[Phylobase-commits] r330 - pkg/inst/doc

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

Author: bbolker
Date: 2008-12-19 16:28:59 +0100 (Fri, 19 Dec 2008)
New Revision: 330

Modified:
   pkg/inst/doc/phylobase.Rnw
Log:
  disabled plotting (temporarily)
  small change to subset example
  update to reflect empty default labels



Modified: pkg/inst/doc/phylobase.Rnw
===================================================================
--- pkg/inst/doc/phylobase.Rnw	2008-12-19 14:34:56 UTC (rev 329)
+++ pkg/inst/doc/phylobase.Rnw	2008-12-19 15:28:59 UTC (rev 330)
@@ -55,6 +55,15 @@
 
 The \code{S4} generic system is too complicated to describe here, but doesn't include the same dot notation.  As a result \code{?plot.phylo4} doesn't work, \code{R} does, however, find the right plotting function.
 
+<<plothack>>= 
+## DISABLE PLOTTING until 
+oldplot <- plot
+plot <- function(...) {
+  oldplot(0:1,0:1)
+  text(0.5,0.5,"plotting temporarily disabled")
+} 
+@ 
+
 <<convtree,fig=FALSE>>=
 library(phylobase)
 # convert rand_tree to a phylo4 object
@@ -113,12 +122,17 @@
 labels(g1)
 @ 
 
-Print internal node labels (R automatically assigns values):
+Print internal node labels (empty):
 <<nodelabelgeodata>>=
 nodeLabels(g1)
 @ 
 
-Print edge labels (also automatically assigned):
+Print node numbers:
+<<nodenumbergeodata>>=
+nodeNumbers(g1)
+@ 
+
+Print edge labels (also empty in this case):
 <<edgelabelgeodata>>=
 edgeLabels(g1)
 @ 
@@ -223,7 +237,7 @@
 <<geoextract,results=hide>>=
 subset(g2,tips.include=c("fuliginosa","fortis","magnirostris",
             "conirostris","scandens"))
-subset(g2,node.subtree="N07")
+subset(g2,node.subtree=21)
 subset(g2,mrca=c("scandens","fortis"))
 @