Prepare and submit a new RevBayes analysis job

Source: R/RevBayes.R

RevBayes() constructs all necessary RevBayes input files for a given project and model specification, synchronizes them with the appropriate GitHub repository, and (optionally) prepares SLURM submission scripts.

RevBayes(pID, scriptID, makeSlurm = FALSE)

Arguments

pID

Character. Project identifier (e.g., "1210").

scriptID

Character. Identifier of the model script to be used. Prefix "rm_" denotes random partitioning.

makeSlurm

Logical. Whether to generate SLURM job scripts immediately. Defaults to FALSE.

Value

RevBayes() invisibly returns TRUE when script generation and Git synchronization succeed. The function is called primarily for its side-effect of populating and committing RevBayes model repositories.

Details

The typical workflow is:

  1. Use PrepareMatrix() to generate standardized .nex matrix files.

  2. Run MakeRepo() to create a GitHub repository for this project–model combination.

  3. Call RevBayes(pID, scriptID) to populate the repository with RevBayes model scripts.

  4. Use MakeSlurm() or makeSlurm = TRUE to create SLURM job files.

The function draws its templates from the rbScripts/ directory, performs placeholder substitution (%PID%, %SCRIPT%, %MATRIXBASE%), and copies the appropriate matrix subsets (neo.nex, trans.nex, or their randomised variants) into the repository.

When makeSlurm = TRUE, both MCMC and marginal-likelihood SLURM job files are generated automatically.