Takes a phylogeny in the form of an object of class
outputs a set of topological constraints for MrBayes as a set of character
strings, either printed in the R console or in a named text file, which
can be used as commands in the MrBayes block of a NEXUS file for use with
(you guessed it!) MrBayes.
An object of class
Filename (possibly with path) as a character string
to a file which will be overwritten with the output constraint lines.
When writing the
partial = TRUE may be useful if the reason for using
createMrBayesConstraints is to constrain a topology containing
some of the taxa in an analysis, while allowing other taxa to freely
vary. For example, Slater (2013) constrained an analysis so extant
taxon relationships were held constant, using a molecular-based topology,
while allowing fossil taxa to freely vary relative to their morphological
NULL, then the constrain commands
are output as a series of character strings.
David W. Bapst, with some inspiration from Graham Slater. This code was produced as part of a project funded by National Science Foundation grant EAR-1147537 to S. J. Carlson.
Slater, G. J. 2013. Phylogenetic evidence for a shift in the mode of mammalian body size evolution at the Cretaceous-Palaeogene boundary. Methods in Ecology and Evolution 4(8):734-744.
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