[Phylobase-commits] r385 - in pkg: R man

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

Author: bbolker
Date: 2008-12-21 18:00:33 +0100 (Sun, 21 Dec 2008)
New Revision: 385

Modified:
   pkg/R/methods-phylo4d.R
   pkg/man/reorder-methods.Rd
Log:
  consistency with new preorder/postorder naming



Modified: pkg/R/methods-phylo4d.R
===================================================================
--- pkg/R/methods-phylo4d.R	2008-12-21 06:16:58 UTC (rev 384)
+++ pkg/R/methods-phylo4d.R	2008-12-21 17:00:33 UTC (rev 385)
@@ -176,7 +176,8 @@
     return(rev(temp))
 })
 
-setMethod("reorder", signature(x = 'phylo4d'), function(x, order = 'cladewise') {
+setMethod("reorder", signature(x = 'phylo4d'),
+          function(x, order = c('preorder','postorder')) {
     ## call orderIndex and use that index to order edges, labels and lengths
     order       <- match.arg(order)
     index       <- orderIndex(x, order)

Modified: pkg/man/reorder-methods.Rd
===================================================================
--- pkg/man/reorder-methods.Rd	2008-12-21 06:16:58 UTC (rev 384)
+++ pkg/man/reorder-methods.Rd	2008-12-21 17:00:33 UTC (rev 385)
@@ -18,7 +18,7 @@
 }
 
 \usage{
-orderIndex(phy, order = 'cladewise')
+orderIndex(phy, order = c('preorder','postorder'))
 \S4method{reorder}{phylo}(x, ...)
 \S4method{reorder}{phylo4}(x, ...)
 \S4method{reorder}{phylo4d}(x, ...)
@@ -27,8 +27,8 @@
 %- maybe also 'usage' for other objects documented here.
 \arguments{
   \item{phy}{a \code{phylo4} or \code{phylo4d} object}
-  \item{order}{(character)}
-  \item{x}{ ~~Describe \code{x} here~~ }
+  \item{x}{a \code{phylo4} or \code{phylo4d} object}
+  \item{order}{'preorder' or 'postorder' for preferred order}
   \item{\dots}{ ~~Describe \code{\dots} here~~ }
 }
 \details{
@@ -42,10 +42,11 @@
   ...
 }
 \references{ ~put references to the literature/web site here ~ }
-\author{ ~~who you are~~ }
-\note{ ~~further notes~~ 
-
- ~Make other sections like Warning with \section{Warning }{....} ~
+\author{Peter Cowan}
+\note{
+  preorder corresponds to 'cladewise' in the ape package,
+  postorder corresponds (almost but close enough?) to 'pruningwise'
+  see ...
 }
 \seealso{ ~~objects to See Also as \code{\link{help}}, ~~~ }
 % Add one or more standard keywords, see file 'KEYWORDS' in the