summary.credibleshiftset {BAMMtools}

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).

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.

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).

Author(s)

Dan Rabosky

References

http://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)