dropTipPartial {motmot}

Drop tips from a phylogenetic tree while preserving deleted nodes

Description

Wrapper for the ape function drop.tip that preserves the number of nodes affecting each branch. For use with the psi and multipsi models.

Usage

dropTipPartial(phy, tip)

Arguments

phy

Phylogenetic tree in phylo format

tip

A vector of mode numeric or character specifying the tips to delete, to be passed to drop.tip

Value

Phylogenetic tree in phylo format, with an added element Shid, a vector of numbers of observed but "missing" speciation events per branch, in the same order as the branches in the phylo object

Author(s)

Travis Ingram

References

Ingram, T. 2011. Speciation along a depth gradient in a marine adaptive radiation. Proc. R. Soc. B 278: 613-618.

See Also

transformPhylo.ML

Examples

## Read in phylogeny and data from Thomas et al. (2009)
data(anolis.tree)
data(anolis.data)
## identify tips to drop
tips.to.go <- anolis.tree$tip.label[1:30]
dropTipPartial(phy=anolis.tree, tip=tips.to.go)