adding the new function 'where'

[ape.git] / R / collapse.singles.R

diff --git a/R/collapse.singles.R b/R/collapse.singles.R
index 4d477ab1f3735e1e57ebea4c27fe3f059555a57b..bbde0a17e003ce464a68dab76afa7d4aa412b416 100644 (file)
--- a/R/collapse.singles.R
+++ b/R/collapse.singles.R
@@ -1,4 +1,4 @@
-## collapse.singles.R (2008-06-19)
+## collapse.singles.R (2010-07-23)
 
 ##    Collapse "Single" Nodes
 
@@ -29,15 +29,15 @@ collapse.singles <- function(tree)
             prev.node <- which(xmat[, 2] == i)
             next.node <- which(xmat[, 1] == i)
             xmat[prev.node, 2] <- xmat[next.node, 2]
-            xmat <- xmat[xmat[, 1] != i, ] ## drop
+            xmat <- xmat[xmat[, 1] != i, ] # drop
             ## changed by EP for the new coding of "phylo" (2006-10-05):
             ## xmat[xmat < i] <- xmat[xmat < i] + 1 ## adjust indices
-            xmat[xmat > i] <- xmat[xmat > i] - 1 ## adjust indices
+            xmat[xmat > i] <- xmat[xmat > i] - 1L ## adjust indices # changed '1' by '1L' (2010-07-23)
             ## END
             elen[prev.node] <- elen[prev.node] + elen[next.node]
             ## added by Elizabeth Purdom (2008-06-19):
             if (!is.null(node.lab)) node.lab <- node.lab[-c(i - ntip)]
-            nnode <- nnode - 1
+            nnode <- nnode - 1L
             ## end
             elen <- elen[-next.node]
         }