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_dmta_parent.html | 467 ++++++++++++++++----------- 1 file changed, 279 insertions(+), 188 deletions(-) (limited to 'docs/articles/prebuilt/2022_dmta_parent.html') diff --git a/docs/articles/prebuilt/2022_dmta_parent.html b/docs/articles/prebuilt/2022_dmta_parent.html index 9fdf75f7..952d028e 100644 --- a/docs/articles/prebuilt/2022_dmta_parent.html +++ b/docs/articles/prebuilt/2022_dmta_parent.html @@ -4,145 +4,104 @@ - + + Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P • mkin - - - + + + - - + - + + Skip to contents -
-
-
-
-

Testing hierarchical parent degradation kinetics -with residue data on dimethenamid and dimethenamid-P

+
+
+

Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P

Johannes Ranke

Last change on 5 January -2023, last compiled on 30 October 2023

+2023, last compiled on 16 November 2023 Source: vignettes/prebuilt/2022_dmta_parent.rmd - - +
2022_dmta_parent.rmd
@@ -1290,9 +1249,9 @@ 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:  1.2.6 
-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 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:59:35 2023 
+Date of summary: Thu Nov 16 04:59:35 2023 
 
 Equations:
 d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1304,7 +1263,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 8.975 s
+Fitted in 4.4 s
 Using 300, 100 iterations and 9 chains
 
 Variance model: Two-component variance function 
@@ -1466,9 +1425,9 @@ Hierarchical mkin fit of the SFO model with error model const
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-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 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:59:26 2023 
+Date of summary: Thu Nov 16 05:00:43 2023 
 
 Equations:
 d_DMTA/dt = - k_DMTA * DMTA
@@ -1478,7 +1437,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 1.899 s
+Fitted in 0.788 s
 Using 300, 100 iterations and 9 chains
 
 Variance model: Constant variance 
@@ -1538,9 +1497,9 @@ Hierarchical mkin fit of the SFO model with error model tc
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-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 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:59:28 2023 
+Date of summary: Thu Nov 16 05:00:43 2023 
 
 Equations:
 d_DMTA/dt = - k_DMTA * DMTA
@@ -1550,7 +1509,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 5.364 s
+Fitted in 2.428 s
 Using 300, 100 iterations and 9 chains
 
 Variance model: Two-component variance function 
@@ -1612,9 +1571,9 @@ Hierarchical mkin fit of the FOMC model with error model const
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-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 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:59:27 2023 
+Date of summary: Thu Nov 16 05:00:43 2023 
 
 Equations:
 d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA
@@ -1624,7 +1583,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 2.944 s
+Fitted in 1.28 s
 Using 300, 100 iterations and 9 chains
 
 Variance model: Constant variance 
@@ -1689,9 +1648,9 @@ Hierarchical mkin fit of the FOMC model with error model tc
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-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 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:59:28 2023 
+Date of summary: Thu Nov 16 05:00:43 2023 
 
 Equations:
 d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA
@@ -1701,7 +1660,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 6.228 s
+Fitted in 2.793 s
 Using 300, 100 iterations and 9 chains
 
 Variance model: Two-component variance function 
@@ -1768,9 +1727,9 @@ Hierarchical mkin fit of the DFOP model with error model const
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-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 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:59:27 2023 
+Date of summary: Thu Nov 16 05:00:43 2023 
 
 Equations:
 d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1782,7 +1741,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 3.231 s
+Fitted in 1.752 s
 Using 300, 100 iterations and 9 chains
 
 Variance model: Constant variance 
@@ -1852,9 +1811,9 @@ Hierarchical mkin fit of the DFOP model with error model tc
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-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 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:59:29 2023 
+Date of summary: Thu Nov 16 05:00:43 2023 
 
 Equations:
 d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1866,7 +1825,7 @@ Data:
 
 Model predictions using solution type analytical 
 
-Fitted in 6.71 s
+Fitted in 3.186 s
 Using 300, 100 iterations and 9 chains
 
 Variance model: Two-component variance function 
@@ -1938,27 +1897,166 @@ Hierarchical mkin fit of the HS model with error model const
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-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 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:59:28 2023 
+Date of summary: Thu Nov 16 05:00:43 2023 
 
 Equations:
-d_DMTA/dt = - ifelse(time 
-

+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 2.28 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
+
+

+

 
 Hierarchical mkin fit of the HS model with error model tc
 
 

 saemix version used for fitting:      3.2 
 mkin version used for pre-fitting:  1.2.6 
-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 
+R version used for fitting:         4.3.2 
+Date of fit:     Thu Nov 16 04:59:29 2023 
+Date of summary: Thu Nov 16 05:00:43 2023 
 
 Equations:
-d_DMTA/dt = - ifelse(time 
-

-

+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 3.658 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    97.76571 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
+
+

+

Hierarchical model convergence plots @@ -2007,23 +2105,23 @@ Convergence plot for the NLHM HS fit with two-component error

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:
@@ -2031,59 +2129,52 @@ 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     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   

+ [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     rprojroot_2.0.3   jsonlite_1.8.4   
+[13] DBI_1.1.3         mclust_6.0.0      gridExtra_2.3     purrr_1.0.1      
+[17] fansi_1.0.4       scales_1.2.1      codetools_0.2-19  textshaping_0.3.6
+[21] jquerylib_0.1.4   cli_3.6.1         rlang_1.1.1       munsell_0.5.0    
+[25] cachem_1.0.8      yaml_2.3.7        tools_4.3.2       memoise_2.0.1    
+[29] dplyr_1.1.2       colorspace_2.1-0  ggplot2_3.4.2     vctrs_0.6.2      
+[33] R6_2.5.1          zoo_1.8-12        lifecycle_1.0.3   stringr_1.5.0    
+[37] fs_1.6.2          MASS_7.3-60       ragg_1.2.5        pkgconfig_2.0.3  
+[41] desc_1.4.2        pkgdown_2.0.7     bslib_0.4.2       pillar_1.9.0     
+[45] gtable_0.3.3      glue_1.6.2        systemfonts_1.0.4 highr_0.10       
+[49] xfun_0.39         tibble_3.2.1      lmtest_0.9-40     tidyselect_1.2.0 
+[53] htmltools_0.5.5   nlme_3.1-163      rmarkdown_2.21    compiler_4.3.2

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

-
- - - +
-
- -- cgit v1.2.1