Merge branch 'prune-dependencies'

hmsc-r · Mar 2, 2021 · 7b9b185 · 7b9b185
2 parents a732ff7 + 1217104
commit 7b9b185
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Showing 5 changed files with 28 additions and 26 deletions.
diff --git a/R/sampleMcmc.R b/R/sampleMcmc.R
@@ -371,7 +371,7 @@ sampleMcmc =
    }
 
    if(nParallel > 1){
-      cl = makeCluster(nParallel, type="SOCK")
+      cl = makeCluster(nParallel)
       clusterExport(cl, c("hM","nChains","transient","samples","thin","verbose","adaptNf","initSeed","initPar","updater",
          "X1", "Tr", "Y", "distr", "Pi", "C", "nr",
          "mGamma", "iUGamma", "V0", "f0", "aSigma", "bSigma", "rhopw",

diff --git a/vignettes/load_libraries.R b/vignettes/load_libraries.R
@@ -1,25 +1,25 @@
 # LOAD PACKAGES (BEGINNING) ######################################################################
-library(devtools)
+#library(devtools)
 #install Rtools to be able to install BayesLogit unless you have it already
 #install_url('https://cran.r-project.org/src/contrib/Archive/BayesLogit/BayesLogit_0.6.tar.gz')
-library(BayesLogit)
-library(withr)
-library(knitr)
-install_github("hmsc-r/HMSC", build_opts = c("--no-resave-data", "--no-manual"))
+#library(BayesLogit)
+#library(withr)
+library(knitr) # kable
+#install_github("hmsc-r/HMSC", build_opts = c("--no-resave-data", "--no-manual"))
 library(Hmsc)
-library(stats)
-library(abind)
-library(corrplot)
-library(ggplot2)
-library(nnet)
-library(coda)
-library(ape)
-library(phytools)
-library(fields)
-library(MASS)
-library(MCMCpack)
+#library(stats)
+#library(abind)
+#library(corrplot)
+#library(ggplot2)
+#library(nnet)
+#library(coda)
+#library(ape)
+#library(phytools)
+#library(fields)
+library(MASS) # mvrnorm
+#library(MCMCpack)
 #install_github("kassambara/easyGgplot2")
-library(easyGgplot2)
-library(pROC)
-library(parallel)
+#library(easyGgplot2)
+#library(pROC)
+#library(parallel)
 # LOAD PACKAGES (END) ############################################################################
diff --git a/vignettes/vignette_3_multivariate_high.Rmd b/vignettes/vignette_3_multivariate_high.Rmd
@@ -33,7 +33,6 @@ library(fields)
 
 ```{r I, message = F}
 library(Hmsc)
-library(parallel)
 library(corrplot)
 set.seed(1)
 ```

diff --git a/vignettes/vignette_5_performance.Rmd b/vignettes/vignette_5_performance.Rmd
@@ -501,10 +501,14 @@ for (case in cases){
 ```
 
 ```{r BLAS, message=F, eval=T, cache=F, echo=F}
-myBLAS <- sessionInfo()$BLAS
-myBLAS <- unlist(strsplit(myBLAS, .Platform$file.sep))
-myBLAS <- myBLAS[length(myBLAS)]
-myBLAS <- unlist(strsplit(myBLAS, "\\."))[1]
+myBLAS <- extSoftVersion()["BLAS"]
+if (myBLAS == "") {
+   myBLAS <- "unknown BLAS"
+} else {
+     myBLAS <- unlist(strsplit(myBLAS, .Platform$file.sep))
+     myBLAS <- myBLAS[length(myBLAS)]
+     myBLAS <- unlist(strsplit(myBLAS, "\\."))[1]
+}
 ```
 
 ### Computational time
@@ -638,7 +642,6 @@ boxplot(toplot, main="rho", names = cases, las = 1)
 \pagebreak
 
 ```{r Data evaluation VIII, message=F, eval=T, cache=F, echo=F}
-library(knitr)
 rhores = matrix(ncol=ncases, nrow=3)
 for (case in 1:ncases){
   rhores[1,case] = mix[[case]]$es.rho

diff --git a/vignettes/vignette_5_performance.pdf b/vignettes/vignette_5_performance.pdf