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Diffstat (limited to 'docs/articles/prebuilt/2022_cyan_pathway.html')
| -rw-r--r-- | docs/articles/prebuilt/2022_cyan_pathway.html | 399 |
1 files changed, 137 insertions, 262 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> |