bamm: bamm: Bayesian Analysis of Macroevolutionary Mixtures

In DomBennett/om..bamm..2.5.0: Outsider module for BAMM

Description

Run bamm through R.

Usage

bamm(control_file, indir, outdir = indir)

Arguments

control_file	File path to control file
indir	File path to directory containting all input files specified in the control file.
outdir	File path to directory where all resulting files will be placed.

Details

control_file is equivalent to the -c option in the command line version of the program. By default, the command-line version looks in the folder where it was launched to find files specified in the control file (e.g. tree file). In this version, the indir determines where input files are contained.

For efficiency, it is based to specify an indir folder that contains only the files required to run the BAMM analysis.

Examples

library(outsider)
bamm <- module_import('bamm', repo = 'dombennett/om..bamm')

# create temp directory to contain test input and output data
wd <- file.path(tempdir(), 'testing_bamm')
if(!dir.exists(wd)) {
  dir.create(wd)
}
# download modified template control file for a "speciation-extinction"
# analysis of whales
url <- 'https://raw.githubusercontent.com/DomBennett/om..bamm/master/test_data/whale_diversification.txt'
control_file <- file.path(wd, 'whale_diversification.txt')
download.file(url = url, destfile = control_file)
# download a tree whales
url <- 'https://raw.githubusercontent.com/DomBennett/om..bamm/master/test_data/whaletree.tre'
download.file(url = url, destfile = file.path(wd, 'whaletree.tre'))

# run bamm in R by specifying the control file and the directory containing the
# whale tree
bamm(control_file = control_file, indir = wd, outdir = wd)

# clean up
unlink(x = wd, recursive = TRUE, force = TRUE)

DomBennett/om..bamm..2.5.0 documentation built on Jan. 19, 2020, 9:52 p.m.