Takes a phylogeny in the form of an object of class phylo and
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.
createMrBayesConstraints(
tree,
partial = TRUE,
file = NULL,
includeIngroupConstraint = FALSE
)If argument file is NULL, then the constrain commands
are output as a series of character strings.
An object of class phylo.
If TRUE (the default), then constraints will
be defined as partial constraints with respect to the rest of the taxa
in the input tree. If FALSE, constraints will be
defined as hard clade membership constraints (i.e. no additional
taxa will be allowed to belong to the nodes present in the observed tree.
Depending on your analysis, partial = TRUE may require additionally
defining an outgroup.
Filename (possibly with path) as a character string
to a file which will be overwritten with the output constraint lines.
If NULL, constraint lines are printed in the console.
When writing the prset line,
should a group named 'ingroup' be included, which presumes an ingroup
constraint was defined by the user for sake or rooting the tree? This is
mainly used for use with paleotree function createMrBayesTIpDatingNexus for automating
the construction of tip-dating analyses, which must constrain the ingroup.
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.
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
character data.
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.
createMrBayesTipDatingNexus, createMrBayesTipCalibrations
set.seed(444)
tree <- rtree(10)
createMrBayesConstraints(tree)
createMrBayesConstraints(tree,partial = FALSE)
if (FALSE) {
createMrBayesConstraints(tree,file = "topoConstraints.txt")
}
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