distinctShiftConfigurations: Identify distinct rate shift configurations

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/distinctShiftConfigurations.R

Description

Identify topologically distinct rate shift configurations that were sampled with BAMM, and assign each sample in the posterior to one of the distinct shift configurations.

Usage

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distinctShiftConfigurations(ephy, expectedNumberOfShifts, threshold, ...)

Arguments

ephy

An object of class bammdata.

expectedNumberOfShifts

The expected number of rate shifts under the prior.

threshold

Threshold value for marginal posterior-to-prior odds ratios, used to identify branches with elevated shift probabilities relative to prior (core vs non-core shifts).

...

Other arguments to distinctShiftConfigurations (possibly deprecated args).

Details

See Rabosky et al (2014) and the BAMM project website for details on the nature of distinct shift configurations and especially the distinction between "core" and "non-core" rate shifts. Note that branches with elevated marginal posterior probabilities relative to the prior (marginal odds ratios) cannot be claimed to have "significant" evidence for a rate shift on the basis of this evidence alone.

Value

An object of class bammshifts. This is a list with the following components:

Results are sorted by frequency:

$frequency[1] gives the most common shift configuration sampled.

$shifts[[1]] gives the corresponding node indices for that configuration.

$samplesets[[1]] gives the indices of samples with this configuration.

Author(s)

Dan Rabosky

See Also

plot.bammshifts, credibleShiftSet

Examples

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data(whales, events.whales)
ed <- getEventData(whales, events.whales, burnin=0.25, nsamples=500)

sc <- distinctShiftConfigurations(ed, expectedNumberOfShifts = 1,
                                  threshold = 5)

plot(sc, ed, rank=1)

BAMMtools documentation built on May 29, 2017, 5:47 p.m.