read.beast: Read Bayesian Trees
In fmichonneau/phyloch: Tools for phylogenetics and taxonomy
Description
Usage
Arguments
Value
Note
Author(s)
References
See Also
Description
Thess functions parse chronograms in NEXUS format as produced by TreeAnnotator or output by MrBayes.
Usage
1
2
3
4
5
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.
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, node.trans, HPDbars to plot highest posterior densities on phylogenies.
fmichonneau/phyloch documentation built on May 16, 2019, 1:45 p.m.
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Description Usage Arguments Value Note Author(s) References See Also
Description
Thess functions parse chronograms in NEXUS format as produced by TreeAnnotator or output by MrBayes.
Usage
1 2 3 4 5 | 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.
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, node.trans, HPDbars to plot highest posterior densities on phylogenies.
R Package Documentation
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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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