BAMMtools (version 2.1.0)

summary.credibleshiftset: Summary of credible set of shift configurations from a BAMM analysis.

Description

Prints summary attributes of the BAMM credible set of shift configurations.

Usage

## S3 method for class 'credibleshiftset':
summary(object, ...)
## S3 method for class 'credibleshiftset':
print(x, ...)

Arguments

object,x

an object of class credibleshiftset.

...

additional arguments (unused).

Value

• summary.credibleshiftset returns (invisibly) a dataframe with a number of rows equal to the number of shift configurations in the credible set and four columns:
• rank
  The ranked index of each shift configuration (ranked by posterior probability)
• probability
  the posterior probability of each shift configuration
• cumulative
  the cumulative probability of each shift configuration
• N_shifts
  the number of rate shifts in each shift configuration (can be zero).

Details

Prints to console summary attributes of the XX% credible set of shift configurations sampled using BAMM. Attributes printed include: the number of distinct configurations in the XX% credible set and the posterior probability, cumulative probability, and number of rate shifts in the 9 most-probable shift configurations.

References

bamm-project.org

See Also

distinctShiftConfigurations, plot.bammshifts, credibleShiftSet

Examples

data(whales, events.whales)

ed <- getEventData(whales, events.whales, nsamples = 500)
cset <- credibleShiftSet(ed, expectedNumberOfShifts = 1, threshold = 5)
summary(cset)