traitgram {picante}R Documentation

Draw phylogeny with nodes at trait positions

Description

Draws a phylogeny where x position of nodes and tips corresponds to value of a continuous trait variable, and y position corresponds to node depth (i.e. age).

Usage

traitgram(x, phy, xaxt = 's', underscore = FALSE, show.names = TRUE,
            show.xaxis.values = TRUE, method = c('ace','pic'), ...)

Arguments

x Trait vector (same order as phy$tip.label, or with taxon names in names)
phy phylo object
xaxt x axis default type
underscore if FALSE remove underscore from taxonomic names
show.names if TRUE show taxon names across tips of phylogeny
show.xaxis.values if TRUE show values for trait on x=axis
method method for calculation of internal trait values. 'ace' = ace maximum likelihood method from ape; 'pic' = independent contrasts method. pic option can be used when ace fails to converge or otherwise seems to fail to correctly reconstruct ancestral values
... Additional arguments passed to plot

Value

Plots a traitgram, no values returned.

Author(s)

David Ackerly <dackerly@berkeley.edu>

See Also

pic3

Examples

randtree <- rcoal(20)
randtraits <- evolve.brownian(randtree)
traitgram(randtraits,randtree)
traitgram(randtraits,randtree,method='pic')

[Package picante version 0.7-0 Index]