some changes for ape 3.0-6

[ape.git] / R / pic.R

diff --git a/R/pic.R b/R/pic.R
index 122b60d3c7fd679acd091b6a694303d965ce0bc2..b1cb20b17921668f98e4375a95093d4ad3fda44b 100644 (file)
--- a/R/pic.R
+++ b/R/pic.R
@@ -1,8 +1,8 @@
-## pic.R (2010-11-15)
+## pic.R (2012-09-11)
 
 ##   Phylogenetically Independent Contrasts
 
-## Copyright 2002-2010 Emmanuel Paradis
+## Copyright 2002-2012 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -22,7 +22,7 @@ pic <- function(x, phy, scaled = TRUE, var.contrasts = FALSE)
     if (any(is.na(x)))
       stop("missing data in 'x': you may consider removing the species with missing data from your tree with the function 'drop.tip'.")
 
-    phy <- reorder(phy, "pruningwise")
+    phy <- reorder(phy, "postorder")
     phenotype <- numeric(nb.tip + nb.node)
 
     if (is.null(names(x))) {
@@ -174,7 +174,7 @@ varCompPhylip <- function(x, phy, exec = NULL)
     odir <- setwd(pfx)
     on.exit(setwd(odir))
     if (file.exists("outfile")) unlink("outfile")
-    system("phylip contrast", intern = TRUE, input = c("W", "A", "Y"))
+    system(exec, intern = TRUE, input = c("W", "A", "Y"))
     varA <- scan("outfile", skip = 7, nlines = p, quiet = TRUE)
     varE <- scan("outfile", skip = 11 + p, nlines = p, quiet = TRUE)
     if (p > 1) {