corHMM (R library)

Overview

corHMM is an R package to fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.

Version 1.22 is installed on the CSF. This will use R 3.4.3.

Restrictions on use

There are no restrictions on accessing the software on the CSF. The software is released under the GNU GPL-v3 license and all usage must adhere to that.

Set up procedure

To access the software you must first load the modulefile:

# This will automatically load the R v3.4.3 modulefile for you

module load apps/gcc/R-packages/3.4.3/corhmm/1.22

Running the application

Please do not run corHMM on the login node. Jobs should be submitted to the compute nodes via batch.

To load the corHMM library in to R once R has started, ensure you run the command:

library(corHMM)

Serial batch job submission

Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings

R CMD BATCH my_script.R my_script.R.o$JOB_ID
        #
        # -- R must be called with both the "CMD" and "BATCH" options which tell it
        #    to run an R *program*, in this case "my_script.R", instead of presenting
        #    an interactive prompt
        #
        # -- Use the following R command in your script to load the scenic library:
        #
        #    library("corhmm")
        #
        # -- the final argument, "my_test.R.o$JOBID", tells R to send output to a 
        #    file with this name (without, R sends output to "my_test.Rout", which
        #    would be over-written by a second submission of "my_test.R" via
        #    "runmyRjob.qsub")

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Further info

• corHMM manual (PDF)

Updates

None.