| 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('ML','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. 'ML' = maximum likelihood method; 'pic' = independent contrasts method. pic option can be used when ML 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>
References
Ackerly, D. D. 2009. Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal. Proceedings of the National Academy of Sciences USA 106:19699-19706. doi: 10.1073/pnas.0901635106.
Evans, M. E. K., S. A. Smith, R. S. Flynn, and M. J. Donoghue. 2009. Climate, Niche Evolution, and Diversification of the "bird-cage" Evening Primroses (Oenothera, Sections Anogra and Kleinia). American Naturalist 173:225-240.
Examples
randtree <- rcoal(20)
randtraits <- rTraitCont(randtree)
traitgram(randtraits,randtree)
traitgram(randtraits,randtree,method='pic')