read.characters2: Read CHARACTERS2 block

In phyext: An extension of some of the classes in phylobase. Tree objects now support subnodes on branches

Description

This function reads raw text in from the nexus file finput. It then writes the TAXA and blockname blocks to a temporary nexus file using CHARACTERS instead of blockname. It then re-reads the temporary nexus file using readNexus(tmpfile,type="data").

Usage

read.characters2(finput, blockname = "characters2")

Arguments

finput
blockname

Details

This function was created mainly to handle reading CHARACTERS2 nexus blocks. These blocks are used by brownie along with CHARACTERS to separate discrete (factor) data from continuous (numeric) data. It is also used because SIMMAP-formatted (version < 1.5) nexus files tend to cause problems with the nexus class library (which phylobase uses)

Value

A data.frame containing the data from blockname.

Author(s)

J. Conrad Stack

See Also

readNexus

phyext documentation built on May 2, 2019, 5:19 p.m.