read.beast: Read Bayesian Trees

In heibl/ips: Interfaces to Phylogenetic Software in R

Read Bayesian Trees

Description

Thess functions parse chronograms in NEXUS format as produced by TreeAnnotator or output by MrBayes.

Usage

read.mrbayes(file, digits = NULL)

read.beast(file, digits = NULL)

read.starbeast(file)

Arguments

file	A character string giving the input file, which must be a TreeAnnotator-generated chronogram in NEXUS format.
digits	NULL or integer, if !is.null(digits) values are rounded to the given integer.

Value

An object of class phylo.

Note

read.starbeast currently parses only skalars and ranges; node statistics with more than two values will be deleted and a warning message will be issued. Future version of read.starbeast will hopefully be able to append list or data frames to phylo objects. If you have any opinion or wishes regarding the question of how this exactly should be managed, send me a message.

read.mrbayes is intended to read single trees with annotated nodes. For reading tree samples from the posterior distribution there is a collection of perl script written by Johan Nylander (https://github.com/nylander/Burntrees).

Author(s)

Christoph Heibl

References

TreeAnnotator: http://beast.bio.ed.ac.uk/TreeAnnotator

Metacomments in NEXUS: http://code.google.com/p/beast-mcmc/wiki/NexusMetacommentFormat

See Also

read.beast.table to extract internal node data from NEXUS file, rbeauti to create XML input for BEAST. HPDbars for plotting highest posterior densities on phylogenies has been moved to package viper.

heibl/ips documentation built on April 18, 2024, 11:59 p.m.