new dist.nodes() with C code

[ape.git] / R / rTrait.R

diff --git a/R/rTrait.R b/R/rTrait.R
index 6731c5cf94526939a767158e9d2f5cebf3bf0174..1b5852d102024a01a9a1a312643e82f57f9c0d76 100644 (file)
--- a/R/rTrait.R
+++ b/R/rTrait.R
@@ -1,8 +1,8 @@
-## rTrait.R (2011-06-16)
+## rTrait.R (2012-02-09)
 
 ##   Trait Evolution
 
-## Copyright 2010-2011 Emmanuel Paradis
+## Copyright 2010-2012 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -64,7 +64,7 @@ rTraitDisc <-
         diag(Q) <- -rowSums(Q)
         for (i in N:1) {
             p <- matexpo(Q * el[i])[x[anc[i]], ]
-            x[des[i]] <- .Internal(sample(k, size = 1, FALSE, prob = p))
+            x[des[i]] <- sample.int(k, size = 1, FALSE, prob = p)
         }
     }
 
@@ -82,7 +82,7 @@ rTraitDisc <-
 
 rTraitCont <-
     function(phy, model = "BM", sigma = 0.1, alpha = 1, theta = 0,
-             ancestor = FALSE, root.value = 0, linear = TRUE, ...)
+             ancestor = FALSE, root.value = 0, ...)
 {
     if (is.null(phy$edge.length))
         stop("tree has no branch length")
@@ -115,7 +115,6 @@ rTraitCont <-
             if (length(theta) == 1) theta <- rep(theta, N)
             else if (length(theta) != N)
                 stop("'theta' must have one or Nedge(phy) elements")
-            if (!linear) model <- model + 1L
         }
         .C("rTraitCont", as.integer(model), as.integer(N),
            as.integer(anc - 1L), as.integer(des - 1L), el,