Performance improvement

[mardukbp]

In the appendix of the documentation it can be seen that fitting the model m1 takes 202 minutes.

Using the optimParallel package running on pqR (instead of GNU R) with 8 cores (Amazon EC2 t3.2xlarge) this model was fitted in 26 minutes.

If you want to experiment with this, do the following:

git clone https://github.com/mardukbp/optimParallel
git clone https://github.com/mardukbp/oSCR.git -b optimParallel
git clone https://github.com/mardukbp/pqR.git -b all-patches

Compile pqR as usual: ./configure && make.

Install the R packages in pqR:

deps <- c("abind", "doParallel", "gdistance", "Formula", "FNN")
sapply(deps, function(x) if(!require(x, character.only=TRUE)) install.packages(x))

setwd(“/path/to/packages”)

install.packages(“optimParallel", repos=NULL, type="source")
install.packages("oSCR", repos=NULL, type="source")