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]