BAMMtools (version 2.1.12)

marginalOddsRatioBranches: Ratio of (marginal) posterior-to-prior probabilities on individual branches

Description

Compute marginal posterior-to-prior odds ratio associated with observing one or more rate shift on a given branch.

Usage

marginalOddsRatioBranches(ephy, expectedNumberOfShifts)

Value

A object of class phylo but where each branch length is equal to the marginal shift odds on each branch.

Arguments

ephy

An object of class bammdata.

expectedNumberOfShifts

Expected number of shifts under the prior alone.

Author

Dan Rabosky

Details

This function returns a copy of a phylogenetic tree where each branch length is equal to the marginal odds ratio in favor of a rate shift on a particular branch. These cannot be interpreted as evidence for a rate shift in an absolute sense. As explained on the website, they are a marginal odds ratio. This function is provided primarily for the purpose of distinguishing core and non-core shifts.

See Also

getBranchShiftPriors, distinctShiftConfigurations, credibleShiftSet

Examples

data(whales, events.whales)
ed <- getEventData(whales, events.whales, burnin=0.1, nsamples=500)
marginalOddsRatioBranches(ed, expectedNumberOfShifts = 1)