[Phylobase-commits] r545 - in pkg: . R man

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

Author: pdc
Date: 2009-08-21 02:02:14 +0200 (Fri, 21 Aug 2009)
New Revision: 545

Removed:
   pkg/R/printphylo-deprecated.R
   pkg/man/deprecated.Rd
Modified:
   pkg/DESCRIPTION
   pkg/NAMESPACE
Log:
printphylo has been deprecated for a while, removing in anticipation of CRAN release

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2009-08-20 21:45:23 UTC (rev 544)
+++ pkg/DESCRIPTION	2009-08-21 00:02:14 UTC (rev 545)
@@ -9,5 +9,5 @@
 Maintainer:  Ben Bolker <bolker at ufl.edu>
 Description: Provides a base S4 class for comparative methods, incorporating one or more trees and trait data
 License: GPL
-Collate: phylo4.R checkdata.R class-multiphylo4.R class-oldclasses.R class-phylo4.R class-phylo4d.R  class-phylomats.R methods-multiphylo4.R methods-oldclasses.R methods-phylo4.R methods-phylo4d.R setAs-Methods.R pdata.R subset.R prune.R treePlot.R identify.R treestruc.R treewalk.R readNexus.R tbind.R zzz.R printphylo-deprecated.R 
+Collate: phylo4.R checkdata.R class-multiphylo4.R class-oldclasses.R class-phylo4.R class-phylo4d.R  class-phylomats.R methods-multiphylo4.R methods-oldclasses.R methods-phylo4.R methods-phylo4d.R setAs-Methods.R pdata.R subset.R prune.R treePlot.R identify.R treestruc.R treewalk.R readNexus.R tbind.R zzz.R
 URL: http://phylobase.R-forge.R-project.org

Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE	2009-08-20 21:45:23 UTC (rev 544)
+++ pkg/NAMESPACE	2009-08-21 00:02:14 UTC (rev 545)
@@ -75,9 +75,6 @@
 export(as_phylo4vcov)
 export(printphylo4)
 
-## deprecated?
-export(printphylo)
-
 ## commented out in source code, probably should be omitted here
 #export(phyloStripchart)
 #export(internEdges, terminEdges, isPoly)

Deleted: pkg/R/printphylo-deprecated.R
===================================================================
--- pkg/R/printphylo-deprecated.R	2009-08-20 21:45:23 UTC (rev 544)
+++ pkg/R/printphylo-deprecated.R	2009-08-21 00:02:14 UTC (rev 545)
@@ -1,46 +0,0 @@
-## Alternative print method for phylo4, showing the contents of the tree data.
-##  Not sure if it works for unrooted trees
-printphylo <- function (x,printlen=6,...) {
-    .Deprecated("print", package="phylobase")
-    printlen <- max(1,printlen)
-    nb.tip <- length(x at tip.label)
-    nb.node <- x at Nnode
-    nb.edge <- length(x at edge.label)
-    cat(paste("\nPhylogenetic tree with", nb.tip, "tips and",
-              nb.node, "internal nodes\n"))
-
-    ## print tip labels
-    cat("\nTips labels:\n")
-    if (nb.tip > printlen) {
-        cat(paste("\t", paste(x at tip.label[1:printlen], collapse = ", "),
-                  ", ...\n", sep = ""))
-    } else print(x at tip.label)
-
-    ## print node labels
-    cat("\nNodes labels:\n")
-    if (nb.node > printlen) {
-        cat(paste("\t", paste(x at node.label[1:printlen], collapse = ", "),
-                  ", ...\n", sep = ""))
-    } else print(x at node.label)
-
-    ## print edge labels
-    cat("\nEdges labels:\n")
-    if (nb.edge > printlen) {
-        cat(paste("\t", paste(x at edge.label[1:printlen], collapse = ", "),
-                  ", ...\n", sep = ""))
-    } else print(x at edge.label)
-
-    ## slots
-    ##     cat("\nSlots:\n")
-    ##     cat(paste("@", names(x)[1:4], sep=""),sep="\t")
-    ##     cat("\n")
-    ##     cat(paste("@", names(x)[5:7], sep=""),sep="\t")
-    ##     cat("\n")
-
-    rlab <- if (isRooted(x)) "Rooted"  else "Unrooted"
-    cat("\n", rlab, "; ", sep = "")
-    blen <- if (hasEdgeLength(x))
-      "includes branch lengths"
-    else       "no branch lengths"
-    cat(blen, "\n\n", sep = "")
-}

Deleted: pkg/man/deprecated.Rd
===================================================================
--- pkg/man/deprecated.Rd	2009-08-20 21:45:23 UTC (rev 544)
+++ pkg/man/deprecated.Rd	2009-08-21 00:02:14 UTC (rev 545)
@@ -1,19 +0,0 @@
-\name{printphylo}
-\alias{printphylo}
-\title{Deprecated functions}
-\description{
-  Functions which are no longer used (or suggested)
-}
-\usage{
-printphylo(x, printlen = 6, ...)
-}
-\arguments{
-  \item{x}{A phylo4 object}
-  \item{printlen}{Maximum number of tip labels to print}
-  \item{\dots}{Included for consistency}
-}
-\value{
-  \code{printphylo} prints a short description of the object
-}
-\author{Ben Bolker (copied from print.phylo in ape package)}
-\keyword{misc}