[Phylobase-commits] r298 - pkg/man

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

Author: bbolker
Date: 2008-11-23 19:12:15 +0100 (Sun, 23 Nov 2008)
New Revision: 298

Modified:
   pkg/man/as-methods.Rd
   pkg/man/multiPhylo-class.Rd
   pkg/man/pdata-class.Rd
   pkg/man/phylo4d-class.Rd
   pkg/man/phylog.Rd
   pkg/man/plot.Rd
Log:
  Various tiny Rd tweaks to eliminate messages & warnings



Modified: pkg/man/as-methods.Rd
===================================================================
--- pkg/man/as-methods.Rd	2008-11-23 18:10:20 UTC (rev 297)
+++ pkg/man/as-methods.Rd	2008-11-23 18:12:15 UTC (rev 298)
@@ -82,8 +82,8 @@
 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_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
 

Modified: pkg/man/multiPhylo-class.Rd
===================================================================
--- pkg/man/multiPhylo-class.Rd	2008-11-23 18:10:20 UTC (rev 297)
+++ pkg/man/multiPhylo-class.Rd	2008-11-23 18:12:15 UTC (rev 298)
@@ -31,8 +31,9 @@
     \item{names}{\code{signature(x = "phylo4")}: gives the slots names}
 }
 }
-\usage{
-  }
+% commented to eliminate Note: on build
+%\usage{
+%  }
   \arguments{
     \item{x}{a phylo4 object}
     \item{printlen}{Maximum number of tip labels to print}

Modified: pkg/man/pdata-class.Rd
===================================================================
--- pkg/man/pdata-class.Rd	2008-11-23 18:10:20 UTC (rev 297)
+++ pkg/man/pdata-class.Rd	2008-11-23 18:12:15 UTC (rev 298)
@@ -36,8 +36,8 @@
     \item{\[\[<-}{\code{signature(x = "pdata")}: set data columns or elements}
     \item{\[\[}{\code{signature(x = "pdata", i = "ANY", j = "ANY")}: access data columns or elements }
     \item{\[\[}{\code{signature(x = "pdata", i = "ANY", j = "missing")}: set data columns or elements }}
-\author{Ben Bolker}
-\examples{
-
-}
+  \author{Ben Bolker}
+  % commented to eliminate Note: on build
+  %\examples{
+%}
 \keyword{classes}

Modified: pkg/man/phylo4d-class.Rd
===================================================================
--- pkg/man/phylo4d-class.Rd	2008-11-23 18:10:20 UTC (rev 297)
+++ pkg/man/phylo4d-class.Rd	2008-11-23 18:12:15 UTC (rev 298)
@@ -4,6 +4,7 @@
 \alias{show,phylo4d-method}
 \alias{print,phylo4d-method}
 \alias{summary,phylo4d-method}
+\alias{phylo4d,phylo4d-method}
 \alias{names,phylo4d-method}
 \alias{[,phylo4d,ANY,ANY,ANY-method}
 \title{phylo4d class}

Modified: pkg/man/phylog.Rd
===================================================================
--- pkg/man/phylog.Rd	2008-11-23 18:10:20 UTC (rev 297)
+++ pkg/man/phylog.Rd	2008-11-23 18:12:15 UTC (rev 298)
@@ -18,6 +18,7 @@
 \seealso{The original \code{\link[pkg:ade4]{phylog}} from the
   \code{ade4} package. 
 }
-\examples{
-}
+% commented to eliminate Note: on build
+%\examples{
+%}
 \keyword{classes}

Modified: pkg/man/plot.Rd
===================================================================
--- pkg/man/plot.Rd	2008-11-23 18:10:20 UTC (rev 297)
+++ pkg/man/plot.Rd	2008-11-23 18:12:15 UTC (rev 298)
@@ -2,6 +2,7 @@
 \docType{methods}
 \alias{plot,phylo4,missing-method}
 \alias{plot,phylo4d,missing-method}
+\alias{plot,pdata,missing-method}
 \title{Plot a phylogenetic tree alone or with data}
 \description{
   These methods display graphics for objects of class \code{phylo4} and