BAMMtools (version 2.1.0)

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)

Arguments

ephy

an object of class bammdata

expectedNumberOfShifts

Expected number of shifts under the prior alone

Value

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

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)
bftree <- marginalOddsRatioBranches(ed, expectedNumberOfShifts = 1)
margprobs <- marginalShiftProbsTree(ed)
plot.new()
par(mfcol = c(1,3))
# Original tree:
plot.phylo(whales, show.tip.label = FALSE)
mtext(side = 3, text = "original tree", cex = 1)

plot.phylo(margprobs, show.tip.label = FALSE)
mtext(side = 3, text = "Marginal probs", cex = 1)

plot.phylo(bftree, show.tip.label = FALSE)
mtext(side = 3, text = "Marginal odds ratio", cex = 1)