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authorJohannes Ranke <jranke@uni-bremen.de>2023-04-15 15:35:06 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2023-04-15 15:35:06 +0200
commitb0b710ee9f9bb9bbe9708676d0c5822465e02203 (patch)
tree537dcf86326ab2e03100a5defb11b264a4b72a17 /inst/rmarkdown
parent50ea6d11f8c79218c98ee8ae56d8bdcd42cc703a (diff)
Make predefined symbols safer
We still need to create a parallel processing cluster _after_ creating a compiled model that is moved to a user defined location, at least I did not find another way to make it work. This is not a problem with parallel processing without a cluster, which is not available on Windows.
Diffstat (limited to 'inst/rmarkdown')
-rw-r--r--inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd24
1 files changed, 20 insertions, 4 deletions
diff --git a/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd
index 38a6bd20..cb328308 100644
--- a/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd
+++ b/inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd
@@ -21,11 +21,18 @@ library(readxl)
```{r n_cores, cache = FALSE}
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
@@ -179,6 +186,10 @@ illparms(parent_best_pH_2)
parms(parent_best_pH_2, ci = TRUE) |> kable(digits = 3)
```
+```{r}
+stopCluster(cl)
+```
+
\clearpage
# Pathway fits
@@ -203,6 +214,7 @@ Separate evaluations of all datasets are performed with constant variance
and using two-component error.
```{r path-1-sep, dependson = c("path-1-degmod", "ds")}
+cl <- start_cluster(n_cores)
sforb_sep_const <- mmkin(list(sforb_path = m_sforb_sfo2), ds,
cluster = cl, quiet = TRUE)
sforb_sep_tc <- update(sforb_sep_const, error_model = "tc")
@@ -268,6 +280,10 @@ plot(path_1_refined)
parms(path_1_refined, ci = TRUE) |> kable(digits = 3)
```
+```{r}
+stopCluster(cl)
+```
+
\clearpage
# Appendix

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