From 78d34a8918edcb91982a3886e4898a63898f52c3 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 20 Apr 2023 21:40:08 +0200 Subject: Update vignettes in dev docs After the post-release fixes to the release version online docs --- docs/dev/articles/index.html | 2 +- docs/dev/articles/prebuilt/2022_cyan_pathway.html | 360 +++++++++++---------- .../figure-html/unnamed-chunk-13-1.png | Bin 363662 -> 363943 bytes .../figure-html/unnamed-chunk-14-1.png | Bin 0 -> 365867 bytes .../figure-html/unnamed-chunk-15-1.png | Bin 0 -> 363662 bytes .../figure-html/unnamed-chunk-20-1.png | Bin 0 -> 378667 bytes .../figure-html/unnamed-chunk-21-1.png | Bin 0 -> 372548 bytes .../figure-html/unnamed-chunk-22-1.png | Bin 0 -> 373913 bytes .../figure-html/unnamed-chunk-7-1.png | Bin 373913 -> 373737 bytes .../figure-html/unnamed-chunk-8-1.png | Bin 0 -> 373913 bytes docs/dev/articles/prebuilt/2022_dmta_pathway.html | 79 +++-- .../figure-html/unnamed-chunk-6-1.png | Bin 400319 -> 393985 bytes .../figure-html/unnamed-chunk-7-1.png | Bin 403164 -> 400319 bytes .../figure-html/unnamed-chunk-8-1.png | Bin 0 -> 403164 bytes docs/dev/articles/web_only/multistart.html | 52 +-- .../figure-html/unnamed-chunk-3-1.png | Bin 64221 -> 66934 bytes .../figure-html/unnamed-chunk-4-1.png | Bin 52914 -> 53020 bytes .../figure-html/unnamed-chunk-5-1.png | Bin 22142 -> 22355 bytes docs/dev/authors.html | 6 +- docs/dev/index.html | 23 +- docs/dev/news/index.html | 60 ++-- docs/dev/pkgdown.yml | 4 +- docs/dev/reference/Rplot001.png | Bin 20512 -> 20558 bytes docs/dev/reference/Rplot002.png | Bin 16766 -> 16467 bytes docs/dev/reference/hierarchical_kinetics.html | 7 +- docs/dev/reference/index.html | 2 +- docs/dev/reference/multistart-1.png | Bin 63843 -> 66388 bytes docs/dev/reference/multistart-2.png | Bin 52220 -> 52865 bytes docs/dev/reference/multistart.html | 2 +- vignettes/web_only/multistart.html | 2 +- vignettes/web_only/multistart.rmd | 2 +- 31 files changed, 341 insertions(+), 260 deletions(-) create mode 100644 docs/dev/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-14-1.png create mode 100644 docs/dev/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-15-1.png create mode 100644 docs/dev/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-20-1.png create mode 100644 docs/dev/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-21-1.png create mode 100644 docs/dev/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-22-1.png create mode 100644 docs/dev/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-8-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-8-1.png diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html index 2aacc53a..c9116643 100644 --- a/docs/dev/articles/index.html +++ b/docs/dev/articles/index.html @@ -17,7 +17,7 @@ mkin - 1.2.3 + 1.2.4 diff --git a/docs/dev/articles/prebuilt/2022_cyan_pathway.html b/docs/dev/articles/prebuilt/2022_cyan_pathway.html index 875f5ac9..7bb0fa5b 100644 --- a/docs/dev/articles/prebuilt/2022_cyan_pathway.html +++ b/docs/dev/articles/prebuilt/2022_cyan_pathway.html @@ -34,7 +34,7 @@ mkin - 1.2.3 + 1.2.4 @@ -135,8 +135,8 @@ residue data on cyantraniliprole

Johannes Ranke

-

Last change on 6 January -2023, last compiled on 16 April 2023

+

Last change on 20 April 2023, +last compiled on 20 April 2023

Source: vignettes/prebuilt/2022_cyan_pathway.rmd @@ -156,7 +156,7 @@ 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 1.2.3 which is currently under +

The mkin package is used in version 1.2.4 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 @@ -174,11 +174,19 @@ processing, the parallel package is used.

library(saemix) library(parallel) n_cores <- detectCores() -if (Sys.info()["sysname"] == "Windows") { - cl <- makePSOCKcluster(n_cores) -} else { - cl <- makeForkCluster(n_cores) -} + +# We need to start a new cluster after defining a compiled model that is +# saved as a DLL to the user directory, therefore we define a function +# This is used again after defining the pathway model +start_cluster <- function(n_cores) { + if (Sys.info()["sysname"] == "Windows") { + ret <- makePSOCKcluster(n_cores) + } else { + ret <- makeForkCluster(n_cores) + } + return(ret) +} +cl <- start_cluster(n_cores)

Test data

@@ -1366,6 +1374,8 @@ when the two-component error model is used.

two-component error model is preferable for all parent models with the exception of DFOP. The lowest AIC and BIC values are are obtained with the FOMC model, followed by SFORB and DFOP.

+

Pathway fits @@ -1378,7 +1388,7 @@ degradation models with different transformation pathway models, a list of mkinmod models is set up below. As in the EU evaluation, parallel formation of metabolites JCZ38 and J9Z38 and secondary formation of metabolite JSE76 from JCZ38 is used.

-
+
 if (!dir.exists("cyan_dlls")) dir.create("cyan_dlls")
 cyan_path_1 <- list(
   sfo_path_1 = mkinmod(
@@ -1411,15 +1421,16 @@ formation of metabolite JSE76 from JCZ38 is used.

     J9Z38 = mkinsub("SFO"),
     JSE76 = mkinsub("SFO"), quiet = TRUE,
     name = "hs_path_1", dll_dir = "cyan_dlls", overwrite = TRUE)
-)

+)
+cl_path_1 <- start_cluster(n_cores)

To obtain suitable starting values for the NLHM fits, separate pathway fits are performed for all datasets.

-
+
 f_sep_1_const <- mmkin(
   cyan_path_1,
   cyan_ds,
   error_model = "const",
-  cluster = cl,
+  cluster = cl_path_1,
   quiet = TRUE)
 status(f_sep_1_const) |> kable()

 
@@ -1474,7 +1485,7 @@ pathway fits are performed for all datasets.

 
 
 

-
+
 f_sep_1_tc <- update(f_sep_1_const, error_model = "tc")
 status(f_sep_1_tc) |> kable()

 
@@ -1539,11 +1550,11 @@ for the parent only fits is used as an argument
 no_random_effect to the mhmkin function. The
 possibility to do so was introduced in mkin version 1.2.2
 which is currently under development.

-
+
 f_saem_1 <- mhmkin(list(f_sep_1_const, f_sep_1_tc),
   no_random_effect = illparms(cyan_saem_full),
-  cluster = cl)

-
+  cluster = cl_path_1)

+
 status(f_saem_1) |> kable()

 

@@ -1586,7 +1597,7 @@ Fisher Information Matrix could not be inverted for the fixed effects
 fits, ill-defined parameters cannot be determined using the
 illparms function, because it relies on the Fisher
 Information Matrix.

-
+
 illparms(f_saem_1) |> kable()

 

 
@@ -1630,7 +1641,7 @@ sd(f_JCZ38_qlogis)

 

 

 
The model comparison below suggests that the pathway fits using DFOP
 or SFORB for the parent compound provide the best fit.

-
+
 anova(f_saem_1) |> kable(digits = 1)

 
@@ -1715,23 +1726,25 @@ or SFORB for the parent compound provide the best fit.

 

 

 
For these two parent model, successful fits are shown below. Plots of
 the fits with the other parent models are shown in the Appendix.

-
+
 plot(f_saem_1[["dfop_path_1", "tc"]])

 

-DFOP pathway fit with two-component error

+DFOP pathway fit with two-component error

 DFOP pathway fit with two-component error
 

 

-
+
 plot(f_saem_1[["sforb_path_1", "tc"]])

 

-SFORB pathway fit with two-component error

+SFORB pathway fit with two-component error

 SFORB pathway fit with two-component error
 

 

 
A closer graphical analysis of these Figures shows that the residues
 of transformation product JCZ38 in the soils Tama and Nambsheim observed
 at later time points are strongly and systematically underestimated.

+
+stopCluster(cl_path_1)

 

 

 
Alternative pathway fits
@@ -1744,7 +1757,7 @@ corresponding amide (Addendum 2014, p. 109). As FOMC provided the best
 fit for the parent, and the biexponential models DFOP and SFORB provided
 the best initial pathway fits, these three parent models are used in the
 alternative pathway fits.

-
+
 cyan_path_2 <- list(
   fomc_path_2 = mkinmod(
     cyan = mkinsub("FOMC", c("JCZ38", "J9Z38")),
@@ -1774,11 +1787,13 @@ alternative pathway fits.

     overwrite = TRUE
   )
 )
+
+cl_path_2 <- start_cluster(n_cores)
 f_sep_2_const <- mmkin(
   cyan_path_2,
   cyan_ds,
   error_model = "const",
-  cluster = cl,
+  cluster = cl_path_2,
   quiet = TRUE)
 
 status(f_sep_2_const) |> kable()

@@ -1820,7 +1835,7 @@ alternative pathway fits.

 
 
Using constant variance, separate fits converge with the exception of
 the fits to the Sassafras soil data.

-
+
 f_sep_2_tc <- update(f_sep_2_const, error_model = "tc")
 status(f_sep_2_tc) |> kable()

 
@@ -1862,11 +1877,11 @@ the fits to the Sassafras soil data.
Using the two-component error model, all separate fits converge with
 the exception of the alternative pathway fit with DFOP used for the
 parent and the Sassafras dataset.

-
+
 f_saem_2 <- mhmkin(list(f_sep_2_const, f_sep_2_tc),
   no_random_effect = illparms(cyan_saem_full[2:4, ]),
-  cluster = cl)

-
+  cluster = cl_path_2)

+
 status(f_saem_2) |> kable()

 

 

@@ -1894,7 +1909,7 @@ parent and the Sassafras dataset.

 

 

 
The hierarchical fits for the alternative pathway completed
 successfully.

-
+
 illparms(f_saem_2) |> kable()

 @@ -1928,7 +1943,7 @@ successfully.
In both fits, the random effects for the formation fractions for the
 pathways from JCZ38 to JSE76, and for the reverse pathway from JSE76 to
 JCZ38 are ill-defined.

-
+
 anova(f_saem_2) |> kable(digits = 1)

 

 

 

@@ -1989,24 +2004,24 @@ and BIC values and are plotted below. Compared with the original
 pathway, the AIC and BIC values indicate a large improvement. This is
 confirmed by the plots, which show that the metabolite JCZ38 is fitted
 much better with this model.

-
+
 plot(f_saem_2[["fomc_path_2", "tc"]])

 

-FOMC pathway fit with two-component error, alternative pathway

+FOMC pathway fit with two-component error, alternative pathway

 FOMC pathway fit with two-component error, alternative pathway
 

 

-
+
 plot(f_saem_2[["dfop_path_2", "tc"]])

 

-DFOP pathway fit with two-component error, alternative pathway

+DFOP pathway fit with two-component error, alternative pathway

 DFOP pathway fit with two-component error, alternative pathway
 

 

-
+
 plot(f_saem_2[["sforb_path_2", "tc"]])

 

-SFORB pathway fit with two-component error, alternative pathway

+SFORB pathway fit with two-component error, alternative pathway

 SFORB pathway fit with two-component error, alternative pathway
 

 

@@ -2021,7 +2036,7 @@ created below that can be indexed by row and column indices, and which
 contains the degradation parameter names for which random effects should
 be excluded for each of the hierarchical fits contained in
 f_saem_2.

-
+
 no_ranef <- matrix(list(), nrow = 3, ncol = 2, dimnames = dimnames(f_saem_2))
 no_ranef[["fomc_path_2", "const"]] <- c("log_beta", "f_JCZ38_qlogis", "f_JSE76_qlogis")
 no_ranef[["fomc_path_2", "tc"]] <- c("cyan_0", "f_JCZ38_qlogis", "f_JSE76_qlogis")
@@ -2031,12 +2046,12 @@ be excluded for each of the hierarchical fits contained in
   "f_JCZ38_qlogis", "f_JSE76_qlogis")
 no_ranef[["sforb_path_2", "tc"]] <- c("cyan_free_0", "log_k_cyan_free_bound",
   "f_JCZ38_qlogis", "f_JSE76_qlogis")
-clusterExport(cl, "no_ranef")
+clusterExport(cl_path_2, "no_ranef")
 
 f_saem_3 <- update(f_saem_2,
   no_random_effect = no_ranef,
-  cluster = cl)

-
+  cluster = cl_path_2)

+
 status(f_saem_3) |> kable()

 

 

@@ -2066,7 +2081,7 @@ be excluded for each of the hierarchical fits contained in
 all updated fits completed successfully. However, the Fisher Information
 Matrix for the fixed effects (Fth) could not be inverted, so no
 confidence intervals for the optimised parameters are available.

-
+
 illparms(f_saem_3) |> kable()

 

 

@@ -2092,7 +2107,7 @@ confidence intervals for the optimised parameters are available.

 

 

 
 

-
+
 anova(f_saem_3) |> kable(digits = 1)

 
@@ -2144,6 +2159,8 @@ confidence intervals for the optimised parameters are available.

 two-component error) are lower than in the previous fits with the
 alternative pathway, the practical value of these refined evaluations is
 limited as no confidence intervals are obtained.

+
+stopCluster(cl_path_2)

@@ -2170,24 +2187,24 @@ Agency are gratefully acknowledged.

 

 
Plots of fits that were not refined further
 

-
+
 plot(f_saem_1[["sfo_path_1", "tc"]])

 

-SFO pathway fit with two-component error

+SFO pathway fit with two-component error

 SFO pathway fit with two-component error
 

 

-
+
 plot(f_saem_1[["fomc_path_1", "tc"]])

 

-FOMC pathway fit with two-component error

+FOMC pathway fit with two-component error

 FOMC pathway fit with two-component error
 

 

-
+
 plot(f_saem_1[["sforb_path_1", "tc"]])

 

-HS pathway fit with two-component error

+HS pathway fit with two-component error

 HS pathway fit with two-component error
 

 

@@ -2203,10 +2220,10 @@ Hierarchical SFO path 1 fit with constant variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 10:07:38 2023 
-Date of summary: Sun Apr 16 08:35:20 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 20:33:05 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan/dt = - k_cyan * cyan
@@ -2219,7 +2236,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1088.473 s
+Fitted in 438.011 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -2331,10 +2348,10 @@ Hierarchical SFO path 1 fit with two-component error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 10:08:17 2023 
-Date of summary: Sun Apr 16 08:35:20 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 20:32:55 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan/dt = - k_cyan * cyan
@@ -2347,7 +2364,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1127.552 s
+Fitted in 427.249 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -2461,10 +2478,10 @@ Hierarchical FOMC path 1 fit with constant variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 10:09:12 2023 
-Date of summary: Sun Apr 16 08:35:20 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 20:33:49 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -2479,7 +2496,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1182.258 s
+Fitted in 481.497 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -2606,10 +2623,10 @@ Hierarchical FOMC path 1 fit with two-component error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 10:09:18 2023 
-Date of summary: Sun Apr 16 08:35:20 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 20:33:59 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -2624,7 +2641,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1188.041 s
+Fitted in 491.071 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -2744,10 +2761,10 @@ Hierarchical DFOP path 1 fit with constant variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 10:10:30 2023 
-Date of summary: Sun Apr 16 08:35:20 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 20:34:33 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -2766,7 +2783,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1260.905 s
+Fitted in 525.551 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -2890,10 +2907,10 @@ Hierarchical DFOP path 1 fit with two-component error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 10:16:28 2023 
-Date of summary: Sun Apr 16 08:35:20 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 20:37:03 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -2912,7 +2929,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1617.774 s
+Fitted in 675.804 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -3036,10 +3053,10 @@ Hierarchical SFORB path 1 fit with constant variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 10:10:49 2023 
-Date of summary: Sun Apr 16 08:35:20 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 20:34:43 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -3057,7 +3074,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1279.472 s
+Fitted in 535.818 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -3201,10 +3218,10 @@ Hierarchical SFORB path 1 fit with two-component error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 10:17:00 2023 
-Date of summary: Sun Apr 16 08:35:20 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 20:37:02 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -3222,7 +3239,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1649.941 s
+Fitted in 674.859 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -3366,10 +3383,10 @@ Hierarchical HS path 1 fit with constant variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 10:11:04 2023 
-Date of summary: Sun Apr 16 08:35:20 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 20:34:41 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan
@@ -3384,7 +3401,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1294.259 s
+Fitted in 533.787 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -3508,10 +3525,10 @@ Hierarchical HS path 1 fit with two-component error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 10:11:24 2023 
-Date of summary: Sun Apr 16 08:35:20 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 20:34:39 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan
@@ -3526,7 +3543,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1313.805 s
+Fitted in 531.084 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -3656,10 +3673,10 @@ Hierarchical FOMC path 2 fit with constant variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 10:34:28 2023 
-Date of summary: Sun Apr 16 08:35:20 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 20:45:51 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -3674,7 +3691,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1030.246 s
+Fitted in 517.002 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -3820,10 +3837,10 @@ Hierarchical FOMC path 2 fit with two-component error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 10:37:36 2023 
-Date of summary: Sun Apr 16 08:35:20 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 20:45:39 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -3838,7 +3855,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1217.619 s
+Fitted in 505.619 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -3966,10 +3983,10 @@ Hierarchical DFOP path 2 fit with constant variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 10:38:34 2023 
-Date of summary: Sun Apr 16 08:35:20 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 20:46:46 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -3989,7 +4006,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1276.128 s
+Fitted in 572.382 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -4157,10 +4174,10 @@ Hierarchical DFOP path 2 fit with two-component error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 10:45:32 2023 
-Date of summary: Sun Apr 16 08:35:20 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 20:49:18 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4180,7 +4197,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1693.767 s
+Fitted in 724.515 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -4348,10 +4365,10 @@ Hierarchical SFORB path 2 fit with constant variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 10:38:37 2023 
-Date of summary: Sun Apr 16 08:35:20 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 20:46:33 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -4369,7 +4386,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1279.102 s
+Fitted in 559.097 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -4544,10 +4561,10 @@ Hierarchical SFORB path 2 fit with two-component error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 10:46:02 2023 
-Date of summary: Sun Apr 16 08:35:20 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 20:49:20 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -4565,7 +4582,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1723.343 s
+Fitted in 726.293 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -4745,10 +4762,10 @@ error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 11:18:41 2023 
-Date of summary: Sun Apr 16 08:35:21 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 21:02:39 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan
@@ -4763,7 +4780,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1957.271 s
+Fitted in 796.615 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -4888,10 +4905,10 @@ variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 11:16:32 2023 
-Date of summary: Sun Apr 16 08:35:21 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 21:04:15 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -4911,7 +4928,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1828.403 s
+Fitted in 893.328 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -5054,10 +5071,10 @@ error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 11:22:28 2023 
-Date of summary: Sun Apr 16 08:35:21 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 21:04:33 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -5077,7 +5094,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 2183.989 s
+Fitted in 910.788 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -5220,10 +5237,10 @@ variance
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 11:17:37 2023 
-Date of summary: Sun Apr 16 08:35:21 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 21:04:09 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -5241,7 +5258,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 1893.29 s
+Fitted in 887.369 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Constant variance 
@@ -5391,10 +5408,10 @@ error
 
 

 saemix version used for fitting:      3.2 
-mkin version used for pre-fitting:  1.2.2 
-R version used for fitting:         4.2.2 
-Date of fit:     Sat Jan 28 11:21:01 2023 
-Date of summary: Sun Apr 16 08:35:21 2023 
+mkin version used for pre-fitting:  1.2.4 
+R version used for fitting:         4.2.3 
+Date of fit:     Thu Apr 20 21:04:32 2023 
+Date of summary: Thu Apr 20 21:04:34 2023 
 
 Equations:
 d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound *
@@ -5412,7 +5429,7 @@ Data:
 
 Model predictions using solution type deSolve 
 
-Fitted in 2097.842 s
+Fitted in 910.017 s
 Using 300, 100 iterations and 10 chains
 
 Variance model: Two-component variance function 
@@ -5582,29 +5599,32 @@ attached base packages:
 [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_1.42 mkin_1.2.4
 
 loaded via a namespace (and not attached):
- [1] pillar_1.9.0      bslib_0.4.2       compiler_4.2.3    jquerylib_0.1.4  
- [5] tools_4.2.3       mclust_6.0.0      digest_0.6.31     tibble_3.2.1     
- [9] jsonlite_1.8.4    evaluate_0.20     memoise_2.0.1     lifecycle_1.0.3  
-[13] nlme_3.1-162      gtable_0.3.3      lattice_0.21-8    pkgconfig_2.0.3  
-[17] rlang_1.1.0       DBI_1.1.3         cli_3.6.1         yaml_2.3.7       
-[21] pkgdown_2.0.7     xfun_0.38         fastmap_1.1.1     gridExtra_2.3    
-[25] dplyr_1.1.1       stringr_1.5.0     generics_0.1.3    desc_1.4.2       
-[29] fs_1.6.1          vctrs_0.6.1       sass_0.4.5        systemfonts_1.0.4
-[33] tidyselect_1.2.0  rprojroot_2.0.3   lmtest_0.9-40     grid_4.2.3       
-[37] inline_0.3.19     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    scales_1.2.1      htmltools_0.5.5   colorspace_2.1-0 
-[49] ragg_1.2.5        utf8_1.2.3        stringi_1.7.12    munsell_0.5.0    
-[53] cachem_1.0.7      zoo_1.8-12       

+ [1] deSolve_1.35      zoo_1.8-12        tidyselect_1.2.0  xfun_0.38        
+ [5] bslib_0.4.2       purrr_1.0.1       lattice_0.21-8    colorspace_2.1-0 
+ [9] vctrs_0.6.1       generics_0.1.3    htmltools_0.5.5   yaml_2.3.7       
+[13] utf8_1.2.3        rlang_1.1.0       pkgbuild_1.4.0    pkgdown_2.0.7    
+[17] jquerylib_0.1.4   pillar_1.9.0      glue_1.6.2        DBI_1.1.3        
+[21] readxl_1.4.2      lifecycle_1.0.3   stringr_1.5.0     munsell_0.5.0    
+[25] gtable_0.3.3      cellranger_1.1.0  ragg_1.2.5        codetools_0.2-19 
+[29] memoise_2.0.1     evaluate_0.20     inline_0.3.19     callr_3.7.3      
+[33] fastmap_1.1.1     ps_1.7.4          lmtest_0.9-40     fansi_1.0.4      
+[37] highr_0.10        scales_1.2.1      cachem_1.0.7      desc_1.4.2       
+[41] jsonlite_1.8.4    systemfonts_1.0.4 fs_1.6.1          textshaping_0.3.6
+[45] gridExtra_2.3     ggplot2_3.4.2     digest_0.6.31     stringi_1.7.12   
+[49] processx_3.8.0    dplyr_1.1.1       grid_4.2.3        rprojroot_2.0.3  
+[53] cli_3.6.1         tools_4.2.3       magrittr_2.0.3    sass_0.4.5       
+[57] tibble_3.2.1      crayon_1.5.2      pkgconfig_2.0.3   prettyunits_1.1.1
+[61] rmarkdown_2.21    R6_2.5.1          mclust_6.0.0      nlme_3.1-162     
+[65] compiler_4.2.3   

 

 

 
Hardware info
 

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

-
MemTotal:       64940452 kB

+
MemTotal:       64936316 kB

 

 

   

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diff --git a/docs/dev/articles/prebuilt/2022_dmta_pathway.html b/docs/dev/articles/prebuilt/2022_dmta_pathway.html
index 0285a193..959f3429 100644
--- a/docs/dev/articles/prebuilt/2022_dmta_pathway.html
+++ b/docs/dev/articles/prebuilt/2022_dmta_pathway.html
@@ -34,7 +34,7 @@
       
       
         mkin
-        1.2.3
+        1.2.4
       
     

 
@@ -135,8 +135,8 @@ residue data on dimethenamid and dimethenamid-P
                         
Johannes
 Ranke

             
-            
Last change on 8 January
-2023, last compiled on 16 April 2023

+            
Last change on 20 April 2023,
+last compiled on 20 April 2023

       
       Source: vignettes/prebuilt/2022_dmta_pathway.rmd
       
@@ -156,7 +156,7 @@ 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 1.2.3, which is currently under
+
The mkin package is used in version 1.2.4, 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
@@ -171,10 +171,17 @@ processing, the parallel package is used.

 library(saemix)
 library(parallel)
 n_cores <- detectCores()
-if (Sys.info()["sysname"] == "Windows") {
-  cl <- makePSOCKcluster(n_cores)
-} else {
-  cl <- makeForkCluster(n_cores)
+
+# We need to start a new cluster after defining a compiled model that is
+# saved as a DLL to the user directory, therefore we define a function
+# This is used again after defining the pathway model
+start_cluster <- function(n_cores) {
+  if (Sys.info()["sysname"] == "Windows") {
+    ret <- makePSOCKcluster(n_cores)
+  } else {
+    ret <- makeForkCluster(n_cores)
+  }
+  return(ret)
 }

@@ -1441,6 +1448,8 @@ of parent models tested here.

   unload = TRUE, overwrite = TRUE,
   quiet = TRUE
 )
+cl <- start_cluster(n_cores)
+
 deg_mods_1 <- list(
   sfo_path_1 = m_sfo_path_1,
   fomc_path_1 = m_fomc_path_1,
@@ -1883,6 +1892,8 @@ SFORB pathway fit with two-component error, reduced parameter model
 
Plots of the remaining fits and listings for all successful fits are
 shown in the Appendix.

+

 
Conclusions
@@ -1921,24 +1932,24 @@ Level with Nonlinear Mixed-Effects Models.” Environments
 

 
Plots of hierarchical fits not selected for refinement
 

-
+
 plot(saem_1[["sfo_path_1", "tc"]])

 

-SFO pathway fit with two-component error

+SFO pathway fit with two-component error

 SFO pathway fit with two-component error
 

 

-
+
 plot(saem_1[["fomc_path_1", "tc"]])

 

-FOMC pathway fit with two-component error

+FOMC pathway fit with two-component error

 FOMC pathway fit with two-component error
 

 

-
+
 plot(saem_1[["sforb_path_1", "tc"]])

 

-HS pathway fit with two-component error

+HS pathway fit with two-component error

 HS pathway fit with two-component error
 

 

@@ -1961,9 +1972,9 @@ error
 
Session info
 

-
R version 4.2.2 Patched (2022-11-10 r83330)
+
R version 4.2.3 (2023-03-15)
 Platform: x86_64-pc-linux-gnu (64-bit)
-Running under: Debian GNU/Linux bookworm/sid
+Running under: Debian GNU/Linux 12 (bookworm)
 
 Matrix products: default
 BLAS:   /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3
@@ -1982,31 +1993,31 @@ attached base packages:
 [8] base     
 
 other attached packages:
-[1] saemix_3.2 npde_3.3   knitr_1.41 mkin_1.2.2
+[1] saemix_3.2 npde_3.3   knitr_1.42 mkin_1.2.4
 
 loaded via a namespace (and not attached):
- [1] deSolve_1.34      zoo_1.8-11        tidyselect_1.2.0  xfun_0.35        
- [5] bslib_0.4.2       purrr_1.0.0       lattice_0.20-45   colorspace_2.0-3 
- [9] vctrs_0.5.1       generics_0.1.3    htmltools_0.5.4   yaml_2.3.6       
-[13] pkgbuild_1.4.0    utf8_1.2.2        rlang_1.0.6       pkgdown_2.0.7    
-[17] jquerylib_0.1.4   pillar_1.8.1      glue_1.6.2        DBI_1.1.3        
-[21] lifecycle_1.0.3   stringr_1.5.0     munsell_0.5.0     gtable_0.3.1     
-[25] ragg_1.2.4        codetools_0.2-18  memoise_2.0.1     evaluate_0.19    
-[29] inline_0.3.19     callr_3.7.3       fastmap_1.1.0     ps_1.7.2         
-[33] lmtest_0.9-40     fansi_1.0.3       highr_0.9         scales_1.2.1     
-[37] cachem_1.0.6      desc_1.4.2        jsonlite_1.8.4    systemfonts_1.0.4
-[41] fs_1.5.2          textshaping_0.3.6 gridExtra_2.3     ggplot2_3.4.0    
-[45] digest_0.6.31     stringi_1.7.8     processx_3.8.0    dplyr_1.0.10     
-[49] grid_4.2.2        rprojroot_2.0.3   cli_3.5.0         tools_4.2.2      
-[53] magrittr_2.0.3    sass_0.4.4        tibble_3.1.8      crayon_1.5.2     
-[57] pkgconfig_2.0.3   prettyunits_1.1.1 assertthat_0.2.1  rmarkdown_2.19   
-[61] R6_2.5.1          mclust_6.0.0      nlme_3.1-161      compiler_4.2.2   

+ [1] deSolve_1.35      zoo_1.8-12        tidyselect_1.2.0  xfun_0.38        
+ [5] bslib_0.4.2       purrr_1.0.1       lattice_0.21-8    colorspace_2.1-0 
+ [9] vctrs_0.6.1       generics_0.1.3    htmltools_0.5.5   yaml_2.3.7       
+[13] utf8_1.2.3        rlang_1.1.0       pkgbuild_1.4.0    pkgdown_2.0.7    
+[17] jquerylib_0.1.4   pillar_1.9.0      glue_1.6.2        DBI_1.1.3        
+[21] lifecycle_1.0.3   stringr_1.5.0     munsell_0.5.0     gtable_0.3.3     
+[25] ragg_1.2.5        codetools_0.2-19  memoise_2.0.1     evaluate_0.20    
+[29] inline_0.3.19     callr_3.7.3       fastmap_1.1.1     ps_1.7.4         
+[33] lmtest_0.9-40     fansi_1.0.4       highr_0.10        scales_1.2.1     
+[37] cachem_1.0.7      desc_1.4.2        jsonlite_1.8.4    systemfonts_1.0.4
+[41] fs_1.6.1          textshaping_0.3.6 gridExtra_2.3     ggplot2_3.4.2    
+[45] digest_0.6.31     stringi_1.7.12    processx_3.8.0    dplyr_1.1.1      
+[49] grid_4.2.3        rprojroot_2.0.3   cli_3.6.1         tools_4.2.3      
+[53] magrittr_2.0.3    sass_0.4.5        tibble_3.2.1      crayon_1.5.2     
+[57] pkgconfig_2.0.3   prettyunits_1.1.1 rmarkdown_2.21    R6_2.5.1         
+[61] mclust_6.0.0      nlme_3.1-162      compiler_4.2.3   

 

 

 
Hardware info
 

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

-
MemTotal:       64940452 kB

+
MemTotal:       64936316 kB

 

 

   

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index 1c81601e..ac5271ec 100644
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diff --git a/docs/dev/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-8-1.png b/docs/dev/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-8-1.png
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index 00000000..1c81601e
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diff --git a/docs/dev/articles/web_only/multistart.html b/docs/dev/articles/web_only/multistart.html
index b5635df2..2de5059c 100644
--- a/docs/dev/articles/web_only/multistart.html
+++ b/docs/dev/articles/web_only/multistart.html
@@ -34,7 +34,7 @@
       
       
         mkin
-        1.2.3
+        1.2.4
       
     

 
@@ -127,13 +127,15 @@
 
       
 
-      

+      

   

     

       
Short demo of the multistart method

-                        
Johannes Ranke

+                        
Johannes
+Ranke

             
-            
Last change 17 April 2023 (rebuilt 2023-04-17)

+            
Last change 20 April 2023
+(rebuilt 2023-04-20)

       
       Source: vignettes/web_only/multistart.rmd
       
@@ -142,7 +144,8 @@
 
     
     
-
The dimethenamid data from 2018 from seven soils is used as example data in this vignette.

+
The dimethenamid data from 2018 from seven soils is used as example
+data in this vignette.

 
 library(mkin)
 dmta_ds <- lapply(1:7, function(i) {
@@ -154,26 +157,34 @@
 names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title)
 dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]])
 dmta_ds[["Elliot 1"]] <- dmta_ds[["Elliot 2"]] <- NULL

-
First, we check the DFOP model with the two-component error model and random effects for all degradation parameters.

+
First, we check the DFOP model with the two-component error model and
+random effects for all degradation parameters.

 
 f_mmkin <- mmkin("DFOP", dmta_ds, error_model = "tc", cores = 7, quiet = TRUE)
 f_saem_full <- saem(f_mmkin)
 illparms(f_saem_full)

 
## [1] "sd(log_k2)"

-
We see that not all variability parameters are identifiable. The illparms function tells us that the confidence interval for the standard deviation of ‘log_k2’ includes zero. We check this assessment using multiple runs with different starting values.

+
We see that not all variability parameters are identifiable. The
+illparms function tells us that the confidence interval for
+the standard deviation of ‘log_k2’ includes zero. We check this
+assessment using multiple runs with different starting values.

 
-f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 8)
+f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16)
 parplot(f_saem_full_multi, lpos = "topleft")

 

-
This confirms that the variance of k2 is the most problematic parameter, so we reduce the parameter distribution model by removing the intersoil variability for k2.

+
This confirms that the variance of k2 is the most problematic
+parameter, so we reduce the parameter distribution model by removing the
+intersoil variability for k2.

 
-f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2")
+f_saem_reduced <- stats::update(f_saem_full, no_random_effect = "log_k2")
 illparms(f_saem_reduced)
-f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cores = 8)
+f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cores = 16)
 parplot(f_saem_reduced_multi, lpos = "topright", ylim = c(0.5, 2))

 

-
The results confirm that all remaining parameters can be determined with sufficient certainty.

-
We can also analyse the log-likelihoods obtained in the multiple runs:

+
The results confirm that all remaining parameters can be determined
+with sufficient certainty.

+
We can also analyse the log-likelihoods obtained in the multiple
+runs:

 
 llhist(f_saem_reduced_multi)

 

@@ -184,11 +195,16 @@
 
## Data: 155 observations of 1 variable(s) grouped in 6 datasets
 ## 
 ##                            npar    AIC    BIC     Lik  Chisq Df Pr(>Chisq)
-## f_saem_reduced                9 663.74 661.87 -322.87                     
-## best(f_saem_reduced_multi)    9 663.60 661.72 -322.80 0.1476  0           
-## f_saem_full                  10 670.35 668.26 -325.17 0.0000  1          1
-## best(f_saem_full_multi)      10 665.61 663.53 -322.80 4.7372  0

-
The reduced model results in lower AIC and BIC values, so it is clearly preferable. Using multiple starting values gives a large improvement in case of the full model, because it is less well-defined, which impedes convergence. For the reduced model, using multiple starting values only results in a small improvement of the model fit.

+## f_saem_reduced                9 663.73 661.86 -322.86                     
+## best(f_saem_reduced_multi)    9 663.69 661.82 -322.85 0.0361  0           
+## f_saem_full                  10 669.77 667.69 -324.89 0.0000  1          1
+## best(f_saem_full_multi)      10 665.56 663.48 -322.78 4.2060  0
+
The reduced model results in lower AIC and BIC values, so it is
+clearly preferable. Using multiple starting values gives a large
+improvement in case of the full model, because it is less well-defined,
+which impedes convergence. For the reduced model, using multiple
+starting values only results in a small improvement of the model
+fit.

   

 
   
 
@@ -132,13 +132,13 @@
 
     
Ranke J (2023).
 mkin: Kinetic Evaluation of Chemical Degradation Data.
-R package version 1.2.3, https://pkgdown.jrwb.de/mkin/. 
+R package version 1.2.4, https://pkgdown.jrwb.de/mkin/. 
 

     
@Manual{,
   title = {mkin: Kinetic Evaluation of Chemical Degradation Data},
   author = {Johannes Ranke},
   year = {2023},
-  note = {R package version 1.2.3},
+  note = {R package version 1.2.4},
   url = {https://pkgdown.jrwb.de/mkin/},
 }

 
diff --git a/docs/dev/index.html b/docs/dev/index.html
index f892841f..59b78ff0 100644
--- a/docs/dev/index.html
+++ b/docs/dev/index.html
@@ -45,7 +45,7 @@
       
       
         mkin
-        1.2.3
+        1.2.4
       
     

 
@@ -245,12 +245,21 @@
 
References
 

 

 

 
 
 
 
 
 
 
 

-
-
-
+
+
+
+
+
+
+
+
+
Ranke J, Wöltjen J, Schmidt J, and Comets E (2021) Taking kinetic evaluations of degradation data to the next level with nonlinear mixed-effects models. Environments 8 (8) 71 doi:10.3390/environments8080071
-
Ranke J, Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data Environments 6 (12) 124 doi:10.3390/environments6120124
-
Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic evaluation of chemical degradation data Environmental Sciences Europe 30 17 doi:10.1186/s12302-018-0145-1
-

+Ranke J, Wöltjen J, Schmidt J, and Comets E (2021) Taking kinetic evaluations of degradation data to the next level with nonlinear mixed-effects models. Environments 8 (8) 71 doi:10.3390/environments8080071
+

+Ranke J, Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data Environments 6 (12) 124 doi:10.3390/environments6120124
+

+Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic evaluation of chemical degradation data Environmental Sciences Europe 30 17 doi:10.1186/s12302-018-0145-1
+

 

 

 

diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index 70eeeed6..93207241 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -17,7 +17,7 @@
       
       
         mkin
-        1.2.3
+        1.2.4
       
     

 
@@ -104,6 +104,13 @@
       Source: NEWS.md
     

 
+    

+
mkin 1.2.4

+

+    

+
mkin 1.2.3.1 (unreleased)

+
  • Small fixes to get the online docs right (example code in R/hierarchical_kinetics, cluster setup in cyantraniliprole and dmta pathway vignettes, graphics and model comparison in multistart vignette), rebuild online docs
    • 
+

     

 
mkin 1.2.3

 
  • ‘R/{endpoints,parms,plot.mixed.mmkin,summary.saem.mmkin}.R’: Calculate parameters and endpoints and plot population curves for specific covariate values, or specific percentiles of covariate values used in saem fits.
    • 
@@ -171,7 +178,8 @@
 

     

 
mkin 1.0.5 (2021-09-15)

-
  • ‘dimethenamid_2018’: Correct the data for the Borstel soil. The five observations from Staudenmaier (2013) that were previously stored as “Borstel 2” are actually just a subset of the 16 observations in “Borstel 1” which is now simply “Borstel”

+
  • ‘dimethenamid_2018’: Correct the data for the Borstel soil. The five observations from Staudenmaier (2013) that were previously stored as “Borstel 2” are actually just a subset of the 16 observations in “Borstel 1” which is now simply “Borstel”
    • 
+

     

 
mkin 1.0.4 (2021-04-20)

 
  • All plotting functions setting graphical parameters: Use on.exit() for resetting graphical parameters
    • 
@@ -180,10 +188,12 @@
 

     

 
mkin 1.0.3 (2021-02-15)

-
  • Review and update README, the ‘Introduction to mkin’ vignette and some of the help pages

+
  • Review and update README, the ‘Introduction to mkin’ vignette and some of the help pages
    • 
+

     

 
mkin 1.0.2 (Unreleased)

-
  • ‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’

+
  • ‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’
    • 
+

     

 
mkin 1.0.1 (2021-02-10)

 
  • ‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults
    • 
@@ -238,7 +248,8 @@
 

     

 
mkin 0.9.49.11 (2020-04-20)

-
  • Increase a test tolerance to make it pass on all CRAN check machines

+
  • Increase a test tolerance to make it pass on all CRAN check machines
    • 
+

     

 
mkin 0.9.49.10 (2020-04-18)

 
  • ‘nlme.mmkin’: An nlme method for mmkin row objects and an associated S3 class with print, plot, anova and endpoint methods
    • 
@@ -353,7 +364,8 @@
 

     

 
mkin 0.9.46 (2017-07-24)

-
  • Remove test_FOMC_ill-defined.R as it is too platform dependent

+
  • Remove test_FOMC_ill-defined.R as it is too platform dependent
    • 
+

     

 
mkin 0.9.45.2 (2017-07-24)

 
  • Rename twa to max_twa_parent to avoid conflict with twa from my pfm package
    • 
@@ -365,7 +377,8 @@
 
    mkin 0.9.45.1 (2016-12-20)
    
 
    
 
    New features
    
-
    • A twa function, calculating maximum time weighted average concentrations for the parent (SFO, FOMC and DFOP).
    
+
    • A twa function, calculating maximum time weighted average concentrations for the parent (SFO, FOMC and DFOP).
      • 
+

 

     

 
mkin 0.9.45 (2016-12-08)

@@ -380,7 +393,8 @@
 
mkin 0.9.44 (2016-06-29)

 

 
Bug fixes

-
  • The test test_FOMC_ill-defined failed on several architectures, so the test is now skipped

+
  • The test test_FOMC_ill-defined failed on several architectures, so the test is now skipped
    • 
+

mkin 0.9.43 (2016-06-28)

@@ -414,7 +428,8 @@

mkin 0.9.42 (2016-03-25)

Major changes

-
  • Add the argument from_max_mean to mkinfit, for fitting only the decline from the maximum observed value for models with a single observed variable
+
  • Add the argument from_max_mean to mkinfit, for fitting only the decline from the maximum observed value for models with a single observed variable
    • +

Minor changes

  • Add plots to compiled_models vignette

    • @@ -434,18 +449,21 @@

    Bug fixes

    • -print.summary.mkinfit(): Avoid an error that occurred when printing summaries generated with mkin versions before 0.9-36
    +print.summary.mkinfit(): Avoid an error that occurred when printing summaries generated with mkin versions before 0.9-36 +

mkin 0.9-40 (2015-07-21)

Bug fixes

  • -endpoints(): For DFOP and SFORB models, where optimize() is used, make use of the fact that the DT50 must be between DT50_k1 and DT50_k2 (DFOP) or DT50_b1 and DT50_b2 (SFORB), as optimize() sometimes did not find the minimum. Likewise for finding DT90 values. Also fit on the log scale to make the function more efficient.
+endpoints(): For DFOP and SFORB models, where optimize() is used, make use of the fact that the DT50 must be between DT50_k1 and DT50_k2 (DFOP) or DT50_b1 and DT50_b2 (SFORB), as optimize() sometimes did not find the minimum. Likewise for finding DT90 values. Also fit on the log scale to make the function more efficient. +

Internal changes

  • -DESCRIPTION, NAMESPACE, R/*.R: Import (from) stats, graphics and methods packages, and qualify some function calls for non-base packages installed with R to avoid NOTES made by R CMD check –as-cran with upcoming R versions.
+DESCRIPTION, NAMESPACE, R/*.R: Import (from) stats, graphics and methods packages, and qualify some function calls for non-base packages installed with R to avoid NOTES made by R CMD check –as-cran with upcoming R versions. +

mkin 0.9-39 (2015-06-26)

@@ -457,7 +475,8 @@

Bug fixes

  • -mkinparplot(): Fix the x axis scaling for rate constants and formation fractions that got confused by the introduction of the t-values of transformed parameters.
+mkinparplot(): Fix the x axis scaling for rate constants and formation fractions that got confused by the introduction of the t-values of transformed parameters. +

mkin 0.9-38 (2015-06-24)

@@ -469,7 +488,8 @@

Bug fixes

  • -mkinmod(): When generating the C code for the derivatives, only declare the time variable when it is needed and remove the ‘-W-no-unused-variable’ compiler flag as the C compiler used in the CRAN checks on Solaris does not know it.
+mkinmod(): When generating the C code for the derivatives, only declare the time variable when it is needed and remove the ‘-W-no-unused-variable’ compiler flag as the C compiler used in the CRAN checks on Solaris does not know it. +

mkin 0.9-36 (2015-06-21)

@@ -482,13 +502,15 @@

Minor changes

-
  • Added a simple showcase vignette with an evaluation of FOCUS example dataset D
+

mkin 0.9-35 (2015-05-15)

Major changes

-
  • Switch from RUnit to testthat for testing
+
  • Switch from RUnit to testthat for testing
    • +

Bug fixes

  • mkinparplot(): Avoid warnings that occurred when not all confidence intervals were available in the summary of the fit

    • @@ -570,13 +592,15 @@

    mkin 0.9-31 (2014-07-14)

    Bug fixes

    -
    • The internal renaming of optimised parameters in Version 0.9-30 led to errors in the determination of the degrees of freedom for the chi2 error level calulations in mkinerrmin() used by the summary function.
    +
    • The internal renaming of optimised parameters in Version 0.9-30 led to errors in the determination of the degrees of freedom for the chi2 error level calulations in mkinerrmin() used by the summary function.
      • +

mkin 0.9-30 (2014-07-11)

New features

-
  • It is now possible to use formation fractions in combination with turning off the sink in mkinmod().
+
  • It is now possible to use formation fractions in combination with turning off the sink in mkinmod().
    • +

Major changes

  • The original and the transformed parameters now have different names (e.g. k_parent and log_k_parent. They also differ in how many they are when we have formation fractions but no pathway to sink.

    • diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index a9ab0c60..c3829f60 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 2.9.2.1 +pandoc: 2.17.1.1 pkgdown: 2.0.7 pkgdown_sha: ~ articles: @@ -16,7 +16,7 @@ articles: dimethenamid_2018: web_only/dimethenamid_2018.html multistart: web_only/multistart.html saem_benchmarks: web_only/saem_benchmarks.html -last_built: 2023-04-17T17:35Z +last_built: 2023-04-20T18:24Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png index 278fd2e2..70d084a3 100644 Binary files a/docs/dev/reference/Rplot001.png and b/docs/dev/reference/Rplot001.png differ diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png index 4b646f22..0f7d4405 100644 Binary files a/docs/dev/reference/Rplot002.png and b/docs/dev/reference/Rplot002.png differ diff --git a/docs/dev/reference/hierarchical_kinetics.html b/docs/dev/reference/hierarchical_kinetics.html index a696916f..7ece90cc 100644 --- a/docs/dev/reference/hierarchical_kinetics.html +++ b/docs/dev/reference/hierarchical_kinetics.html @@ -24,7 +24,7 @@ includes them.'>