contMap: Map continuous trait evolution on the tree

Description

Function plots a tree with a mapped continuous character. The mapping is accomplished by estimating states at internal nodes using ML with fastAnc, and the interpolating the states along each edge using equation [2] of Felsenstein (1985).

Usage

contMap(tree, x, res=100, fsize=NULL, ftype=NULL, lwd=4, legend=NULL,
     lims=NULL, outline=TRUE, sig=3)

Arguments

tree

object of class "phylo".

vector of phenotypic trait values for species. names(x) should contain the species names and match tree$tip.label.

res

resolution for gradient plotting. Larger numbers indicate a finer (smoother) gradient.

fsize

relative font size - can be a vector with the second element giving the font size for the legend.

ftype

font type - see options in plotSimmap. As with fsize, can be a vector with the second element giving font type for the legend.

lwd

line width for branches.

legend

if FALSE no legend is plotted; if a numeric value, it gives the length of the legend in units of branch length. Default is 0.5 times the total tree length.

lims

range for the color map. By default, this will be c(min(x),max(x)), and should always include this range.

outline

logical value indicating whether or not to outline the branches of the tree in black.

sig

the number of decimal places to show on the legend limits.

Value

plots a tree.

References

Revell, L. J. Submitted. Two new graphical methods for mapping trait evolution on phylogenies. Felsenstein, J. 1985. Phylogenies and the comparative method. American Naturalist, 125, 1-15.

Description

Usage

Arguments

Value

References

See Also