traitgram {picante} | R Documentation |
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).
traitgram(x, phy, xaxt = 's', underscore = FALSE, show.names = TRUE, show.xaxis.values = TRUE, method = c('ace','pic'), ...)
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 |
Plots a traitgram, no values returned.
David Ackerly <dackerly@berkeley.edu>
randtree <- rcoal(20) randtraits <- evolve.brownian(randtree) traitgram(randtraits,randtree) traitgram(randtraits,randtree,method='pic')