repaint: Paint the Branches of a Tree

In surface: Fitting Hansen Models to Investigate Convergent Evolution

Description

A wrapper to the paint function in ouch to ensure that regime paintings are automatically formatted for SURFACE analysis (painting the stem branch of a clade and ensuring that the root is assigned a regime)

Usage

repaint(otree, regshifts, stem = TRUE)

Arguments

otree	Phylogenetic tree in ouchtree format
regshifts	Named character vector of regime shifts
stem	A logical indicating whether the painting of a clade should include the stem branch; defaults to TRUE, and is set to TRUE during all calls within the surface functions

Value

A named character vector of regime assignments for each branch, as returned by paint

Author(s)

Travis Ingram

References

Butler, M.A. & King, A.A. (2004) Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist 164: 683-695.

Ingram, T. & Mahler, D.L. (2013) SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise AIC. Methods in Ecology and Evolution 4: 416-425.

Examples

data(surfaceDemo)
tree<-surfaceDemo$tree
dat<-surfaceDemo$sim$dat
olist<-convertTreeData(tree,dat)
otree<-olist[[1]]
repaint(otree, regshifts = c(c("1"="a","6"="b","17"="c")))

surface documentation built on Dec. 18, 2020, 5:08 p.m.