diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2023-02-17 09:30:37 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2023-02-17 09:30:37 +0100 |
| commit | beb8e5a107f8bacca5e6b956cc6847c661cd20b0 (patch) | |
| tree | 20f2769107876bb11b2f2e2549e00499bb86d3ee | |
| parent | 19861806ed790dc55380c64c6a5e27ba7ecd52de (diff) | |
| parent | c7cc91c47f9b074521fcaaa05a020525d719c2d9 (diff) | |
Merge remote-tracking branch 'origin/main' into faster_lsoda
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | GNUmakefile | 3 | ||||
| -rw-r--r-- | R/mmkin.R | 7 | ||||
| -rw-r--r-- | vignettes/dmta_parent_2022_prebuilt.rnw | 2 |
4 files changed, 7 insertions, 6 deletions
@@ -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')" @@ -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} |