get.subs {treeio} | R Documentation |
get substitution information
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, ...)
object |
paml_rst object |
type |
one of 'marginal_subs', 'marginal_AA_subs', 'joint_subs' or 'joint_AA_subs'. |
... |
additional parameter |
data.frame
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")