check.identify {OUwie}

A test of regime identifiability

Description

Ho and Ane test for determining whether all regimes form connected subtrees, making both the ancestral state and the regime optima unidentifiable.

Usage

check.identify(phy, data, simmap.tree=FALSE, quiet=FALSE)

Arguments

phy

a phylogenetic tree, in ape “phylo” format and with internal nodes labeled denoting the ancestral selective regimes.

data

a data.frame containing species information (see Details).

simmap.tree

a logical indicating whether the input tree is in SIMMAP format. The default is FALSE.

quiet

a logical indicating whether messages should be written to the screen. The default is FALSE.

Value

This returns a vector with two elements, with the first being an indicator of identifiability (0=unidentifiable, 1=identifiable, and if get.penalty=TRUE, the second is the penalty used for the modified BIC.

Author(s)

Jeremy M. Beaulieu and Brian C. O'Meara

References

Ho, L.S.T., and C. Ane. 2014. Intrinsic inference difficulties for trait evolution with Ornstein-Uhlenbeck models. Methods in Ecology and Evolution, 5: 1133-1146.