[Phylobase-commits] r571 - pkg/man

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

Author: pdc
Date: 2009-08-23 19:36:40 +0200 (Sun, 23 Aug 2009)
New Revision: 571

Modified:
   pkg/man/readNexus.Rd
Log:
tweak documentation, describe{} allows \item{label}{description} whereas itemize{} only accepts \item{test}

Modified: pkg/man/readNexus.Rd
===================================================================
--- pkg/man/readNexus.Rd	2009-08-23 16:46:36 UTC (rev 570)
+++ pkg/man/readNexus.Rd	2009-08-23 17:36:40 UTC (rev 571)
@@ -27,7 +27,7 @@
 }
 \details{
   The options for \code{check.node.labels} can take the values:
-  \itemize{
+  \describe{
      \item{keep}{the node labels of the Nexus file will be passed as node labels in the phylo4 object}
      \item{drop}{the node labels of the Nexus file will be ignored in the phylo4 object}
      \item{asdata}{the node labels will passed to the phylo4 object as data.}
@@ -41,10 +41,9 @@
 \seealso{the \linkS4class{phylo4d} class, the \linkS4class{phylo4} class}
 \author{Brian O'Meara, Derrick Zwickl}
 \note{
-  This relies on Version 2.0 of the Nexus Class Library by Paul Lewis and Mark Holder.
-  Tree reading is done initially using a function from APE; this function can be 
-  confused if the tree name has the word (\dQuote{tree}) in it. Also note that edge
-  and node labels (except for terminal nodes) are NOT yet loaded into the \code{phylo4}
-  object.
+  This relies on Version 2.0 of the Nexus Class Library by Paul Lewis and Mark Holder. Tree reading
+  is done initially using the \code{APE} function \link[ape]{read.nexus}; this function can be
+  confused if the tree name has the word (\dQuote{tree}) in it. Also note that edge and node labels
+  (except for terminal nodes) are NOT yet loaded into the \code{phylo4} object.
 }
 \keyword{misc}