[Phylobase-commits] r161 - pkg/man

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

Author: pdc
Date: 2008-03-08 08:30:46 +0100 (Sat, 08 Mar 2008)
New Revision: 161

Modified:
   pkg/man/as-methods.Rd
Log:
tidy help file

Modified: pkg/man/as-methods.Rd
===================================================================
--- pkg/man/as-methods.Rd	2008-03-08 07:22:02 UTC (rev 160)
+++ pkg/man/as-methods.Rd	2008-03-08 07:30:46 UTC (rev 161)
@@ -34,53 +34,53 @@
 
     \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{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{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{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{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}.}
+        \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. 
+\seealso{ generic \code{\link[methods]{as}}, \code{\link{phylo4}}, \code{\link{phylo4d}}, \code{\link{extract.tree}}, the original \code{\link[ade4]{phylog}} from the
+  \code{ade4} package and \code{\link[ape]{as.phylo}} from the \code{ape} package. 
 }
 \examples{
-    library(ape)
-  example(read.tree)
+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
+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.
+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}