traitgram: Draw phylogeny with nodes at trait positions

In picante: Integrating Phylogenies and Ecology

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 <[e-mail]>

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')

Example output

Loading required package: ape
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-3
Loading required package: nlme
Warning message:
In sqrt(diag(solve(h))) : NaNs produced

picante documentation built on July 1, 2020, 10:57 p.m.