[Phylobase-commits] r890 - pkg/R

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

Author: francois
Date: 2014-03-20 17:41:54 +0100 (Thu, 20 Mar 2014)
New Revision: 890

Modified:
   pkg/R/class-phylomats.R
   pkg/R/methods-phylo4.R
Log:
fix docs

Modified: pkg/R/class-phylomats.R
===================================================================
--- pkg/R/class-phylomats.R	2014-03-20 16:41:15 UTC (rev 889)
+++ pkg/R/class-phylomats.R	2014-03-20 16:41:54 UTC (rev 890)
@@ -28,10 +28,12 @@
 #'   ## topologically identical ...
 #' 
 #'   ## edge matrices are in a different order:
-#'   ## cf. o2 at edge and o3 at edge
+#'   ## cf. edges(o2) and edges(o3)
 #'   ## BUT the edge matrices are otherwise identical
-#'   identical(o2 at edge[order(o2 at edge[,2]),],
-#'             o3 at edge[order(o3 at edge[,2]),])
+#'   o2edges <- edges(o2)
+#'   o3edges <- edges(o3)
+#'   identical(o2edges[order(o2edges[,2]),],
+#'             o3edges[order(o3edges[,2]),])
 #' 
 #'   ## There is left/right ambiguity here in the tree orders:
 #'   ## in o2 the 5->6->7->1 lineage

Modified: pkg/R/methods-phylo4.R
===================================================================
--- pkg/R/methods-phylo4.R	2014-03-20 16:41:15 UTC (rev 889)
+++ pkg/R/methods-phylo4.R	2014-03-20 16:41:54 UTC (rev 890)
@@ -599,7 +599,7 @@
 #' follows: root first, then other internal nodes, and finally tips.\cr The
 #' returned data.frame has the following columns:\cr \item{label}{Label for the
 #' taxon at the node (usually species name).} \item{node}{Node number, i.e. the
-#' number identifying the node in \code{x at edge}.} \item{ancestor}{Node number
+#' number identifying the node in edge matrix.} \item{ancestor}{Node number
 #' of the node's ancestor.} \item{branch.length}{The branch length connecting
 #' the node to its ancestor (NAs if missing).} \item{node.type}{"root",
 #' "internal", or "tip". (internally generated)} \item{data}{phenotypic data