[Phylobase-commits] r306 - in pkg: R inst/doc man tests

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Dec 9 06:18:07 CET 2008 

Author: bbolker
Date: 2008-12-09 06:18:07 +0100 (Tue, 09 Dec 2008)
New Revision: 306

Modified:
   pkg/R/checkdata.R
   pkg/inst/doc/phylobase.pdf
   pkg/man/treewalk.Rd
   pkg/tests/phylotorture.R
Log:
 fixed small bug (introduced by more stringent checking) identified
by Jim Regetz; added corresponding test; documentation tweak in 
treewalk.Rd



Modified: pkg/R/checkdata.R
===================================================================
--- pkg/R/checkdata.R	2008-11-28 11:50:19 UTC (rev 305)
+++ pkg/R/checkdata.R	2008-12-09 05:18:07 UTC (rev 306)
@@ -23,7 +23,7 @@
     intnodes <- nodes[!nodes %in% tips]
     if (!(all(tips==1:ntips) && all(nodes=(ntips+1):(ntips+length(intnodes)))))
       return("tips and nodes incorrectly numbered")
-    nAncest <- tabulate(E[, 2])
+    nAncest <- tabulate(E[, 2],nbins=max(nodes)) ## bug fix from Jim Regetz
     nDesc <- tabulate(E[,1])
     nTips <- sum(nDesc==0)
     if (!all(nDesc[1:nTips]==0))

Modified: pkg/inst/doc/phylobase.pdf
===================================================================
--- pkg/inst/doc/phylobase.pdf	2008-11-28 11:50:19 UTC (rev 305)
+++ pkg/inst/doc/phylobase.pdf	2008-12-09 05:18:07 UTC (rev 306)
@@ -112,18 +112,22 @@
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 trailer
 << /Size 236
 /Root 234 0 R
 /Info 235 0 R
-/ID [<FCC374C8B790D347C9311A0BAFDB4722> <FCC374C8B790D347C9311A0BAFDB4722>] >>
+/ID [<2935E71425B5F713713C9FE2FFC1F6CB> <2935E71425B5F713713C9FE2FFC1F6CB>] >>
 startxref
-142149
+141892
 %%EOF

Modified: pkg/man/treewalk.Rd
===================================================================
--- pkg/man/treewalk.Rd	2008-11-28 11:50:19 UTC (rev 305)
+++ pkg/man/treewalk.Rd	2008-12-09 05:18:07 UTC (rev 306)
@@ -30,7 +30,6 @@
   \item{phy}{a \linkS4class{phylo4} object (or one inheriting from
     \linkS4class{phylo4}, e.g. a \linkS4class{phylo4d} object)
   }
-  \item{x}{a \code{phylo4} object}
   \item{node}{a node number (or name)}
   \item{which}{(\code{ancestors}) specify whether to return just direct
     ancestor ("parent"), all ancestor nodes ("all"), or all ancestor

Modified: pkg/tests/phylotorture.R
===================================================================
--- pkg/tests/phylotorture.R	2008-11-28 11:50:19 UTC (rev 305)
+++ pkg/tests/phylotorture.R	2008-12-09 05:18:07 UTC (rev 306)
@@ -108,3 +108,11 @@
 
 foo at tip.label <- rep('blah',10)
 foo at node.label <- rep("",9)
+
+#####
+## tree with only 2 tips: will fail under previous versions
+## with "Error in if (which(nAncest == 0) != nTips + 1) { : 
+##  argument is of length zero"
+
+edge <- matrix(c(3,1,3,2),byrow=TRUE,ncol=2)
+p2 <- phylo4(edge)

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