Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

No Format
source /usr/local/bin/s3proxy.sh
module load anaconda3/2024.06
conda create --name myRenv R=4.3.1
source activate myRenv

To install packes like "tidyverse","lubridate","ggplot2", "tmap", "ggmap", "sf", "ggsci", "remotes", "raster", "readxl", "terra"
Simply google with the package name and conda as search strings e.g. tidyverse conda
You will see instructions to install these packages:

conda install r::r-lubridate
conda install r::r-tidyverse
conda install conda-forge::r-ggplot2
conda install conda-forge::r-tmap
conda install conda-forge::r-ggmap
conda install conda-forge::r-sf
conda install conda-forge::r-ggsci
conda install conda-forge::r-remotes
conda install conda-forge::r-raster
conda install conda-forge::r-readxl
conda install conda-forge::r-terra

Or simply:
conda create --name myRenv r=4.3.1 r-tidyverse r-ggplot2 r-tmap r-ggmap r-sf r-ggsci r-remotes r-raster r-readxl r-terra -c conda-forge 

Here is a sample pbs script:
#!/bin/bash
#PBS -m abe
#PBS -M XXXX@griffithuni.edu.au
#PBS -N MyTest
#PBS -q workq
#PBS -l select=1:ncpus=1:mem=4gb,walltime=01:00:00
module load anaconda3/2024.06
source activate myRenv
module list
cd $PBS_O_WORKDIR
R CMD BATCH '--args a=1 b=c(2,5,6)' test.R test.out
echo "test Done"
echo "Done with job"

save' <MAIN_CODEmodel1.R
##sleep 22
echo "Done with job"
>>>>>

R script can start with loading the packages like this:
package_names <- c("tidyverse","lubridate","ggplot2", "tmap", "ggmap", "sf", "ggsci", "remotes", "raster", "readxl", "terra")

# Loop to load the packages
for (package_name in package_names) {
if (!requireNamespace(package_name, quietly = TRUE)) {
message(paste("Installing and loading", package_name))
install.packages(package_name, dependencies = TRUE)
}
library(package_name, character.only = TRUE)
}

<snip>



Reference

1. http://yusung.blogspot.com.au/2009/01/install-jags-and-rjags-in-fedora.html

...