R: get.subs method

get.subs {treeio}

R Documentation

get.subs method

Description

get substitution information

Usage

get.subs(object, type, ...)

## S4 method for signature 'codeml'
get.subs(object, type, ...)

## S4 method for signature 'hyphy'
get.subs(object, type, ...)

## S4 method for signature 'paml_rst'
get.subs(object, type, ...)

## S4 method for signature 'phangorn'
get.subs(object, type, ...)

Arguments

`object`	paml_rst object
`type`	one of 'marginal_subs', 'marginal_AA_subs', 'joint_subs' or 'joint_AA_subs'.
`...`	additional parameter

Value

data.frame

Examples

nwk <- system.file("extdata/HYPHY", "labelledtree.tree", package="treeio")
ancseq <- system.file("extdata/HYPHY", "ancseq.nex", package="treeio")
tipfas <- system.file("extdata", "pa.fas", package="treeio")
hy <- read.hyphy(nwk, ancseq, tipfas)
get.subs(hy, type="AA_subs")

[Package treeio version 1.2.2 Index]