Update static docs

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 &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>