repaint {surface} | R Documentation |
Paint the Branches of a Tree
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 |
regshifts |
Named character vector of regime shifts |
stem |
A logical indicating whether the painting of a clade should include the stem branch; defaults to |
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")))