-html/saem-sforb-path-1-tc-reduced-convergence-1.png Binary files differindex f1019504..a7187abc 100644 --- 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alt=""><h1>Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change on 4 August 2023, -last compiled on 13 Oktober 2023</h4> +last compiled on 16 November 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2023_mesotrione_parent.rmd" class="external-link"><code>vignettes/prebuilt/2023_mesotrione_parent.rmd</code></a></small> - <div class="hidden name"><code>2023_mesotrione_parent.rmd</code></div> - + <div class="d-none name"><code>2023_mesotrione_parent.rmd</code></div> </div> @@ -2480,7 +2439,7 @@ further refined to make them fully identifiable.</p> <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 4.3.1 (2023-06-16) +<pre><code>R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 12 (bookworm) @@ -2509,19 +2468,18 @@ other attached packages: 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_4.3.1 fastmap_1.1.1 cellranger_1.1.0 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 codetools_0.2-19 -[21] textshaping_0.3.6 jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1 -[25] munsell_0.5.0 cachem_1.0.8 yaml_2.3.7 tools_4.3.1 -[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 MASS_7.3-60 ragg_1.2.5 -[41] pkgconfig_2.0.3 desc_1.4.2 pkgdown_2.0.7 bslib_0.4.2 -[45] pillar_1.9.0 gtable_0.3.3 glue_1.6.2 systemfonts_1.0.4 -[49] highr_0.10 xfun_0.39 tibble_3.2.1 lmtest_0.9-40 -[53] tidyselect_1.2.0 htmltools_0.5.5 nlme_3.1-162 rmarkdown_2.21 -[57] compiler_4.3.1 readxl_1.4.2 </code></pre> + [9] grid_4.3.2 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.4 +[13] DBI_1.1.3 mclust_6.0.0 gridExtra_2.3 purrr_1.0.1 +[17] fansi_1.0.4 scales_1.2.1 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_4.3.2 memoise_2.0.1 dplyr_1.1.2 +[29] colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.2 R6_2.5.1 +[33] zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 fs_1.6.2 +[37] MASS_7.3-60 ragg_1.2.5 pkgconfig_2.0.3 desc_1.4.2 +[41] pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 gtable_0.3.3 +[45] glue_1.6.2 systemfonts_1.0.4 xfun_0.39 tibble_3.2.1 +[49] lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5 nlme_3.1-163 +[53] rmarkdown_2.21 compiler_4.3.2 </code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> @@ -2530,34 +2488,27 @@ loaded via a namespace (and not attached): <pre><code>MemTotal: 64928100 kB</code></pre> </div> </div> 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