phytools: read.simmap – R documentation

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phytools

read.simmap

Read SIMMAP style trees from file

Description

This reads one or multiple SIMMAP style trees from file.

Usage

read.simmap(file="", text, format="nexus", rev.order=TRUE, version=1)

Arguments

`file`	name of text file with one or multiple SIMMAP v1.0 or v1.5 style trees.
`text`	character string containing the tree. If `version=1.5` this argument is ignored. (This format tree can only be read from file in the present version.)
`format`	format of the trees: either `"phylip"` or `"nexus"` - the latter is the default output from SIMMAP. If `version=1.5` this argument is ignored.
`rev.order`	a logical value indicating whether the states and times along each branch is given (from root to tip) in right-to-left order (if TRUE) or in left-to-right order. If `version=1.5` this argument is ignored.
`version`	version of SIMMAP for input tree. If the tree(s) was/were simulated in SIMMAP v1.0 or written to file by `link{make.simmap}` then `version=1.0`; if the tree(s) was/were simulated using SIMMAP v1.5 then `version=1.5`.

Details

This function now accepts trees in both SIMMAP v1.0 and SIMMAP v1.5 format. In addition, it can read a more flexible format than is produced by SIMMAP (for instance, multi-character mapped states and more than 7 mapped states). Uses some modified code from read.nexus from the "ape" package to read the NEXUS block created by SIMMAP. Also creates the attribute "map.order" which indicates whether the stochastic map was read in from left to right or right to left. This attribute is used by default by write.simmap to write the tree in the same order.

Value

A modified object of class "phylo" (or list of class "multiPhylo") with the following additional elements:

`maps`	a list of named vectors containing the times spent in each state on each branch, in the order in which they occur.
`mapped.edge`	a matrix containing the total time spent in each state along each edge of the tree.

Author(s)

Liam Revell liam.revell@umb.edu

References

Bollback, J. P. (2006) Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics, 7, 88.

Paradis, E., J. Claude, and K. Strimmer (2004) APE: Analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-290.

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.