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

In BAMMtools: Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees

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)

BAMMtools documentation built on Sept. 13, 2024, 1:10 a.m.