JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. JAGS was written with three aims in mind:

  • To have a cross-platform engine for the BUGS language.

  • To be extensible, allowing users to write their own functions, distributions and samplers.

  • To be a platform for experimentation with ideas in Bayesian modeling.

Interactive Usage

After connecting to Bessemer (see Establishing a SSH connection), start an interactive session with the srun --pty bash -i command.

The latest version of JAGS (currently version 4.3.0) is made available with the command:

$ module load JAGS/4.3.0-foss-2020a

After this the JAGS command can be run from the terminal prompt:

$ jags
Welcome to JAGS 4.3.0 on Thu Mar 24 15:43:13 2022
JAGS is free software and comes with ABSOLUTELY NO WARRANTY
Loading module: basemod: ok
Loading module: bugs: ok

The rjags and runjags interfaces in R

rjags and runjags are CRAN packages that provide an R interface to JAGS. They are not installed in R by default.

After connecting to Bessemer (see Establishing a SSH connection), start an interactive session with the srun --pty bash -i command.

Run the following module commands :

$ module load JAGS/4.3.0-foss-2020a
$ module load R/4.0.0-foss-2020a

Launch R by typing R and pressing return. Within R, execute the following commands


and follow the on-screen inctructions. Answer y to any questions about the creation of a personal library should they be asked.

The packages will be stored in a directory called R within your home directory.

You should only need to run the install.packages commands once. When you log into the system in future, you will only need to run the module commands above to make JAGS available to the system.

You load the rjags packages the same as you would any other R package



If you received an error message such as :

Error : .onLoad failed in loadNamespace() for 'rjags', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/home/te1st/R/x86_64-unknown-linux-gnu-library/3.2/rjags/libs/rjags.so':
libjags.so.3: cannot open shared object file: No such file or directory
Error: package or namespace load failed for 'rjags'

The most likely cause is that you forget to load the necessary modules before starting R.

Installation notes

Installation method

JAGS version 4.3.0 was installed using Easybuild 4.4.0, build details can be found in /usr/local/packages/live/eb/JAGS/4.3.0-foss-2020a/easybuild