traitgram function

Draw phylogeny with nodes at trait positions

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('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

Returns

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')