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.
An object of class
The expected number of rate shifts under the prior.
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
An object of class
bammshifts. This is a list with the
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
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 gives the most common shift configuration sampled.
$shifts[] gives the corresponding node indices for that configuration.
$samplesets[] gives the indices of samples with this configuration.
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