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authorJohannes Ranke <jranke@uni-bremen.de>2023-02-17 09:30:37 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2023-02-17 09:30:37 +0100
commitbeb8e5a107f8bacca5e6b956cc6847c661cd20b0 (patch)
tree20f2769107876bb11b2f2e2549e00499bb86d3ee
parent19861806ed790dc55380c64c6a5e27ba7ecd52de (diff)
parentc7cc91c47f9b074521fcaaa05a020525d719c2d9 (diff)
Merge remote-tracking branch 'origin/main' into faster_lsoda
-rw-r--r--.gitignore1
-rw-r--r--GNUmakefile3
-rw-r--r--R/mmkin.R7
-rw-r--r--vignettes/dmta_parent_2022_prebuilt.rnw2
4 files changed, 7 insertions, 6 deletions
diff --git a/.gitignore b/.gitignore
index 5bec45e6..6cf7f403 100644
--- a/.gitignore
+++ b/.gitignore
@@ -31,4 +31,3 @@ vignettes/*_files/
vignettes/prebuilt/*_cache
vignettes/prebuilt/*_files
vignettes/prebuilt/*_dlls
-vignettes/prebuilt/*.pdf
diff --git a/GNUmakefile b/GNUmakefile
index 9f268335..42df55d5 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -99,6 +99,9 @@ testcheck: roxygen test check
README.html: README.md
"$(RBIN)/Rscript" -e "rmarkdown::render('README.md', output_format = 'html_document', output_options = list(mathjax = NULL))"
+vignettes/%.pdf: vignettes/references.bib vignettes/%.rnw
+ "$(RBIN)/Rscript" -e "tools::buildVignette(file = 'vignettes/$*.rnw', dir = 'vignettes')"
+
vignettes/%.html: vignettes/mkin_vignettes.css vignettes/references.bib vignettes/%.rmd
"$(RBIN)/Rscript" -e "tools::buildVignette(file = 'vignettes/$*.rmd', dir = 'vignettes')"
diff --git a/R/mmkin.R b/R/mmkin.R
index 01e53290..e1537685 100644
--- a/R/mmkin.R
+++ b/R/mmkin.R
@@ -62,16 +62,15 @@
#' # allow to plot the observed variables separately
#' plot(fits.0[1, 1])
#'
-#' # On Windows, we can use multiple cores by making a cluster using the parallel
-#' # package, which gets loaded with mkin, and passing it to mmkin, e.g.
-#' cl <- makePSOCKcluster(12)
+#' # On Windows, we can use multiple cores by making a cluster first
+#' cl <- parallel::makePSOCKcluster(12)
#' f <- mmkin(c("SFO", "FOMC", "DFOP"),
#' list(A = FOCUS_2006_A, B = FOCUS_2006_B, C = FOCUS_2006_C, D = FOCUS_2006_D),
#' cluster = cl, quiet = TRUE)
#' print(f)
#' # We get false convergence for the FOMC fit to FOCUS_2006_A because this
#' # dataset is really SFO, and the FOMC fit is overparameterised
-#' stopCluster(cl)
+#' parallel::stopCluster(cl)
#' }
#'
#' @export mmkin
diff --git a/vignettes/dmta_parent_2022_prebuilt.rnw b/vignettes/dmta_parent_2022_prebuilt.rnw
index cbfa6897..6267bffc 100644
--- a/vignettes/dmta_parent_2022_prebuilt.rnw
+++ b/vignettes/dmta_parent_2022_prebuilt.rnw
@@ -3,5 +3,5 @@
%\VignetteIndexEntry{Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P}
\begin{document}
-\includepdf[pages=-, fitpaper=true]{2022_wp_1/2022_dmta_parent.pdf}
+\includepdf[pages=-, fitpaper=true]{prebuilt/2022_dmta_parent.pdf}
\end{document}

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