View source: R/distinctShiftConfigurations.R
distinctShiftConfigurations | R Documentation |
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.
distinctShiftConfigurations(ephy, expectedNumberOfShifts, threshold, ...)
ephy |
An object of class |
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). |
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.
An object of class bammshifts
. This is a list with the
following components:
marg.probs: A list of the marginal probability of a shift occurring at each node of the phylogeny for each distinct rate shift configuration.
marginal_odd_ratio: Marginal posterior-to-prior odds ratios for one or more rate shifts an a given branch.
shifts: A list of the set of shift nodes for each distinct rate configuration.
samplesets: A list of sample indices that reduce to each of the unique shift sets.
frequency: A vector of frequencies of each distinct shift configuration.
coreshifts: A vector of node numbers corresponding to the
core shifts. All of these nodes have a marginal odds ratio of
at least threshold
supporting a rate shift.
threshold: A single numeric value giving the marginal posterior:prior odds ratio threshold used during enumeration of distinct shift configurations.
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.
Dan Rabosky
plot.bammshifts
, credibleShiftSet
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)
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