[Phylobase-commits] r323 - pkg/man

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

Author: bcomeara
Date: 2008-12-19 08:08:42 +0100 (Fri, 19 Dec 2008)
New Revision: 323

Removed:
   pkg/man/NexusToDataFrame.Rd
   pkg/man/NexusToPhylo4.Rd
   pkg/man/NexusToPhylo4D.Rd
Log:
removd help for old ioNCL methods, added help for new method

Deleted: pkg/man/NexusToDataFrame.Rd
===================================================================
--- pkg/man/NexusToDataFrame.Rd	2008-12-19 07:07:28 UTC (rev 322)
+++ pkg/man/NexusToDataFrame.Rd	2008-12-19 07:08:42 UTC (rev 323)
@@ -1,34 +0,0 @@
-\name{NexusToDataFrame}
-\docType{methods}
-\alias{NexusToDataFrame}
-\title{Load data from a Nexus file}
-\description{
-  \code{NexusToDataFrame} reads a Nexus file and outputs a data.frame with data.
-}
-\section{Methods}{
-  \describe{
-\item{x = "NexusToDataFrame"}{creates a data.frame from a Nexus file}
-
-   }
- }
- \usage{
-NexusToDataFrame(fileToRead, allchar = FALSE, polymorphictomissing = TRUE, levelsall = TRUE)
-}
-\arguments{
-  \item{fileToRead}{a Nexus file}
-\item{allchar}{if TRUE, load all characters, even excluded ones}
-\item{polymorphictomissing}{if TRUE, convert polymorphic data to missing data}
-\item{levelsall}{categorical data are loaded with the same levels, even
-  if one character is missing a state}
-}
-\value{
-  A dataframe suitable to use with \linkS4class{phylo4d}.
-}
-\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.
-  If using Nexus files from Mesquite with continuous data, there must not be an 
-  (\dQuote{Items = ()}) command in the file; delete it if present.
-}
-\keyword{misc}

Deleted: pkg/man/NexusToPhylo4.Rd
===================================================================
--- pkg/man/NexusToPhylo4.Rd	2008-12-19 07:07:28 UTC (rev 322)
+++ pkg/man/NexusToPhylo4.Rd	2008-12-19 07:08:42 UTC (rev 323)
@@ -1,33 +0,0 @@
-\name{NexusToPhylo4}
-\docType{methods}
-\alias{NexusToPhylo4}
-\title{Load a tree from a Nexus file}
-\description{
-  \code{NexusToPhylo4} reads a Nexus file and outputs a \code{phylo4} tree.
-}
-\section{Methods}{
-  \describe{
-\item{x = "NexusToPhylo4"}{creates a \code{phylo4} tree from a Nexus file}
-
-   }
- }
- \usage{
-NexusToPhylo4(fileToRead, multi = FALSE)
-}
-\arguments{
-  \item{fileToRead}{a Nexus file}
-\item{multi}{if TRUE, return a list of \code{phylo4} trees}
-}
-\value{
-  A \linkS4class{phylo4} tree, or a list of trees if multi=TRUE.
-}
-\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}

Deleted: pkg/man/NexusToPhylo4D.Rd
===================================================================
--- pkg/man/NexusToPhylo4D.Rd	2008-12-19 07:07:28 UTC (rev 322)
+++ pkg/man/NexusToPhylo4D.Rd	2008-12-19 07:08:42 UTC (rev 323)
@@ -1,39 +0,0 @@
-\name{NexusToPhylo4D}
-\docType{methods}
-\alias{NexusToPhylo4D}
-\title{Load data and a tree from a Nexus file}
-\description{
-  \code{NexusToPhylo4D} reads a Nexus file and outputs a \code{phylo4d} object.
-}
-\section{Methods}{
-  \describe{
-\item{x = "NexusToPhylo4D"}{creates a \code{phylo4d} object from a Nexus file}
-
-   }
- }
- \usage{
-NexusToPhylo4D(fileToRead, multi=FALSE, allchar=FALSE, polymorphictomissing=TRUE, levelsall=TRUE)
-}
-\arguments{
-  \item{fileToRead}{a Nexus file}
-\item{multi}{if TRUE, return a list of \code{phylo4} trees}
-\item{allchar}{if TRUE, load all characters, even excluded ones}
-\item{polymorphictomissing}{if TRUE, convert polymorphic data to missing data}
-\item{levelsall}{categorical data are loaded with the same levels, even
-  if one character is missing a state}
-}
-\value{
-  A \linkS4class{phylo4d} object.
-}
-\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.
-  If using Nexus files from Mesquite with continuous data, there must not be an 
-  (\dQuote{Items = ()}) command in the file; delete it if present.
-  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{phylo4d}
-  object.
-}
-\keyword{misc}