marginalOddsRatioBranches {BAMMtools} | R Documentation |
Compute marginal posterior-to-prior odds ratio associated with observing one or more rate shift on a given branch.
marginalOddsRatioBranches(ephy, expectedNumberOfShifts)
ephy |
An object of class |
expectedNumberOfShifts |
Expected number of shifts under the prior alone. |
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.
A object of class phylo
but where each branch length is
equal to the marginal shift odds on each branch.
Dan Rabosky
getBranchShiftPriors
,
distinctShiftConfigurations
,
credibleShiftSet
#Produce a blank template control file generateControlFile(file = 'traitcontrol.txt', type='trait') #Produce a customized control file data(whales) #get bamm priors to supply to control file priors <- setBAMMpriors(whales, outfile = NULL) generateControlFile(file = 'divcontrol.txt', params = list( treefile = 'whales.tre', globalSamplingFraction = '1', numberOfGenerations = '100000', overwrite = '1', lambdaInitPrior = as.numeric(priors['lambdaInitPrior']), lambdaShiftPrior = as.numeric(priors['lambdaShiftPrior']), muInitPrior = as.numeric(priors['muInitPrior']), expectedNumberOfShifts = '1'))