A test of regime identifiability

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

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.

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.

Author

Jeremy M. Beaulieu and Brian C. O'Meara