[Phylobase-commits] r352 - pkg/man

[noreply at r-forge.r-project.org]

Author: bcomeara
Date: 2008-12-20 00:17:25 +0100 (Sat, 20 Dec 2008)
New Revision: 352

Added:
   pkg/man/readNexus.Rd
Log:
Thought I added this documentation last night, but apparently not

Added: pkg/man/readNexus.Rd
===================================================================
--- pkg/man/readNexus.Rd	                        (rev 0)
+++ pkg/man/readNexus.Rd	2008-12-19 23:17:25 UTC (rev 352)
@@ -0,0 +1,37 @@
+\name{readNexus}
+\docType{methods}
+\alias{readNexus}
+\title{Parse a Nexus file for one or more tree(s) and/or tip data}
+\description{
+  \code{readNexus} reads a Nexus file and outputs a \code{data.frame}, \code{phylo4}, or \code{phylo4d} object.
+}
+\section{Methods}{
+  \describe{
+\item{x = "readNexus"}{creates a \code{data.frame}, \code{phylo4}, or \code{phylo4d} object from a Nexus file}
+
+   }
+ }
+ \usage{
+readNexus(file, simplify=TRUE, which=c("all","tree","data"), char.all=FALSE, polymorphic.convert=TRUE, levels.uniform=TRUE)
+}
+\arguments{
+  \item{file}{a Nexus file}
+  \item{simplify}{If FALSE, returns a list. If TRUE, returns a list if there are multiple trees, a single object otherwise}
+  \item{which}{Determines which objects to return, if present}
+  \item{char.all}{If TRUE, returns all characters, even those excluded in the NEXUS file}
+  \item{polymorphic.convert}{If TRUE, converts polymorphic DNA characters to missing data}
+  \item{levels.uniform}{If TRUE, uses the same levels for all characters}
+}
+\value{
+  A \linkS4class{phylo4} tree, \linkS4class{phylo4d} object, or a list of trees if simplify=FALSE or there is more than one tree, or a data.frame.
+}
+\seealso{the \linkS4class{phylo4d} class, the \linkS4class{phylo4} class}
+\author{Brian O'Meara, Derrick Zwickl}
+\note{
+  This relies on Version 2.0 of the Nexus Class Library by Paul Lewis and Mark Holder.
+  Tree reading is done initially using a function from APE; this function can be 
+  confused if the tree name has the word (\dQuote{tree}) in it. Also note that edge
+  and node labels (except for terminal nodes) are NOT yet loaded into the \code{phylo4}
+  object.
+}
+\keyword{misc}