Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/createMrBayesConstraints.R
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.
1 2 | createMrBayesConstraints(tree, partial = TRUE, file = NULL,
includeIngroupConstraint = FALSE)
|
tree |
An object of class |
partial |
If |
file |
Filename (possibly with path) as a character string
to a file which will be overwritten with the output constraint lines.
If |
includeIngroupConstraint |
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
character data.
If argument file
is 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.
createMrBayesTipDatingNexus
, createMrBayesTipCalibrations
1 2 3 4 5 6 7 8 9 10 11 | set.seed(444)
tree<-rtree(10)
createMrBayesConstraints(tree)
createMrBayesConstraints(tree,partial=FALSE)
## Not run:
createMrBayesConstraints(tree,file="topoConstraints.txt")
## End(Not run)
|
Loading required package: ape
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
[1] "constraint node1 partial = t1 t6 : t5 t10 t9 t2 t8 t7 t3 t4;"
[2] "constraint node2 partial = t5 t10 t9 t2 t8 t7 t3 t4 : t1 t6;"
[3] "constraint node3 partial = t5 t10 : t1 t6 t9 t2 t8 t7 t3 t4;"
[4] "constraint node4 partial = t9 t2 t8 t7 t3 t4 : t1 t6 t5 t10;"
[5] "constraint node5 partial = t9 t2 : t1 t6 t5 t10 t8 t7 t3 t4;"
[6] "constraint node6 partial = t8 t7 t3 t4 : t1 t6 t5 t10 t9 t2;"
[7] "constraint node7 partial = t8 t7 : t1 t6 t5 t10 t9 t2 t3 t4;"
[8] "constraint node8 partial = t3 t4 : t1 t6 t5 t10 t9 t2 t8 t7;"
[9] ""
[10] "prset topologypr = constraints(node1,node2,node3,node4,node5,node6,node7,node8);"
[1] "constraint node1 = t1 t6;"
[2] "constraint node2 = t5 t10 t9 t2 t8 t7 t3 t4;"
[3] "constraint node3 = t5 t10;"
[4] "constraint node4 = t9 t2 t8 t7 t3 t4;"
[5] "constraint node5 = t9 t2;"
[6] "constraint node6 = t8 t7 t3 t4;"
[7] "constraint node7 = t8 t7;"
[8] "constraint node8 = t3 t4;"
[9] ""
[10] "prset topologypr = constraints(node1,node2,node3,node4,node5,node6,node7,node8);"
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