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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

Run `BAMM` through `outsider` in R

Bayesian Analysis of Macroevolutionary Mixtures: multimodel inference on speciation and trait evolution.

Install and look up help

library(outsider)
module_install(repo = "DomBennett/om..bamm")
#module_help(repo = "DomBennett/om..bamm")

A detailed example

The example below is taken from the "Quickstart" guide to BAMM

# ------
# Import
# ------
library(outsider)
bamm <- module_import(fname = 'bamm', repo = "DomBennett/om..bamm")

# ----
# Data
# ----
# 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
# --------
# 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)

# ------
# Verify
# ------
# Double check the output, all resulting files are stored in outdir
list.files(wd)
# peek into the mcmc_out.txt
print(read.csv(file.path(wd, 'mcmc_out.txt')))

# delete temp dir
if ('wd' %in% ls() && dir.exists(wd)) {
 unlink(x = wd, recursive = TRUE, force = TRUE) 
}
module_uninstall(repo = "DomBennett/om..bamm")

Key arguments

The bamm function in R has three arguments:

control_file: File path to the text file that specifies all of the parameters of the analysis
indir: File path to the directory containing all of the input files (e.g. the tree file). (It's best to make this folder contain only the input files.)
outdir: File path to the directory which will collect all the output files.

Links

Find out more by visiting the BAMM documentation website.

Please cite

Rabosky DL (2014) Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees. PLOS ONE 9(2): e89543. https://doi.org/10.1371/journal.pone.0089543
Rabosky, D., Santini, F., Eastman, J. et al. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nat Commun 4, 1958 (2013) doi:10.1038/ncomms2958
Daniel L. Rabosky, Stephen C. Donnellan, Michael Grundler, Irby J. Lovette, Analysis and Visualization of Complex Macroevolutionary Dynamics: An Example from Australian Scincid Lizards, Systematic Biology, Volume 63, Issue 4, July 2014, Pages 610–627, https://doi.org/10.1093/sysbio/syu025
Shi, J.J. and Rabosky, D.L. (2015), Speciation dynamics during the global radiation of extant bats. Evolution, 69: 1528-1545. doi:10.1111/evo.12681
Bennett et al. (2020). outsider: Install and run programs, outside of R, inside of R. Journal of Open Source Software, In review