[Phylobase-commits] r130 - pkg/man

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

Author: jombart
Date: 2008-02-28 18:41:41 +0100 (Thu, 28 Feb 2008)
New Revision: 130

Modified:
   pkg/man/check.phylo4d.Rd
Log:
Minor fixes/adds in check_data documentation.


Modified: pkg/man/check.phylo4d.Rd
===================================================================
--- pkg/man/check.phylo4d.Rd	2008-02-28 13:50:51 UTC (rev 129)
+++ pkg/man/check.phylo4d.Rd	2008-02-28 17:41:41 UTC (rev 130)
@@ -4,6 +4,7 @@
 \title{Validity checking for phylo4d objects}
 \description{
   Basic checks on the validity of S4 phylogenetic plus data objects
+  (i.e. \linkS4class{phylo4d} objects).
 }
 \usage{
 check_data(object, use.tip.names=TRUE, missing.tip.data=c("fail","OK","warn"), extra.tip.data=c("fail","OK","warn"), default.tip.names=c("warn","OK","fail"), use.node.names=FALSE, missing.node.data=c("OK","warn","fail"), extra.node.data=c("OK","warn","fail"), default.node.names=c("warn","OK","fail"),\dots)
@@ -13,7 +14,7 @@
 }
 
 \arguments{
-  \item{object}{A phylo4 object}
+  \item{object}{A phylo4d object}
   \item{use.tip.names}{Use tip data names if present (default=\code{TRUE})}
   \item{missing.tip.data}{Can tip data taxa be a subset of tree taxa? (default=\code{fail})}
   \item{extra.tip.data}{Can tip data taxa be a superset of tree taxa? (default=\code{fail})}
@@ -54,6 +55,7 @@
 p4 <- as(p3,"phylo4")
 #create phylo4d objects with tip data
 p4d <- phylo4d(p4,dat)
+check_data(p4d)
 p4d.sorted <- phylo4d(p4,dat[5:1,])
 try(p4d.nonames <- phylo4d(p4,dat.defaultnames))
 p4d.nonames <- phylo4d(p4,dat.defaultnames,use.tip.names=FALSE)