From b7901aac76df753ec1213cb02bebea055965ee87 Mon Sep 17 00:00:00 2001
From: Ranke Johannes Last change 31 January 2019
-(rebuilt 2023-05-19)
+(rebuilt 2023-10-30)
Source: vignettes/FOCUS_D.rmd
FOCUS_D.rmd
mkinparplot
function.
summary
method for mkinfit
objects.
summary(fit)
## mkin version used for fitting: 1.2.4
-## R version used for fitting: 4.3.0
-## Date of fit: Fri May 19 09:20:23 2023
-## Date of summary: Fri May 19 09:20:23 2023
+## mkin version used for fitting: 1.2.6
+## R version used for fitting: 4.3.1
+## Date of fit: Mon Oct 30 09:40:58 2023
+## Date of summary: Mon Oct 30 09:40:58 2023
##
## Equations:
## d_parent/dt = - k_parent * parent
@@ -248,7 +251,7 @@ the mkinparplot
function.
##
## Model predictions using solution type analytical
##
-## Fitted using 401 model solutions performed in 0.048 s
+## Fitted using 401 model solutions performed in 0.123 s
##
## Error model: Constant variance
##
diff --git a/docs/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/articles/FOCUS_D_files/figure-html/plot-1.png
index c0832a1a..f0b51c1f 100644
Binary files a/docs/articles/FOCUS_D_files/figure-html/plot-1.png and b/docs/articles/FOCUS_D_files/figure-html/plot-1.png differ
diff --git a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png
index 02cfcfb4..f6180470 100644
Binary files a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png and b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png differ
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 @@
@@ -73,6 +73,9 @@
Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P
+
+ Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione
+
Testing hierarchical pathway kinetics with residue data on cyantraniliprole
@@ -135,7 +138,7 @@ residue data on cyantraniliprole
Ranke
Last change on 20 April 2023,
-last compiled on 19 Mai 2023
+last compiled on 30 October 2023
Source: vignettes/prebuilt/2022_cyan_pathway.rmd
2022_cyan_pathway.rmd
@@ -155,7 +158,7 @@ be fitted with the mkin package.
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.
-The mkin package is used in version 1.2.4 which is currently under
+
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
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
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
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
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
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
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
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
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
saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.4
-R version used for fitting: 4.3.0
-Date of fit: Fri May 19 09:28:57 2023
-Date of summary: Fri May 19 09:57:33 2023
+mkin version used for pre-fitting: 1.2.6
+R version used for fitting: 4.3.1
+Date of fit: Mon Oct 30 10:02:52 2023
+Date of summary: Mon Oct 30 11:18:27 2023
Equations:
-d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan
-d_JCZ38/dt = + f_cyan_to_JCZ38 * ifelse(time <= tb, k1, k2) * cyan -
- k_JCZ38 * JCZ38
-d_J9Z38/dt = + f_cyan_to_J9Z38 * ifelse(time <= tb, k1, k2) * cyan -
- k_J9Z38 * J9Z38
-d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76
-
-Data:
-433 observations of 4 variable(s) grouped in 5 datasets
-
-Model predictions using solution type deSolve
-
-Fitted in 485.304 s
-Using 300, 100 iterations and 10 chains
-
-Variance model: Constant variance
-
-Starting values for degradation parameters:
- cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1
- 102.8845 -3.4495 -4.9355 -5.6040 0.6468
- f_cyan_ilr_2 f_JCZ38_qlogis log_k1 log_k2 log_tb
- 1.2396 9.7220 -2.9079 -4.1810 1.7813
-
-Fixed degradation parameter values:
-None
-
-Starting values for random effects (square root of initial entries in omega):
- cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1
-cyan_0 5.406 0.00 0.00 0.000 0.0000
-log_k_JCZ38 0.000 2.33 0.00 0.000 0.0000
-log_k_J9Z38 0.000 0.00 1.59 0.000 0.0000
-log_k_JSE76 0.000 0.00 0.00 1.013 0.0000
-f_cyan_ilr_1 0.000 0.00 0.00 0.000 0.6367
-f_cyan_ilr_2 0.000 0.00 0.00 0.000 0.0000
-f_JCZ38_qlogis 0.000 0.00 0.00 0.000 0.0000
-log_k1 0.000 0.00 0.00 0.000 0.0000
-log_k2 0.000 0.00 0.00 0.000 0.0000
-log_tb 0.000 0.00 0.00 0.000 0.0000
- f_cyan_ilr_2 f_JCZ38_qlogis log_k1 log_k2 log_tb
-cyan_0 0.000 0.00 0.0000 0.0000 0.0000
-log_k_JCZ38 0.000 0.00 0.0000 0.0000 0.0000
-log_k_J9Z38 0.000 0.00 0.0000 0.0000 0.0000
-log_k_JSE76 0.000 0.00 0.0000 0.0000 0.0000
-f_cyan_ilr_1 0.000 0.00 0.0000 0.0000 0.0000
-f_cyan_ilr_2 2.038 0.00 0.0000 0.0000 0.0000
-f_JCZ38_qlogis 0.000 10.33 0.0000 0.0000 0.0000
-log_k1 0.000 0.00 0.7006 0.0000 0.0000
-log_k2 0.000 0.00 0.0000 0.8928 0.0000
-log_tb 0.000 0.00 0.0000 0.0000 0.6773
-
-Starting values for error model parameters:
-a.1
- 1
-
-Results:
-
-Likelihood computed by importance sampling
- AIC BIC logLik
- 2427 2419 -1194
-
-Optimised parameters:
- est. lower upper
-cyan_0 101.9660 1.005e+02 1.035e+02
-log_k_JCZ38 -3.4698 -4.716e+00 -2.224e+00
-log_k_J9Z38 -5.0947 -5.740e+00 -4.450e+00
-log_k_JSE76 -5.5977 -6.321e+00 -4.875e+00
-f_cyan_ilr_1 0.6595 3.734e-01 9.456e-01
-f_cyan_ilr_2 0.5905 1.664e-01 1.015e+00
-f_JCZ38_qlogis 25.8627 -4.224e+05 4.225e+05
-log_k1 -3.0884 -3.453e+00 -2.723e+00
-log_k2 -4.3877 -4.778e+00 -3.998e+00
-log_tb 2.3057 1.715e+00 2.896e+00
-a.1 3.3228 NA NA
-SD.log_k_JCZ38 1.4071 NA NA
-SD.log_k_J9Z38 0.5774 NA NA
-SD.log_k_JSE76 0.6214 NA NA
-SD.f_cyan_ilr_1 0.3058 NA NA
-SD.f_cyan_ilr_2 0.3470 NA NA
-SD.f_JCZ38_qlogis 0.0644 NA NA
-SD.log_k1 0.3994 NA NA
-SD.log_k2 0.4373 NA NA
-SD.log_tb 0.6419 NA NA
-
-Correlation is not available
-
-Random effects:
- est. lower upper
-SD.log_k_JCZ38 1.4071 NA NA
-SD.log_k_J9Z38 0.5774 NA NA
-SD.log_k_JSE76 0.6214 NA NA
-SD.f_cyan_ilr_1 0.3058 NA NA
-SD.f_cyan_ilr_2 0.3470 NA NA
-SD.f_JCZ38_qlogis 0.0644 NA NA
-SD.log_k1 0.3994 NA NA
-SD.log_k2 0.4373 NA NA
-SD.log_tb 0.6419 NA NA
-
-Variance model:
- est. lower upper
-a.1 3.323 NA NA
-
-Backtransformed parameters:
- est. lower upper
-cyan_0 1.020e+02 1.005e+02 1.035e+02
-k_JCZ38 3.112e-02 8.951e-03 1.082e-01
-k_J9Z38 6.129e-03 3.216e-03 1.168e-02
-k_JSE76 3.706e-03 1.798e-03 7.639e-03
-f_cyan_to_JCZ38 5.890e-01 NA NA
-f_cyan_to_J9Z38 2.318e-01 NA NA
-f_JCZ38_to_JSE76 1.000e+00 0.000e+00 1.000e+00
-k1 4.558e-02 3.164e-02 6.565e-02
-k2 1.243e-02 8.417e-03 1.835e-02
-tb 1.003e+01 5.557e+00 1.811e+01
-
-Resulting formation fractions:
- ff
-cyan_JCZ38 5.890e-01
-cyan_J9Z38 2.318e-01
-cyan_sink 1.793e-01
-JCZ38_JSE76 1.000e+00
-JCZ38_sink 5.861e-12
-
-Estimated disappearance times:
- DT50 DT90 DT50back DT50_k1 DT50_k2
-cyan 29.02 158.51 47.72 15.21 55.77
-JCZ38 22.27 73.98 NA NA NA
-J9Z38 113.09 375.69 NA NA NA
-JSE76 187.01 621.23 NA NA NA
-
-
-
+d_cyan/dt = - ifelse(time
+
+
Pathway 2
@@ -3514,10 +3389,10 @@ Hierarchical FOMC path 2 fit with two-component error
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
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
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
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
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
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
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
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
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
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
Session info
-R version 4.3.0 Patched (2023-05-18 r84448)
+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
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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 @@
@@ -73,6 +73,9 @@
Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P
+
+ Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione
+
Testing hierarchical pathway kinetics with residue data on cyantraniliprole
@@ -135,7 +138,7 @@ with residue data on dimethenamid and dimethenamid-P
Ranke
Last change on 5 January
-2023, last compiled on 19 Mai 2023
+2023, last compiled on 30 October 2023
Source: vignettes/prebuilt/2022_dmta_parent.rmd
2022_dmta_parent.rmd
@@ -154,7 +157,7 @@ FOMC, DFOP and HS can be fitted with the mkin package.
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.
-The mkin package is used in version 1.2.4. It contains the test data
+
The mkin package is used in version 1.2.6. It contains the test data
and the functions used in the evaluations. The saemix
package is used as a backend for fitting the NLHM, but is also loaded to
make the convergence plot function available.
@@ -1005,7 +1008,7 @@ updated assuming two-component error.
DFOP
OK
OK
-C
+OK
OK
C
OK
@@ -1013,7 +1016,7 @@ updated assuming two-component error.
HS
OK
-C
+OK
OK
OK
OK
@@ -1111,9 +1114,9 @@ the best fits.
FOMC tc
8
-720.4
-718.8
--352.2
+720.7
+719.1
+-352.4
DFOP const
@@ -1132,9 +1135,9 @@ the best fits.
DFOP tc
10
-665.5
-663.4
--322.8
+665.7
+663.6
+-322.9
HS tc
@@ -1215,12 +1218,12 @@ achieved with the argument test = TRUE
to the
kable(format.args = list(digits = 4))
-
-
+
+
-
+
@@ -1238,8 +1241,8 @@ achieved with the argument test = TRUE
to the
f_saem_dfop_tc_no_ranef_k2
9
-663.8
-661.9
+663.7
+661.8
-322.9
NA
NA
@@ -1248,12 +1251,12 @@ achieved with the argument test = TRUE
to the
f_saem[[“DFOP”, “tc”]]
10
-665.5
-663.4
--322.8
-0.2809
+665.7
+663.6
+-322.9
+0
+1
1
-0.5961
@@ -1286,10 +1289,10 @@ Plot of the final NLHM DFOP fit
summary(f_saem_dfop_tc_no_ranef_k2)
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
+ DT50 DT90 DT50back DT50_k1 DT50_k2
+DMTA 11.45 41.32 12.44 10.82 81.85
Alternative check of parameter identifiability
@@ -1462,10 +1465,10 @@ Hierarchical mkin fit of the SFO model with error model const
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
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
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
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
@@ -1764,10 +1767,10 @@ Hierarchical mkin fit of the DFOP model with error model const
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
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
@@ -1934,167 +1937,28 @@ Hierarchical mkin fit of the HS model with error model const
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 <= 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
-
-
-
+d_DMTA/dt = - ifelse(time
+
Hierarchical mkin fit of the HS model with error model tc
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 <= 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
-
-
-
+d_DMTA/dt = - ifelse(time
+
+
Hierarchical model convergence plots
@@ -2143,50 +2007,53 @@ Convergence plot for the NLHM HS fit with two-component error
Session info
-R version 4.2.3 (2023-03-15)
+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
+ [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
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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 @@
@@ -73,6 +73,9 @@
Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P
+
+ Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione
+
Testing hierarchical pathway kinetics with residue data on cyantraniliprole
@@ -135,7 +138,7 @@ residue data on dimethenamid and dimethenamid-P
Ranke
Last change on 20 April 2023,
-last compiled on 19 Mai 2023
+last compiled on 30 October 2023
Source: vignettes/prebuilt/2022_dmta_pathway.rmd
2022_dmta_pathway.rmd
@@ -155,7 +158,7 @@ can be fitted with the mkin package.
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.
-The mkin package is used in version 1.2.4, which is currently under
+
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 saemix
package is used as a backend for
fitting the NLHM, but is also loaded to make the convergence plot
@@ -1976,23 +1979,23 @@ error
Session info
-R version 4.3.0 Patched (2023-05-18 r84448)
+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
+[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
Hardware info
-CPU model: AMD Ryzen 9 7950X 16-Core Processor
-MemTotal: 64925476 kB
+CPU model: Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz
+MemTotal: 247605564 kB
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+++ b/docs/articles/twa.html
@@ -33,7 +33,7 @@
@@ -73,6 +73,9 @@
Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P
+
+ Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione
+
Testing hierarchical pathway kinetics with residue data on cyantraniliprole
@@ -135,7 +138,7 @@ concentrations with mkin
Ranke
Last change 18 September 2019
-(rebuilt 2023-05-19)
+(rebuilt 2023-10-30)
Source: vignettes/twa.rmd
twa.rmd
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@@ -33,7 +33,7 @@
@@ -73,6 +73,9 @@
Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P
+
+ Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione
+
Testing hierarchical pathway kinetics with residue data on cyantraniliprole
@@ -134,7 +137,7 @@
Ranke
Last change 16 January 2018
-(rebuilt 2023-05-19)
+(rebuilt 2023-10-30)
Source: vignettes/web_only/FOCUS_Z.rmd
FOCUS_Z.rmd
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@@ -33,7 +33,7 @@
@@ -73,6 +73,9 @@
Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P
+
+ Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione
+
Testing hierarchical pathway kinetics with residue data on cyantraniliprole
@@ -135,7 +138,7 @@ to the US EPA SOP for the NAFTA guidance
Ranke
26 February 2019 (rebuilt
-2023-05-19)
+2023-10-30)
Source: vignettes/web_only/NAFTA_examples.rmd
NAFTA_examples.rmd
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Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P
+
+ Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione
+
Testing hierarchical pathway kinetics with residue data on cyantraniliprole
@@ -134,7 +137,7 @@
Ranke
Last change 17 February 2023
-(rebuilt 2023-05-19)
+(rebuilt 2023-10-30)
Source: vignettes/web_only/benchmarks.rmd
benchmarks.rmd
@@ -231,7 +234,15 @@ systems. All trademarks belong to their respective owners.
Constant variance (t1) and two-component error model (t2) for four
models fitted to two datasets, i.e. eight fits for each test.
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