getEventData Reads shift configuration data (the "event data" output) from a BAMM analysis and creates a bammdata object. The bammdata object is fundamental for extracting information about macroevolutionary rate variation through time and among lineages.
● Data Source:
CranContrib
● Keywords: models
● Alias: getEventData
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getCladeRates
(Package: BAMMtools) :
Compute clade-specific mean rates
Computes marginal clade-specific rates of speciation, extinction, or (if relevant) trait evolution from BAMM output.
● Data Source:
CranContrib
● Keywords: models
● Alias: getCladeRates
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summary.bammdata
(Package: BAMMtools) :
Summary of rate shift results from code{BAMM
Summarizes the posterior distribution on the number of shifts.
● Data Source:
CranContrib
● Keywords: models
● Alias: summary.bammdata
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Calculates the likelihood of a phylogeny exactly as is done by BAMM, given a set of events.
● Data Source:
CranContrib
● Keywords:
● Alias: BAMMlikelihood
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Subsets a bammdata object. Returns a bammdata object after extracting a specified set of samples from the posterior.
● Data Source:
CranContrib
● Keywords: manip
● Alias: subsetEventData
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getBestShiftConfiguration
(Package: BAMMtools) :
Get the best (sampled) rate shift configuration from a code{BAMM
Get the rate shift configuration with the maximum a posteriori probability, e.g., the shift configuration that was sampled most frequently with BAMM.
● Data Source:
CranContrib
● Keywords: models
● Alias: getBestShiftConfiguration
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2 images
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Deprecated function. Please use rich.colors instead.
● Data Source:
CranContrib
● Keywords:
● Alias: richColors
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Adds symbols to a plotted tree to mark the location(s) where there is a shift in the macroevolutionary dynamics of diversification or trait evolution.
● Data Source:
CranContrib
● Keywords: graphics
● Alias: addBAMMshifts
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2 images
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Computes pairwise Bayes factors for a set of macroevolutionary models sampled using BAMM, using MCMC simulation output.
● Data Source:
CranContrib
● Keywords: models
● Alias: computeBayesFactors
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getTipRates
(Package: BAMMtools) :
Compute tip-specific macroevolutionary rates from code{bammdata
Return speciation, extinction, net diversification, or Brownian motion trait rates for all species in the phylogeny from BAMM output.
● Data Source:
CranContrib
● Keywords: models
● Alias: getTipRates
●
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