[Phylobase-commits] r125 - in pkg: R man

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

Author: bbolker
Date: 2008-02-26 22:51:42 +0100 (Tue, 26 Feb 2008)
New Revision: 125

Modified:
   pkg/R/plot.R
   pkg/man/pdata-class.Rd
   pkg/man/phylo4-class.Rd
   pkg/man/phylo4d-class.Rd
Log:

  changed check_phylo4d (nonexistent) to check_phylo4 in plot.R
  adding aliases for missing methods (but no real docs!) for [



Modified: pkg/R/plot.R
===================================================================
--- pkg/R/plot.R	2008-02-26 16:58:18 UTC (rev 124)
+++ pkg/R/plot.R	2008-02-26 21:51:42 UTC (rev 125)
@@ -30,7 +30,7 @@
           function(x, treetype=c("phylogram","cladogram"), symbol=c("circles", "squares"), center=TRUE, scale=TRUE, legend=TRUE, grid=TRUE, box=TRUE, show.tip.label=TRUE, show.node.label=TRUE, show.var.label=TRUE, ratio.tree=1/3, font=3, tip.label=x at tip.label, var.label=colnames(x at tip.data), cex.symbol=1, cex.label=1, cex.legend=1, ...){
               
     #### preliminary stuff and checks
-    invisible(check_phylo4d(x))
+    invisible(check_phylo4(x))
     if(!require(ape)) stop("the ape package is required")
     ## if(ncol(tdata(x,which="tip")) == 0) stop("no data in this phylo4d object")
     

Modified: pkg/man/pdata-class.Rd
===================================================================
--- pkg/man/pdata-class.Rd	2008-02-26 16:58:18 UTC (rev 124)
+++ pkg/man/pdata-class.Rd	2008-02-26 21:51:42 UTC (rev 125)
@@ -4,6 +4,7 @@
 \alias{pdata-class}
 \alias{[<-,pdata-method}
 \alias{[,pdata-method}
+\alias{[,pdata,ANY,ANY,ANY-method}
 \alias{[[,pdata-method}
 \alias{[[<-,pdata-method}
 \alias{[[,pdata,ANY,ANY-method}

Modified: pkg/man/phylo4-class.Rd
===================================================================
--- pkg/man/phylo4-class.Rd	2008-02-26 16:58:18 UTC (rev 124)
+++ pkg/man/phylo4-class.Rd	2008-02-26 21:51:42 UTC (rev 125)
@@ -4,6 +4,7 @@
 \alias{phylo4-class}
 \alias{$,phylo4-method}
 \alias{$<-,phylo4-method}
+\alias{[,phylo4,ANY,missing,missing-method}
 \alias{print,phylo4-method}
 \alias{show,phylo4-method}
 \alias{summary,phylo4-method}

Modified: pkg/man/phylo4d-class.Rd
===================================================================
--- pkg/man/phylo4d-class.Rd	2008-02-26 16:58:18 UTC (rev 124)
+++ pkg/man/phylo4d-class.Rd	2008-02-26 21:51:42 UTC (rev 125)
@@ -5,6 +5,7 @@
 \alias{print,phylo4d-method}
 \alias{summary,phylo4d-method}
 \alias{names,phylo4d-method}
+\alias{[,phylo4d,ANY,ANY,ANY-method}
 \title{phylo4d class}
 \description{S4 class for phylogenetic tree and data.}
 \section{Objects from the Class}{