[Adephylo-commits] r126 - in pkg: R man

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

Author: jombart
Date: 2009-11-05 12:05:15 +0100 (Thu, 05 Nov 2009)
New Revision: 126

Modified:
   pkg/R/partition.R
   pkg/R/table.phylo4d.R
   pkg/man/table.phylo4d.Rd
Log:
removed calls to @tip.label


Modified: pkg/R/partition.R
===================================================================
--- pkg/R/partition.R	2009-11-05 10:59:43 UTC (rev 125)
+++ pkg/R/partition.R	2009-11-05 11:05:15 UTC (rev 126)
@@ -63,7 +63,7 @@
     ## main computations
     temp <- listTips(x)
     res <- data.frame(lapply(temp,fDum))
-    row.names(res) <- x at tip.label
+    row.names(res) <- tipLabels(x)
     res <- res[,-1]
 
     if(result=="dummy"){
@@ -135,7 +135,7 @@
     res <- res[,-1] # keep only centred vectors; orthogonal for identity
     res <- res * sqrt(n) # render vectors orthogonal for 1/n
 
-    rownames(res) <- x at tip.label
+    rownames(res) <- tipLabels(x)
     colnames(res) <- paste("V",1:ncol(res))
 
     return(as.data.frame(res))

Modified: pkg/R/table.phylo4d.R
===================================================================
--- pkg/R/table.phylo4d.R	2009-11-05 10:59:43 UTC (rev 125)
+++ pkg/R/table.phylo4d.R	2009-11-05 11:05:15 UTC (rev 126)
@@ -5,7 +5,7 @@
                       repVar=1:ncol(tdata(x, type="tip")), 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(tdata(x,type="tip")),
+                      tip.label=tipLabels(x), var.label=colnames(tdata(x,type="tip")),
                       cex.symbol=1, cex.label=1, cex.legend=1, coord.legend=NULL, ...)
 {
 
@@ -86,7 +86,7 @@
     y.inset <- SYMBSCALE * cex.symbol * usr.height / par("pin")[2]
     x.base <- plotres$x.lim[2] + x.inset # start plotting from x.base rightwards
     if(show.tip.label){
-        temp <- x at tip.label[which.max(nchar(x at tip.label))] # longest tip label
+        temp <- x at tip.label[which.max(nchar(tipLabels(x)))] # longest tip label
         lab.width <- strwidth(temp, units="user", cex=cex.label) # compute the width to keep for tip labels
     } else{
         lab.width <- 0

Modified: pkg/man/table.phylo4d.Rd
===================================================================
--- pkg/man/table.phylo4d.Rd	2009-11-05 10:59:43 UTC (rev 125)
+++ pkg/man/table.phylo4d.Rd	2009-11-05 11:05:15 UTC (rev 126)
@@ -15,11 +15,12 @@
 }
 \usage{
 table.phylo4d(x, treetype=c("phylogram","cladogram"), symbol=c("circles", "squares"),
-          repVar=1:ncol(x at tip.data), 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, coord.legend=NULL, \dots)
+                      repVar=1:ncol(tdata(x, type="tip")), 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(tdata(x,type="tip")),
+                      cex.symbol=1, cex.label=1, cex.legend=1,
+  coord.legend=NULL, \dots)
 }
 \arguments{
   \item{x}{a \linkS4class{phylo4d} object}