[Phylobase-commits] r930 - pkg/R

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

Author: francois
Date: 2014-05-06 22:16:38 +0200 (Tue, 06 May 2014)
New Revision: 930

Modified:
   pkg/R/checkdata.R
Log:
added test for reticulation (apparently forgotten)

Modified: pkg/R/checkdata.R
===================================================================
--- pkg/R/checkdata.R	2014-04-09 20:05:13 UTC (rev 929)
+++ pkg/R/checkdata.R	2014-05-06 20:16:38 UTC (rev 930)
@@ -69,12 +69,12 @@
 
     ## Storage of error/warning messages
     err <- wrn <- character(0)
-
+    
     ## Matrix is integer
     if (!is.integer(object at edge)) {
         err <- c(err, "Edge matrix needs to be integer.")
     }
-
+    
     ## Matrix doesn't have NAs
     if (any(is.na(object at edge))) {
         err <- c(err, "Edge matrix cannot have NAs at this time.",
@@ -102,6 +102,16 @@
     
     res <- checkTreeCpp(object, opts=opt)
 
+    if (hasRetic(object)) {
+        msg <- "Tree is reticulated."
+        if (identical(opt$retic, "fail")) {
+            err <- c(err, msg)
+        }
+        if (identical(opt$retic, "warn")) {
+            wrn <- c(wrn, msg)
+        }
+    }
+
     if (hasEdgeLength(object) && any(is.na(edgeLength(object)))) {
         naElen <- names(which(is.na(object at edge.length)))
         if (! identical(naElen, edgeId(object, "root")))