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-rw-r--r--docs/articles/prebuilt/2022_cyan_pathway.html399
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-rw-r--r--docs/articles/prebuilt/2022_dmta_parent.html475
-rw-r--r--docs/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-dfop-const-1.pngbin130847 -> 128165 bytes
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-rw-r--r--docs/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-dfop-tc-no-ranef-k2-1.pngbin128564 -> 117456 bytes
-rw-r--r--docs/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-fomc-const-1.pngbin101690 -> 100175 bytes
-rw-r--r--docs/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-fomc-tc-1.pngbin97397 -> 92215 bytes
-rw-r--r--docs/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-hs-const-1.pngbin132456 -> 129829 bytes
-rw-r--r--docs/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-hs-tc-1.pngbin102390 -> 98778 bytes
-rw-r--r--docs/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-sfo-const-1.pngbin76259 -> 75641 bytes
-rw-r--r--docs/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-sfo-tc-1.pngbin64271 -> 62897 bytes
-rw-r--r--docs/articles/prebuilt/2022_dmta_parent_files/figure-html/multistart-full-par-1.pngbin72048 -> 74368 bytes
-rw-r--r--docs/articles/prebuilt/2022_dmta_parent_files/figure-html/multistart-reduced-par-1.pngbin66652 -> 70345 bytes
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-rw-r--r--docs/articles/prebuilt/2022_dmta_pathway.html65
-rw-r--r--docs/articles/prebuilt/2022_dmta_pathway_files/figure-html/saem-sforb-path-1-tc-reduced-convergence-1.pngbin160917 -> 155608 bytes
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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 &lt;= tb, k1, k2) * cyan
-d_JCZ38/dt = + f_cyan_to_JCZ38 * ifelse(time &lt;= tb, k1, k2) * cyan -
- k_JCZ38 * JCZ38
-d_J9Z38/dt = + f_cyan_to_J9Z38 * ifelse(time &lt;= 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>
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index 48bfc544..2693b983 100644
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+++ b/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-7-1.png
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index cc7d0126..55a517f0 100644
--- a/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-8-1.png
+++ b/docs/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-8-1.png
Binary files differ
diff --git a/docs/articles/prebuilt/2022_dmta_parent.html b/docs/articles/prebuilt/2022_dmta_parent.html
index 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 &lt;= 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 &lt;= 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>
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index 1f8eb9f0..277b7c18 100644
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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>
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