X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=R%2FrTrait.R;h=ec055dcb58a643798cc51976938cc1e19ff4f6af;hb=d5b85d181648e2761cecc91d75c4c66fa05e4508;hp=2c04dc6dd0855e246de03107d4b70017386baab3;hpb=f295ab19440298e543db5a270e54f10a84382197;p=ape.git

diff --git a/R/rTrait.R b/R/rTrait.R
index 2c04dc6..ec055dc 100644
--- a/R/rTrait.R
+++ b/R/rTrait.R
@@ -1,8 +1,8 @@
-## rTrait.R (2010-07-26)
+## rTrait.R (2011-04-02)
 
 ##   Trait Evolution
 
-## Copyright 2010 Emmanuel Paradis
+## Copyright 2010-2011 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -10,7 +10,7 @@
 rTraitDisc <-
     function(phy, model = "ER", k = if (is.matrix(model)) ncol(model) else 2,
              rate = 0.1, states = LETTERS[1:k], freq = rep(1/k, k),
-             ancestor = FALSE, root.value = 1)
+             ancestor = FALSE, root.value = 1, ...)
 {
     if (is.null(phy$edge.length))
         stop("tree has no branch length")
@@ -56,7 +56,7 @@ rTraitDisc <-
 
     if (is.function(model)) {
         environment(model) <- environment() # to find 'k'
-        for (i in N:1) x[des[i]] <- model(x[anc[i]], el[i])
+        for (i in N:1) x[des[i]] <- model(x[anc[i]], el[i], ...)
     } else {
         freq <- rep(freq, each = k)
         Q <- Q * freq
@@ -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, linear = TRUE, ...)
 {
     if (is.null(phy$edge.length))
         stop("tree has no branch length")
@@ -102,7 +102,7 @@ rTraitCont <-
 
     if (is.function(model)) {
         environment(model) <- environment()
-        for (i in N:1) x[des[i]] <- model(x[anc[i]], el[i])
+        for (i in N:1) x[des[i]] <- model(x[anc[i]], el[i], ...)
     } else {
         model <- pmatch(toupper(model), c("BM", "OU"))
         if (length(sigma) == 1) sigma <- rep(sigma, N)
@@ -117,7 +117,10 @@ rTraitCont <-
                 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, sigma, alpha, theta, x, DUP = FALSE, NAOK = TRUE, PACKAGE = "ape")
+        .C("rTraitCont", as.integer(model), as.integer(N),
+           as.integer(anc - 1L), as.integer(des - 1L), el,
+           as.double(sigma), as.double(alpha), as.double(theta), x,
+           DUP = FALSE, NAOK = TRUE, PACKAGE = "ape")
     }
 
     if (ancestor) {