paleotree (version 1.0)

plotTraitgram: Plot a Traitgram for Continuous Traits

Description

This function uses maximum-likelihood ancestral trait estimation to plot a 'traitgram' (Ackerly, 2009) given a tree and a set of continuous trait values.

Usage

plotTraitgram(trait, tree, trait.name = "'trait'", conf.int = T, lwd = 1.5)

Arguments

trait

a vector of continuous trait values

tree

a phylo object

trait.name

The name of the trait plotted, used for the figure's main title

conf.int

if true, confidence intervals are plotted

lwd

The line width used for the figure

Value

• Returns no value, just plots the traitgram.

Details

By default, this function uses ace from the library ape to reconstruct ancestral traits and confidence intervals with maximum likelihood. If confidence intervals are turned off, a somewhat faster function getAncStates from geiger is used. As with many functions in the paleotree library, absolute time is always decreasing, i.e. the present day is zero.

References

Ackerly, D. 2009. Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal. Proceedings of the National Academy of Sciences 106(Supplement 2):19699-19706.

See Also

ace,getAncStates, Also see the function traitgram in the library picante.

Examples

require(geiger)
set.seed(444)
tree<-rtree(10)
trait<-rTraitCont(tree)
plotTraitgram(trait,tree)