[Phylobase-commits] r166 - pkg/man

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

Author: pdc
Date: 2008-03-16 01:18:02 +0100 (Sun, 16 Mar 2008)
New Revision: 166

Removed:
   pkg/man/coerce-methods.Rd
Modified:
   pkg/man/as-methods.Rd
Log:
combine .Rd files, these are redundant, 
hopefully aliasing allows us to delete one please let me know if any one has issues

Modified: pkg/man/as-methods.Rd
===================================================================
--- pkg/man/as-methods.Rd	2008-03-16 00:16:47 UTC (rev 165)
+++ pkg/man/as-methods.Rd	2008-03-16 00:18:02 UTC (rev 166)
@@ -11,6 +11,16 @@
 \alias{as,phylo4d,phylo-method}
 \alias{as,phylo4,data.frame-method}
 \alias{as,phylo4d,data.frame-method}
+\alias{coerce-methods}
+\alias{coerce,phylo,phylo4-method}
+\alias{coerce,phylo,phylo4d-method}
+\alias{coerce,multiPhylo4,multiPhylo-method}
+\alias{coerce,multiPhylo,multiPhylo4-method}
+\alias{coerce,multiPhylo4d,multiPhylo-method}
+\alias{coerce,phylo4,phylo-method}
+\alias{coerce,phylo4d,phylo-method}
+\alias{coerce,phylo4,data.frame-method}
+\alias{coerce,phylo4d,data.frame-method}
 
 \title{Converting between phylo4 and other phylogenetic trees}
 

Deleted: pkg/man/coerce-methods.Rd
===================================================================
--- pkg/man/coerce-methods.Rd	2008-03-16 00:16:47 UTC (rev 165)
+++ pkg/man/coerce-methods.Rd	2008-03-16 00:18:02 UTC (rev 166)
@@ -1,77 +0,0 @@
-\name{coerce-methods}
-\docType{methods}
-\alias{coerce-methods}
-
-\alias{coerce,phylo,phylo4-method}
-\alias{coerce,phylo,phylo4d-method}
-\alias{coerce,multiPhylo4,multiPhylo-method}
-\alias{coerce,multiPhylo,multiPhylo4-method}
-\alias{coerce,multiPhylo4d,multiPhylo-method}
-\alias{coerce,phylo4,phylo-method}
-\alias{coerce,phylo4d,phylo-method}
-\alias{coerce,phylo4,data.frame-method}
-\alias{coerce,phylo4d,data.frame-method}
-
-\title{Converting between phylo4 and other phylogenetic trees}
-\description{
-  Translation functions to convert between phylobase trees or trees+data objects (\code{phylo4}, \code{phylo4d}), and objects used by other comparative methods packages in R:  \code{ape} objects
-  (\code{phylo}, \code{multiPhylo}) \code{ade4} objects (\code{phylog}), and to \code{data.frame} respresentation. 
-}
-\section{Methods}{
-  \item{coerce}{from one object class to another using \code{as(object,"Class")}, where the \code{object} is of the old class and the returned object is of the new class \code{"Class"}. The \code{as} function examines the class of \code{object} and the new \code{"Class"} specified to choose the proper conversion without additional information from the user. Conversions exist for combinations:
-  \describe{
-
-    \item{\code{phylobase} to \code{phylobase} formats:}{
-      \describe{
-        \item{\code{as(object,"phylo4d")}}{where object is of class \linkS4class{phylo4} and returns an object of class \linkS4class{phylo4d}, with empty data.}
-        \item{\code{as(object,"phylo4")}}{where object is of class \linkS4class{phylo4d} and returns an object of class \linkS4class{phylo4}, dropping data with warning.}
-      }
-    }
-    \item{\code{phylobase} to \code{ape} formats:}{
-      \describe{
-        \item{\code{as(object,"phylo")}}{where object is of class \linkS4class{phylo4} or \linkS4class{phylo4d} and returns an object of class \code{phylo}, with data dropped in the case of \code{phylo4d} conversion (with warning).}
-        \item{\code{as(object,"multiPhylo")}}{ ~~Not implemented yet. where object is of class \linkS4class{multiPhylo4} and returns an object of class \code{multiPhylo}. }
-      }
-    }
-    \item{\code{ape} to \code{phylobase} formats:}{
-      \describe{
-        \item{\code{as(object,"phylo4")}}{where object is of class \code{phylo} and returns an object of class \code{phylo4}.}
-        \item{\code{as(object,"phylo4d")}}{where object is of class \code{phylo} and returns an object of class \code{phylo4d}, with empty data.}
-        \item{\code{as(object,"multiPhylo4")}}{ ~~Not implemented yet. where object is of class \code{multiPhylo} and returns an object of class \code{multiPhylo4}. }
-      }
-    }
-    \item{\code{phylobase} to \code{ade4} formats:}{
-      \describe{
-        \item{\code{as(object,"phylog")}}{where object is of class \code{phylo4} and returns an object of class \linkS4class{phylog}.}
-      }
-    }
-    \item{\code{phylobase} format to \code{data.frame}:}{
-      \describe{
-        \item{\code{as(object,"data.frame")}}{where object is of class \code{phylo4} or \code{phylo4d} and returns an object of class \code{data.frame}, with data included in the case of \code{phylo4d}.}
-      }
-    }
-  }}
-}
-
-\author{Ben Bolker, Thibaut Jombart \email{jombart at biomserv.univ-lyon1.fr}, Marguerite Butler}
-\seealso{ generic \code{\link[methods]{as}}, \code{\link{phylo4}}, \code{\link{phylo4d}}, \code{\link{extract.tree}}, the original \link[ade4]{phylog} from the
-  \code{ade4} package and \link[ape]{as.phylo} from the \code{ape} package. 
-}
-\examples{
-    library(ape)
-  example(read.tree)
-## round trip conversion 
-  tree_in_phylo = tree.owls               # tree is a phylo object 
-  tree_in_phylo4 = as(tree.owls,"phylo4")  # phylo converted to phylo4 
-  tree_in_phylo4
-  identical(tree_in_phylo,as(tree_in_phylo4,"phylo")) # test if phylo, and phlyo4 converted to phylo are identical
-
-  as(tree_in_phylo4, "phylog")     # conversion to phylog (ade4)
-  as(tree_in_phylo4, "data.frame")  # conversion to data.frame
-  as(tree_in_phylo4, "phylo")      # conversion to phylo (ape)
-  as(tree_in_phylo4, "phylo4d")    # conversion to phylo4d, but without data so data slots empty.
-}
-\keyword{methods}
-\concept{phylo4 tree formats}
-\concept{convert tree formats}
-\concept{conversion between tree formats}
\ No newline at end of file