BPPmultitool

BPPmultitool is a collection of R scripts that is useful to analyze the output of BPPmulti which can be found here: http://github.com/eberlejonas/BPPmulti

Currently supported is:

• automatic reading of BPPmulti settings
• plotting guide trees
• parsing ESS (effective sampling size) values
• writing of summarizing result tables
• extraction of single analysis results
• plots of single analysis results
• summarizing plots of species delimitation results from multiple guide trees and repeated runs

Requirements

An R installation with the packages ape and stringr installed. Use install.packages("ape") and install.packages("stringr") in the R console if you don't have them installed already.

Usage

1. Download all BPPmultitool files to a folder on your computer.
2. Open template.R in a texteditor
3. Search for the command setwd("/home/jonas/my_BPPmulti_run") (line 21) and put the path to the working directory inside the quotes (the one you also specified in your BPPmulti analysis). On Windows you can for instance write setwd("C:/Users/jonas/my_BPPmulti_run").
4. Execute all desired commands in template.R on the R console. source("subs.R"), setwd("..."), settings <- getSettings(), and BPPresults <- parseBPPmulti(settings) are obligatory.

Please also refer to the comments in template.R.