[Phylobase-commits] r579 - pkg/R

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

Author: francois
Date: 2009-08-25 00:47:46 +0200 (Tue, 25 Aug 2009)
New Revision: 579

Modified:
   pkg/R/readNexus.R
Log:
fixed small bug/typo in readNexus

Modified: pkg/R/readNexus.R
===================================================================
--- pkg/R/readNexus.R	2009-08-24 21:35:46 UTC (rev 578)
+++ pkg/R/readNexus.R	2009-08-24 22:47:46 UTC (rev 579)
@@ -4,7 +4,8 @@
                        check.node.labels=c("keep", "drop", "asdata")) {
 
     ## file = input nexus file
-    ## simplify =
+    ## simplify = if TRUE only keeps the first tree, if several trees are found in
+    ##            the Nexus file
     ## type = specify whether to return trees+data as phylo4d object ("all") if
     ##        both are found, returning a data.frame or phylo4 object if only one
     ##        is found, "tree": return a phylo4 object only, regardless of
@@ -59,13 +60,13 @@
                                 "check.node.labels because there are no ",
                                 "labels associated with the tree ", i)
                         check.node.labels <- "drop"
-                    }
+                    }                  
                     trees[[i]] <- phylo4d(intreesphylolist[[i]],
                                           check.node.labels=check.node.labels)
                 }
                 else {
                     trees[[i]] <- phylo4(intreesphylolist[[i]],
-                                         check.node.labels="keep")
+                                         check.node.labels=check.node.labels)
                 }
             }
         }