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Last data update: 2014.03.03

R: Summary of rate shift results from 'BAMM' analysis

summary.bammdata

R Documentation

Summary of rate shift results from `BAMM` analysis

Description

Summarizes the posterior distribution on the number of shifts.

Usage

## S3 method for class 'bammdata'
summary(object, display = 10, print = T, ...)

Arguments

`object`	An object of class `bammdata`.
`display`	An integer for the number of rows of the posterior to display.
`print`	Print summary of shift distribution in console window?
`...`	Additional arguments (currently unused).

Details

Prints to console the number of posterior samples and the posterior distribution on the number of shifts, which is just the fraction of samples in the posterior having 0, 1, 2,...n shifts.

Value

Returns (invisibly) a dataframe with 2 components:

`shifts`	The number of shifts.
`prob`	The corresponding posterior probability of a model with a given number of rate shifts.

Author(s)

Mike Grundler, Dan Rabosky

References

http://bamm-project.org

Examples

data(whales, events.whales)
ephy <- getEventData(whales, events.whales, nsamples=100)
summary(ephy)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(BAMMtools)
Loading required package: ape
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/BAMMtools/summary.bammdata.Rd_%03d_medium.png", width=480, height=480)
> ### Name: summary.bammdata
> ### Title: Summary of rate shift results from 'BAMM' analysis
> ### Aliases: summary.bammdata
> ### Keywords: models
> 
> ### ** Examples
> 
> data(whales, events.whales)
> ephy <- getEventData(whales, events.whales, nsamples=100)
Processing event data from data.frame

Discarded as burnin: GENERATIONS <  0
Analyzing  100  samples from posterior

Setting recursive sequence on tree...

Done with recursive sequence

> summary(ephy)

Analyzed 100 posterior samples
Shift posterior distribution:

         0       0.07
         1       0.69
         2       0.19
         3       0.04
         4       0.01

Compute credible set of shift configurations for more information:
	See ?credibleShiftSet and ?getBestShiftConfiguration
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>

Summary of rate shift results from BAMM analysis