read.beast.table: Extract node data from BEAST chronogram

In ips: Interfaces to Phylogenetic Software in R

Extract node data from BEAST chronogram

Description

This function reads a BEAST chronogram such as produced by TreeAnnotator and extracts time, rate, and support values for internal and external nodes. Nodes in the resulting data frame are ordered exactly like in the NEXUS file.

Usage

read.beast.table(file, digits = 2)

Arguments

file	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

A matrix; each row corresponds to an internal node, the (ape!)number of which is given in the first column; the remaining columns list the node values extracted from the chronogram.

Author(s)

Christoph Heibl

See Also

read.beast to parse TreeAnnotator output, rbeauti to create XML input for BEAST. HPDbars for plotting highest posterior densities on phylogenies has been moved to package viper.

ips documentation built on May 29, 2024, 4:39 a.m.