Paint the Branches of a Tree

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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

1
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.