Post release changes to the docs

The cyantraniliprole and dmta pathway vignettes were not working any
more with the latest changes in deSolve and mkin. All docs need a
rebuild.

4 files changed, 54 insertions, 17 deletions

diff --git a/R/hierarchical_kinetics.R b/R/hierarchical_kinetics.R
index ae60d43c..46623356 100644
--- a/R/hierarchical_kinetics.R
+++ b/R/hierarchical_kinetics.R
@@ -30,7 +30,9 @@
 #'
 #' \dontrun{
 #' library(rmarkdown)
-#' draft("example_analysis.rmd", template = "hierarchical_kinetics", package = "mkin")
+#' # The following is now commented out after the relase of v1.2.3 for the generation
+#' # of online docs, as the command creates a directory and opens an editor
+#' #draft("example_analysis.rmd", template = "hierarchical_kinetics", package = "mkin")
 #' }
 #'
 #' @export
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 5c67d88f..6bf7c14a 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -1,8 +1,8 @@
 url: https://pkgdown.jrwb.de/mkin
 
 development:
-  mode: devel
-  version_label: info
+  mode: release
+  version_label: default
 
 template:
   bootswatch: spacelab
diff --git a/vignettes/prebuilt/2022_cyan_pathway.rmd b/vignettes/prebuilt/2022_cyan_pathway.rmd
index df34a6f2..d0b2c889 100644
--- a/vignettes/prebuilt/2022_cyan_pathway.rmd
+++ b/vignettes/prebuilt/2022_cyan_pathway.rmd
@@ -50,11 +50,19 @@ library(knitr)
 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)
 ```
 
 \clearpage
@@ -135,6 +143,10 @@ illparms(cyan_saem_reduced)
 anova(cyan_saem_reduced) |> kable(digits = 1)
 ```
 
+```{r}
+stopCluster(cl)
+```
+
 # Pathway fits
 
 ## Evaluations with pathway established previously
@@ -178,6 +190,7 @@ cyan_path_1 <- list(
     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.
@@ -187,7 +200,7 @@ 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()
 
@@ -209,7 +222,7 @@ currently under development.
 ```{r, f-saem-1, dependson = "f-sep-1"}
 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)
 ```
 
 ```{r dependson = "f-saem-1"}
@@ -253,6 +266,9 @@ at later time points are strongly and systematically underestimated.
 
 \clearpage
 
+```{r}
+stopCluster(cl_path_1)
+```
 
 ## Alternative pathway fits
 
@@ -294,11 +310,13 @@ cyan_path_2 <- list(
     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()
@@ -319,7 +337,7 @@ Sassafras dataset.
 ```{r f-saem-2, dependson = c("f-sep-2-const", "f-sep-2-tc")}
 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)
 ```
 
 ```{r dependson = "f-saem-2"}
@@ -384,11 +402,11 @@ no_ranef[["sforb_path_2", "const"]] <- c("cyan_free_0",
   "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)
 ```
 
 ```{r dependson = "f-saem-3"}
@@ -413,6 +431,10 @@ 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.
 
+```{r}
+stopCluster(cl_path_2)
+```
+
 \clearpage
 
 # Conclusion
diff --git a/vignettes/prebuilt/2022_dmta_pathway.rmd b/vignettes/prebuilt/2022_dmta_pathway.rmd
index ff2b527c..f787daf2 100644
--- a/vignettes/prebuilt/2022_dmta_pathway.rmd
+++ b/vignettes/prebuilt/2022_dmta_pathway.rmd
@@ -45,10 +45,17 @@ library(knitr)
 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)
 }
 ```
 
@@ -163,6 +170,8 @@ m_hs_path_1 <- mkinmod(
   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,
@@ -332,6 +341,10 @@ plot(saem_sforb_path_1_tc_reduced)
 Plots of the remaining fits and listings for all successful fits are shown in
 the Appendix.
 
+```{r}
+stopCluster(cl)
+```
+
 
 # Conclusions