[Phylobase-commits] r588 - pkg/man

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

Author: pdc
Date: 2009-08-25 05:20:50 +0200 (Tue, 25 Aug 2009)
New Revision: 588

Modified:
   pkg/man/as-methods.Rd
Log:
What is really wanted here are \describe sections 
\itemize should only contain \item{bullet points with text}
\describe takes another term \item{phrase}{definition of said phrase}

Modified: pkg/man/as-methods.Rd
===================================================================
--- pkg/man/as-methods.Rd	2009-08-25 02:25:56 UTC (rev 587)
+++ pkg/man/as-methods.Rd	2009-08-25 03:20:50 UTC (rev 588)
@@ -58,62 +58,47 @@
   additional information from the user. Conversions exist for
   combinations:
 
-  \itemize{
-  
-    \item{}{\code{phylobase} to \code{phylobase} formats:}
-    \itemize{   
-      \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}. If data are dropped during the conversion, a
-	warning message is produced. A similar conversion can be done by
-	using the function \code{extractTree}, but in this case, no error
-	message is produced.}
-    }
+  \describe{
+    \item{\code{phylobase} to \code{phylobase} formats:}{
+    \describe{
     
-    \item{}{\code{phylobase} to \code{ape} formats:}
-    \itemize{
-      \item{}{\code{as(object, "phylo")}}{where object is of class
-	\linkS4class{phylo4} or \linkS4class{phylo4d} and returns an
-	object of class \code{phylo}. If data are dropped during the
-	conversion from a \code{phylo4d} object, a warning message is
-	produced.}
-      \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, "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}. If data are dropped during the conversion, a warning message is produced. A similar conversion can be done by using the function \code{extractTree}, but in this case, no error message is produced.}
+    }} %end phylobase to phylobase
     
-    \item{}{\code{ape} to \code{phylobase} formats:}
-    \itemize{
-      \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{ape} formats:}{
+    \describe{
     
-    \item{}{\code{phylobase} to \code{ade4} formats:}
-    \itemize{
-      \item{}{\code{as(object, "phylog")}}{where object is of class
-	\code{phylo4} and returns an object of class \linkS4class{phylog}.} 
-    }
+      \item{\code{as(object, "phylo")}}{where object is of class \linkS4class{phylo4} or \linkS4class{phylo4d} and returns an object of class \code{phylo}. If data are dropped during the conversion from a \code{phylo4d} object, a warning message is produced.}
+      
+      \item{\code{as(object, "multiPhylo")}}{~~Not implemented yet. where object is of class \linkS4class{multiPhylo4} and returns an object of class \code{multiPhylo}.}
+    }} % end phylobase to ape
     
-    \item{}{\code{phylobase} format to \code{data.frame}:}
-    \itemize{
-      \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{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}. }
+    }} % end ape to phylobase
+    
+    \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}.}
+    }} % end phylobase to ade4
+    
+    \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}.}
+    }} % end phylobase to dataframe
+  } % end main description
+} % end methods
 
-
 \author{Ben Bolker, Thibaut Jombart, Marguerite Butler, Steve Kembel}
 \seealso{ generic \code{\link[methods]{as}}, \code{\link{phylo4}},
   \code{\link{phylo4d}}, \code{\link{extractTree}}, the original