[Phylobase-commits] r525 - in pkg: R tests

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

Author: bbolker
Date: 2009-08-20 05:07:38 +0200 (Thu, 20 Aug 2009)
New Revision: 525

Modified:
   pkg/R/class-phylomats.R
   pkg/R/setAs-Methods.R
   pkg/tests/roundtrip.R
Log:
  make phylo4vcov -> phylo4 order correctly
  comment tweaks
  test tweaking



Modified: pkg/R/class-phylomats.R
===================================================================
--- pkg/R/class-phylomats.R	2009-08-19 23:23:46 UTC (rev 524)
+++ pkg/R/class-phylomats.R	2009-08-20 03:07:38 UTC (rev 525)
@@ -79,9 +79,10 @@
         ## add root node to edge matrix and branch lengths
         temptree$edgemat <- rbind(temptree$edgemat,c(NA,rootnode))
         temptree$edgelens <- c(temptree$edgelens,NA)
-        phylo4(temptree$edgemat,edge.length=temptree$edgelens,
+        reorder(phylo4(temptree$edgemat,edge.length=temptree$edgelens,
                tip.label=rownames(from),
-               edge.label=from at edge.label,order=from at order)
+               edge.label=from at edge.label,order="unknown"),
+                "preorder")
       })
 
 

Modified: pkg/R/setAs-Methods.R
===================================================================
--- pkg/R/setAs-Methods.R	2009-08-19 23:23:46 UTC (rev 524)
+++ pkg/R/setAs-Methods.R	2009-08-20 03:07:38 UTC (rev 525)
@@ -69,7 +69,7 @@
 ## BMB: adding an explicit as method, and the warning,
 ##  here is a very bad idea, because
 ##   even implicit conversions from phylo4d to phylo4 (e.g.
-##  to use inhertied methods) will produce the warning
+##  to use inherited methods) will produce the warning
 
 ## setAs("phylo4d", "phylo4",function(from,to) {
 ##   warning("losing data while coercing phylo4d to phylo")
@@ -116,6 +116,7 @@
         y$edge.length <- NULL
     if (length(y$node.label) == 0)
         y$node.label <- NULL
+    ## how do we tell if there is an explicit root edge?
     if (isRooted(from)) {
         root.edge <- brlen0[rootNode(from)]
         if (!is.na(root.edge)) y$root.edge <- root.edge

Modified: pkg/tests/roundtrip.R
===================================================================
--- pkg/tests/roundtrip.R	2009-08-19 23:23:46 UTC (rev 524)
+++ pkg/tests/roundtrip.R	2009-08-20 03:07:38 UTC (rev 525)
@@ -10,8 +10,8 @@
 t5 <- as(t1,"phylo")
 stopifnot(identical(t0,t5))
 
-## t2<-as(t1,"phylo4vcov")
-## t3<-as(t2,"phylo4")
-## t4<-as(t3,"phylo")
+t2<-as(t1,"phylo4vcov")
+t3<-as(t2,"phylo4")
+t4<-as(t3,"phylo")
+## stopifnot(identical(t0,t4))
 
-## plot(test.tree) #CRASHES R!