Pulls out a subtree from bammdata object

Description

Given a set of tips or a node, this function extracts the corresponding subtree from the bammdata object. User should specify either a set of tips or a node, and the node will overwrite the tips if both are given.

Usage

subtreeBAMM(ephy, tips = NULL, node = NULL)

Arguments

Details

This function allows users to extract a subtree from a big bammdata object, and examine the subset using plot.bammdata

Value

An object of class bammdata.

Author(s)

Huateng Huang

See Also

getmrca, plot.bammdata

Examples

data(whales, events.whales)
ephy <- getEventData(whales, events.whales, burnin=0.25, nsamples=500)

# specify a set of tips for the subtree
tips <- sample(ephy$tip.label,size=20,replace=FALSE)
subphy <- subtreeBAMM(ephy,tips=tips)

# specify a innernode for subsetting
subphy <- subtreeBAMM(ephy,node=103)

# plot the subtree
plot(subphy)

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/subtreeBAMM.Rd_%03d_medium.png", width=480, height=480)
> ### Name: subtreeBAMM
> ### Title: Pulls out a subtree from 'bammdata' object
> ### Aliases: subtreeBAMM
> ### Keywords: graphics
> 
> ### ** Examples
> 
> data(whales, events.whales)
> ephy <- getEventData(whales, events.whales, burnin=0.25, nsamples=500)
Processing event data from data.frame

Discarded as burnin: GENERATIONS <  2495000
Analyzing  500  samples from posterior

Setting recursive sequence on tree...

Done with recursive sequence

> 
> # specify a set of tips for the subtree
> tips <- sample(ephy$tip.label,size=20,replace=FALSE)
> subphy <- subtreeBAMM(ephy,tips=tips)
> 
> # specify a innernode for subsetting
> subphy <- subtreeBAMM(ephy,node=103)
> 
> # plot the subtree
> plot(subphy)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>