[Phylobase-commits] r541 - pkg/R

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

Author: francois
Date: 2009-08-20 21:56:18 +0200 (Thu, 20 Aug 2009)
New Revision: 541

Modified:
   pkg/R/checkdata.R
Log:
expanded warning message for reticulated trees, and leftovers from adding rownamesAsLabels

Modified: pkg/R/checkdata.R
===================================================================
--- pkg/R/checkdata.R	2009-08-20 19:14:57 UTC (rev 540)
+++ pkg/R/checkdata.R	2009-08-20 19:56:18 UTC (rev 541)
@@ -148,7 +148,8 @@
         if ("retic" %in% err)
           return(paste("tree is reticulated:",msg))
         if ("retic" %in% warn)
-          warning("tree is reticulated:",msg)
+          warning("tree is reticulated, most functions in phylobase haven't ",
+                  "been tested with reticulated trees: ", msg)
     }
     return(TRUE)
 }
@@ -183,10 +184,10 @@
 
 
 formatData <- function(phy, dt, type=c("tip", "internal", "all"),
-                       match.data=TRUE, label.type=c("rownames", "column"),
+                       match.data=TRUE, rownamesAsLabels=FALSE,
+                       label.type=c("rownames", "column"),
                        label.column=1, missing.data=c("fail", "warn", "OK"),
-                       extra.data=c("warn", "OK", "fail"),
-                       rownamesAsLabels=FALSE
+                       extra.data=c("warn", "OK", "fail")
                        ) {
 
     type <- match.arg(type)