read.beast: Read Bayesian Trees
In ips: Interfaces to Phylogenetic Software in R
read.beast R Documentation
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.community/treeannotator
Metacomments in NEXUS: https://code.google.com/archive/p/beast-mcmc/wikis/NexusMetacommentFormat.wiki
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.
ips documentation built on May 29, 2024, 4:39 a.m.
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| read.beast | R Documentation |
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 |
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.community/treeannotator
Metacomments in NEXUS: https://code.google.com/archive/p/beast-mcmc/wikis/NexusMetacommentFormat.wiki
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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