[Phylobase-commits] r423 - in pkg: R inst/doc man

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

Author: bbolker
Date: 2009-01-03 19:31:18 +0100 (Sat, 03 Jan 2009)
New Revision: 423

Modified:
   pkg/R/methods-phylo4.R
   pkg/inst/doc/phylobase.Rnw
   pkg/man/check.phylo4d.Rd
Log:
  clean up glitches from previous changes



Modified: pkg/R/methods-phylo4.R
===================================================================
--- pkg/R/methods-phylo4.R	2009-01-03 17:26:41 UTC (rev 422)
+++ pkg/R/methods-phylo4.R	2009-01-03 18:31:18 UTC (rev 423)
@@ -39,7 +39,8 @@
 setMethod("edges", "phylo4", function(x, order, drop.root=FALSE, ...) {
   e <- x at edge
   if (drop.root) e <- e[!is.na(e[,1]),]
-}
+  e
+})
 
 setMethod("edgeOrder", "phylo4", function(x, ...) {
     x at order

Modified: pkg/inst/doc/phylobase.Rnw
===================================================================
--- pkg/inst/doc/phylobase.Rnw	2009-01-03 17:26:41 UTC (rev 422)
+++ pkg/inst/doc/phylobase.Rnw	2009-01-03 18:31:18 UTC (rev 423)
@@ -376,7 +376,6 @@
   }
 nodevals <- data.frame(nodevals)
 treed2 <- phylo4d(tree,all.data=nodevals)
-}
 @ 
 
 

Modified: pkg/man/check.phylo4d.Rd
===================================================================
--- pkg/man/check.phylo4d.Rd	2009-01-03 17:26:41 UTC (rev 422)
+++ pkg/man/check.phylo4d.Rd	2009-01-03 18:31:18 UTC (rev 423)
@@ -92,6 +92,7 @@
 #create phylo4 objects with node and tip data
 p4d.all1 <- phylo4d(p4, node.data = nod.dat, tip.data = dat,
   which = "all")
+nodeLabels(p4) <- as.character(sort(nodeId(p4)))
 p4d.all2 <- phylo4d(p4, all.data = rbind(dat, nod.dat), which = "all")
 }
 \keyword{misc}