From 8b7edd4eaf0d196e674a085f744d1a69260a6c91 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 16 Nov 2023 06:02:05 +0100 Subject: Update pkgdown docs to bootstrap 5 with search --- docs/articles/prebuilt/2022_cyan_pathway.html | 552 +++++++++++++++----------- 1 file changed, 316 insertions(+), 236 deletions(-) (limited to 'docs/articles/prebuilt/2022_cyan_pathway.html') diff --git a/docs/articles/prebuilt/2022_cyan_pathway.html b/docs/articles/prebuilt/2022_cyan_pathway.html index c22b07e4..5325018a 100644 --- a/docs/articles/prebuilt/2022_cyan_pathway.html +++ b/docs/articles/prebuilt/2022_cyan_pathway.html @@ -4,145 +4,104 @@ - + + Testing hierarchical pathway kinetics with residue data on cyantraniliprole • mkin - - - + + + - - + - + + Skip to contents -
-
-
-
-

Testing hierarchical pathway kinetics with -residue data on cyantraniliprole

+ +
+
+

Testing hierarchical pathway kinetics with residue data on cyantraniliprole

Johannes Ranke

Last change on 20 April 2023, -last compiled on 30 October 2023

+last compiled on 16 November 2023 Source: vignettes/prebuilt/2022_cyan_pathway.rmd - - +
2022_cyan_pathway.rmd
@@ -2209,9 +2168,9 @@ Hierarchical SFO path 1 fit with constant variance 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 10:03:13 2023 
-Date of summary: Mon Oct 30 11:18:26 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:27:41 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
 d_cyan/dt = - k_cyan * cyan
@@ -2224,7 +2183,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1273.632 s
+Fitted in 421.347 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -2337,9 +2296,9 @@ Hierarchical SFO path 1 fit with two-component error
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 09:58:51 2023 
-Date of summary: Mon Oct 30 11:18:26 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:27:55 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
 d_cyan/dt = - k_cyan * cyan
@@ -2352,7 +2311,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1011.299 s
+Fitted in 435.122 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -2467,9 +2426,9 @@ Hierarchical FOMC path 1 fit with constant variance
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 10:04:48 2023 
-Date of summary: Mon Oct 30 11:18:26 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:28:33 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -2484,7 +2443,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1368.338 s
+Fitted in 473.357 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -2612,9 +2571,9 @@ Hierarchical FOMC path 1 fit with two-component error
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 10:00:40 2023 
-Date of summary: Mon Oct 30 11:18:26 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:28:46 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -2629,7 +2588,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1120.168 s
+Fitted in 486.031 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -2750,9 +2709,9 @@ Hierarchical DFOP path 1 fit with constant variance
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 10:02:52 2023 
-Date of summary: Mon Oct 30 11:18:26 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:29:15 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -2771,7 +2730,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1252.502 s
+Fitted in 514.477 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -2896,9 +2855,9 @@ Hierarchical DFOP path 1 fit with two-component error
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 10:12:10 2023 
-Date of summary: Mon Oct 30 11:18:26 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:31:58 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -2917,7 +2876,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1809.832 s
+Fitted in 677.928 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -3042,9 +3001,9 @@ Hierarchical SFORB path 1 fit with constant variance
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 10:02:30 2023 
-Date of summary: Mon Oct 30 11:18:26 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:29:33 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -3062,7 +3021,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1230.946 s
+Fitted in 532.937 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -3207,9 +3166,9 @@ Hierarchical SFORB path 1 fit with two-component error
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 10:09:13 2023 
-Date of summary: Mon Oct 30 11:18:26 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:31:58 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -3227,7 +3186,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1633.433 s
+Fitted in 677.936 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -3372,14 +3331,142 @@ Hierarchical HS path 1 fit with constant variance
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 10:02:52 2023 
-Date of summary: Mon Oct 30 11:18:27 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:29:18 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
-d_cyan/dt = - ifelse(time 
-

-

+d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan
+d_JCZ38/dt = + f_cyan_to_JCZ38 * ifelse(time <= tb, k1, k2) * cyan -
+           k_JCZ38 * JCZ38
+d_J9Z38/dt = + f_cyan_to_J9Z38 * ifelse(time <= tb, k1, k2) * cyan -
+           k_J9Z38 * J9Z38
+d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76
+
+Data:
+433 observations of 4 variable(s) grouped in 5 datasets
+
+Model predictions using solution type deSolve 
+
+Fitted in 518.128 s
+Using 300, 100 iterations and 10 chains
+
+Variance model: Constant variance 
+
+Starting values for degradation parameters:
+        cyan_0    log_k_JCZ38    log_k_J9Z38    log_k_JSE76   f_cyan_ilr_1 
+      102.8845        -3.4495        -4.9355        -5.6040         0.6468 
+  f_cyan_ilr_2 f_JCZ38_qlogis         log_k1         log_k2         log_tb 
+        1.2396         9.7220        -2.9079        -4.1810         1.7813 
+
+Fixed degradation parameter values:
+None
+
+Starting values for random effects (square root of initial entries in omega):
+               cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1
+cyan_0          5.406        0.00        0.00       0.000       0.0000
+log_k_JCZ38     0.000        2.33        0.00       0.000       0.0000
+log_k_J9Z38     0.000        0.00        1.59       0.000       0.0000
+log_k_JSE76     0.000        0.00        0.00       1.013       0.0000
+f_cyan_ilr_1    0.000        0.00        0.00       0.000       0.6367
+f_cyan_ilr_2    0.000        0.00        0.00       0.000       0.0000
+f_JCZ38_qlogis  0.000        0.00        0.00       0.000       0.0000
+log_k1          0.000        0.00        0.00       0.000       0.0000
+log_k2          0.000        0.00        0.00       0.000       0.0000
+log_tb          0.000        0.00        0.00       0.000       0.0000
+               f_cyan_ilr_2 f_JCZ38_qlogis log_k1 log_k2 log_tb
+cyan_0                0.000           0.00 0.0000 0.0000 0.0000
+log_k_JCZ38           0.000           0.00 0.0000 0.0000 0.0000
+log_k_J9Z38           0.000           0.00 0.0000 0.0000 0.0000
+log_k_JSE76           0.000           0.00 0.0000 0.0000 0.0000
+f_cyan_ilr_1          0.000           0.00 0.0000 0.0000 0.0000
+f_cyan_ilr_2          2.038           0.00 0.0000 0.0000 0.0000
+f_JCZ38_qlogis        0.000          10.33 0.0000 0.0000 0.0000
+log_k1                0.000           0.00 0.7006 0.0000 0.0000
+log_k2                0.000           0.00 0.0000 0.8928 0.0000
+log_tb                0.000           0.00 0.0000 0.0000 0.6773
+
+Starting values for error model parameters:
+a.1 
+  1 
+
+Results:
+
+Likelihood computed by importance sampling
+   AIC  BIC logLik
+  2427 2419  -1194
+
+Optimised parameters:
+                      est.      lower      upper
+cyan_0            101.9660  1.005e+02  1.035e+02
+log_k_JCZ38        -3.4698 -4.716e+00 -2.224e+00
+log_k_J9Z38        -5.0947 -5.740e+00 -4.450e+00
+log_k_JSE76        -5.5977 -6.321e+00 -4.875e+00
+f_cyan_ilr_1        0.6595  3.734e-01  9.456e-01
+f_cyan_ilr_2        0.5905  1.664e-01  1.015e+00
+f_JCZ38_qlogis     25.8627 -4.224e+05  4.225e+05
+log_k1             -3.0884 -3.453e+00 -2.723e+00
+log_k2             -4.3877 -4.778e+00 -3.998e+00
+log_tb              2.3057  1.715e+00  2.896e+00
+a.1                 3.3228         NA         NA
+SD.log_k_JCZ38      1.4071         NA         NA
+SD.log_k_J9Z38      0.5774         NA         NA
+SD.log_k_JSE76      0.6214         NA         NA
+SD.f_cyan_ilr_1     0.3058         NA         NA
+SD.f_cyan_ilr_2     0.3470         NA         NA
+SD.f_JCZ38_qlogis   0.0644         NA         NA
+SD.log_k1           0.3994         NA         NA
+SD.log_k2           0.4373         NA         NA
+SD.log_tb           0.6419         NA         NA
+
+Correlation is not available
+
+Random effects:
+                    est. lower upper
+SD.log_k_JCZ38    1.4071    NA    NA
+SD.log_k_J9Z38    0.5774    NA    NA
+SD.log_k_JSE76    0.6214    NA    NA
+SD.f_cyan_ilr_1   0.3058    NA    NA
+SD.f_cyan_ilr_2   0.3470    NA    NA
+SD.f_JCZ38_qlogis 0.0644    NA    NA
+SD.log_k1         0.3994    NA    NA
+SD.log_k2         0.4373    NA    NA
+SD.log_tb         0.6419    NA    NA
+
+Variance model:
+     est. lower upper
+a.1 3.323    NA    NA
+
+Backtransformed parameters:
+                      est.     lower     upper
+cyan_0           1.020e+02 1.005e+02 1.035e+02
+k_JCZ38          3.112e-02 8.951e-03 1.082e-01
+k_J9Z38          6.129e-03 3.216e-03 1.168e-02
+k_JSE76          3.706e-03 1.798e-03 7.639e-03
+f_cyan_to_JCZ38  5.890e-01        NA        NA
+f_cyan_to_J9Z38  2.318e-01        NA        NA
+f_JCZ38_to_JSE76 1.000e+00 0.000e+00 1.000e+00
+k1               4.558e-02 3.164e-02 6.565e-02
+k2               1.243e-02 8.417e-03 1.835e-02
+tb               1.003e+01 5.557e+00 1.811e+01
+
+Resulting formation fractions:
+                   ff
+cyan_JCZ38  5.890e-01
+cyan_J9Z38  2.318e-01
+cyan_sink   1.793e-01
+JCZ38_JSE76 1.000e+00
+JCZ38_sink  5.861e-12
+
+Estimated disappearance times:
+        DT50   DT90 DT50back DT50_k1 DT50_k2
+cyan   29.02 158.51    47.72   15.21   55.77
+JCZ38  22.27  73.98       NA      NA      NA
+J9Z38 113.09 375.69       NA      NA      NA
+JSE76 187.01 621.23       NA      NA      NA
+
+

+

Pathway 2 @@ -3390,9 +3477,9 @@ Hierarchical FOMC path 2 fit with two-component error 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 10:32:26 2023 
-Date of summary: Mon Oct 30 11:18:27 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:40:28 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -3407,7 +3494,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1185.728 s
+Fitted in 499.317 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -3556,9 +3643,9 @@ Hierarchical DFOP path 2 fit with constant variance
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 10:34:49 2023 
-Date of summary: Mon Oct 30 11:18:27 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:41:25 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -3578,7 +3665,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1329.843 s
+Fitted in 555.724 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -3747,9 +3834,9 @@ Hierarchical DFOP path 2 fit with two-component error
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 10:41:05 2023 
-Date of summary: Mon Oct 30 11:18:27 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:44:08 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -3769,7 +3856,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1705.043 s
+Fitted in 718.988 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -3938,9 +4025,9 @@ Hierarchical SFORB path 2 fit with constant variance
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 10:35:39 2023 
-Date of summary: Mon Oct 30 11:18:27 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:41:22 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -3958,7 +4045,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1379.466 s
+Fitted in 553.276 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -4134,9 +4221,9 @@ Hierarchical SFORB path 2 fit with two-component error
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 10:41:39 2023 
-Date of summary: Mon Oct 30 11:18:27 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:44:02 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -4154,7 +4241,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1739.402 s
+Fitted in 713.14 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -4335,9 +4422,9 @@ error
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 11:12:56 2023 
-Date of summary: Mon Oct 30 11:18:27 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:57:07 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -4352,7 +4439,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1872.856 s
+Fitted in 776.732 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -4478,9 +4565,9 @@ variance
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 11:17:06 2023 
-Date of summary: Mon Oct 30 11:18:27 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:58:51 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4500,7 +4587,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 2122.961 s
+Fitted in 880.94 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -4577,12 +4664,12 @@ f_JSE76_qlogis     1.9658      NA     NA
 log_k1            -1.9503      NA     NA
 log_k2            -4.4745      NA     NA
 g_qlogis          -0.4967      NA     NA
-a.1                2.7461 2.59886 2.8932
+a.1                2.7461 2.59274 2.8994
 SD.log_k_JCZ38     1.3178 0.47602 2.1596
 SD.log_k_J9Z38     0.7022 0.15061 1.2538
-SD.log_k_JSE76     0.6566 0.15614 1.1570
+SD.log_k_JSE76     0.6566 0.15613 1.1570
 SD.f_cyan_ilr_1    0.3409 0.11666 0.5652
-SD.f_cyan_ilr_2    0.4385 0.09483 0.7821
+SD.f_cyan_ilr_2    0.4385 0.09482 0.7821
 SD.log_k1          0.7381 0.25599 1.2202
 SD.log_k2          0.5133 0.18152 0.8450
 SD.g_qlogis        0.9866 0.35681 1.6164
@@ -4593,16 +4680,16 @@ Random effects:
                   est.   lower  upper
 SD.log_k_JCZ38  1.3178 0.47602 2.1596
 SD.log_k_J9Z38  0.7022 0.15061 1.2538
-SD.log_k_JSE76  0.6566 0.15614 1.1570
+SD.log_k_JSE76  0.6566 0.15613 1.1570
 SD.f_cyan_ilr_1 0.3409 0.11666 0.5652
-SD.f_cyan_ilr_2 0.4385 0.09483 0.7821
+SD.f_cyan_ilr_2 0.4385 0.09482 0.7821
 SD.log_k1       0.7381 0.25599 1.2202
 SD.log_k2       0.5133 0.18152 0.8450
 SD.g_qlogis     0.9866 0.35681 1.6164
 
 Variance model:
      est. lower upper
-a.1 2.746 2.599 2.893
+a.1 2.746 2.593 2.899
 
 Backtransformed parameters:
                       est. lower upper
@@ -4644,9 +4731,9 @@ error
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 11:17:59 2023 
-Date of summary: Mon Oct 30 11:18:27 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:58:58 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4666,7 +4753,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 2175.807 s
+Fitted in 887.853 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -4810,9 +4897,9 @@ variance
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 11:17:04 2023 
-Date of summary: Mon Oct 30 11:18:27 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:58:49 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -4830,7 +4917,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 2121.218 s
+Fitted in 878.878 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -4981,9 +5068,9 @@ error
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-R version used for fitting:         4.3.1 
-Date of fit:     Mon Oct 30 11:18:24 2023 
-Date of summary: Mon Oct 30 11:18:27 2023 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:59:10 2023 
+Date of summary: Thu Nov 16 04:59:11 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -5001,7 +5088,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 2200.603 s
+Fitted in 899.539 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -5150,23 +5237,23 @@ JSE76  25.44  84.51       NA           NA           NA
 

 
Session info
 

-
R version 4.3.1 (2023-06-16)
+
R version 4.3.2 (2023-10-31)
 Platform: x86_64-pc-linux-gnu (64-bit)
-Running under: Ubuntu 22.04.3 LTS
+Running under: Debian GNU/Linux 12 (bookworm)
 
 Matrix products: default
-BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
-LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
+BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 
+LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
 
 locale:
- [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
- [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
- [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
- [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
+ [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
+ [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8    
+ [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8   
+ [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
-[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
+[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       
 
-time zone: Europe/Zurich
+time zone: Europe/Berlin
 tzcode source: system (glibc)
 
 attached base packages:
@@ -5174,62 +5261,55 @@ attached base packages:
 [8] base     
 
 other attached packages:
-[1] saemix_3.2 npde_3.3   knitr_1.44 mkin_1.2.6
+[1] saemix_3.2 npde_3.3   knitr_1.42 mkin_1.2.6
 
 loaded via a namespace (and not attached):
- [1] sass_0.4.7        utf8_1.2.3        generics_0.1.3    stringi_1.7.12   
- [5] lattice_0.21-9    digest_0.6.33     magrittr_2.0.3    evaluate_0.22    
- [9] grid_4.3.1        fastmap_1.1.1     cellranger_1.1.0  rprojroot_2.0.3  
-[13] jsonlite_1.8.7    processx_3.8.2    pkgbuild_1.4.2    deSolve_1.35     
-[17] mclust_6.0.0      ps_1.7.5          gridExtra_2.3     purrr_1.0.1      
-[21] fansi_1.0.4       scales_1.2.1      codetools_0.2-19  textshaping_0.3.6
-[25] jquerylib_0.1.4   cli_3.6.1         crayon_1.5.2      rlang_1.1.1      
-[29] munsell_0.5.0     cachem_1.0.8      yaml_2.3.7        inline_0.3.19    
-[33] tools_4.3.1       memoise_2.0.1     dplyr_1.1.2       colorspace_2.1-0 
-[37] ggplot2_3.4.2     vctrs_0.6.3       R6_2.5.1          zoo_1.8-12       
-[41] lifecycle_1.0.3   stringr_1.5.0     fs_1.6.3          MASS_7.3-60      
-[45] ragg_1.2.5        callr_3.7.3       pkgconfig_2.0.3   desc_1.4.2       
-[49] pkgdown_2.0.7     bslib_0.5.1       pillar_1.9.0      gtable_0.3.3     
-[53] glue_1.6.2        systemfonts_1.0.4 xfun_0.40         tibble_3.2.1     
-[57] lmtest_0.9-40     tidyselect_1.2.0  rstudioapi_0.15.0 htmltools_0.5.6.1
-[61] nlme_3.1-163      rmarkdown_2.23    compiler_4.3.1    prettyunits_1.2.0
-[65] readxl_1.4.2     

+ [1] sass_0.4.6        utf8_1.2.3        generics_0.1.3    stringi_1.7.12   
+ [5] lattice_0.21-8    digest_0.6.31     magrittr_2.0.3    evaluate_0.21    
+ [9] grid_4.3.2        fastmap_1.1.1     cellranger_1.1.0  rprojroot_2.0.3  
+[13] jsonlite_1.8.4    processx_3.8.1    pkgbuild_1.4.0    deSolve_1.35     
+[17] DBI_1.1.3         mclust_6.0.0      ps_1.7.5          gridExtra_2.3    
+[21] purrr_1.0.1       fansi_1.0.4       scales_1.2.1      codetools_0.2-19 
+[25] textshaping_0.3.6 jquerylib_0.1.4   cli_3.6.1         crayon_1.5.2     
+[29] rlang_1.1.1       munsell_0.5.0     cachem_1.0.8      yaml_2.3.7       
+[33] inline_0.3.19     tools_4.3.2       memoise_2.0.1     dplyr_1.1.2      
+[37] colorspace_2.1-0  ggplot2_3.4.2     vctrs_0.6.2       R6_2.5.1         
+[41] zoo_1.8-12        lifecycle_1.0.3   stringr_1.5.0     fs_1.6.2         
+[45] MASS_7.3-60       ragg_1.2.5        callr_3.7.3       pkgconfig_2.0.3  
+[49] desc_1.4.2        pkgdown_2.0.7     bslib_0.4.2       pillar_1.9.0     
+[53] gtable_0.3.3      glue_1.6.2        systemfonts_1.0.4 highr_0.10       
+[57] xfun_0.39         tibble_3.2.1      lmtest_0.9-40     tidyselect_1.2.0 
+[61] htmltools_0.5.5   nlme_3.1-163      rmarkdown_2.21    compiler_4.3.2   
+[65] prettyunits_1.1.1 readxl_1.4.2     

 

 

 
Hardware info
 

-
CPU model: Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz

-
MemTotal:       247605564 kB

+
CPU model: AMD Ryzen 9 7950X 16-Core Processor

+
MemTotal:       64927712 kB

-
- - - +
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- -- cgit v1.2.1