Connect R to JAGS

Mac OSX (10.11+)

1. Use Just Another Gibbs Sampler (JAGS)
2. Install JAGS 4.3.2 (or 4.2.0 - currently it is slightly slower for 4.3.2, which was updated to be compatible with R 4.3.x); Download here
3. Install R; Download from here
4. Fire up R, run R command install.packages("rjags")
5. Run R command library(rjags) in R console; If the installations are successful, you’ll see some notes like this:

>library(rjags)
Loading required package: coda
Linked to JAGS 4.x.0
Loaded modules: basemod,bugs

• Run R command library(baker). If the package ks cannot be loaded due to failure of loading package rgl, first install X11 by going here, followed by

install.packages("http://download.r-forge.r-project.org/src/contrib/rgl_0.95.1504.tar.gz",repo=NULL,type="source")

Unix (Build from source without administrative privilege)

Here we use JHPCE as an example. The complete installation guide offers extra information.

1. Download source code for JAGS 4.2.0; The workflow would be similar for later versions of JAGS.

2. Suppose you’ve downloaded it in ~/local/jags/4.2.0. Follow the bash commands below:

   # change to the directory with the newly downloaded source files:
   cd ~/local/jags/4.2.0
   
   # create a new folder named "usr"
   mkdir usr
   
   # decompress files:
   tar zxvf JAGS-4.2.0.tar.gz
   
   # change to the directory with newly decompressed files:
   cd ~/local/jags/4.2.0/JAGS-4.2.0
   
   
   
   # specify new JAGS home:
   export JAGS_HOME=$HOME/local/jags/4.2.0/usr
   export PATH=$JAGS_HOME/bin:$PATH
   
   # link to BLAS and LAPACK:
   # Here I have used "/usr/lib64/atlas/" and "/usr/lib64/" on JHPCE that give me
   # access to libblas.so.3 and liblapack.so.3. Please modify to paths on your system.
   LDFLAGS="-L/usr/lib64/atlas/ -L/usr/lib64/" ./configure --prefix=$JAGS_HOME --libdir=$JAGS_HOME/lib64 
   
   # if you have 8 cores:
   make -j8
   make install
   
   # prepare to install R package, rjags:
   export PKG_CONFIG_PATH=$HOME/local/jags/4.2.0/usr/lib64/pkgconfig 
   
   module load R
   R> install.packages("rjags")
   # or if the above fails, try:
   R>install.packages("rjags", configure.args="--enable-rpath")
   

3. Also check out the INSTALLATION file for rjags package.

#!/bin/bash
#$ -M [email protected]
#$ -N baker_regression_perch
#$ -o /users/zhwu/baker_regression/data_analysis/baker_regression_test.txt
#$ -e /users/zhwu/baker_regression/data_analysis/baker_regression_test.txt

export JAGS_HOME=$HOME/local/jags/4.2.0/usr
export PATH=$JAGS_HOME/bin:$PATH

export LD_LIBRARY_PATH=$JAGS_HOME/lib64

cd /users/zhwu/baker_regression/data_analysis
#$ -cwd

echo "**** Job starts ****"
date
echo "**** JHPCE info ****"
echo "User: ${USER}"
echo "Job id: ${JOB_ID}"
echo "Job name: ${JOB_NAME}"
echo "Hostname: ${HOSTNAME}" 

Rscript real_regression_data_jhpce.R

echo "**** Job ends ****" 
date