X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=R%2FrTrait.R;h=8cc48e17c9e45296c082b33ca33f29e01c3f3296;hb=dfabbb4721bc499ee9e5ee9aadcfd59ff3d4f223;hp=3359df6f71da40c3b8a5d7a254844bafb50b79e3;hpb=24fc6c03893f85a3f9ab3d088201b3731f3035b4;p=ape.git

diff --git a/R/rTrait.R b/R/rTrait.R
index 3359df6..8cc48e1 100644
--- a/R/rTrait.R
+++ b/R/rTrait.R
@@ -1,4 +1,4 @@
-## rTrait.R (2010-01-11)
+## rTrait.R (2010-05-06)
 
 ##   Trait Evolution
 
@@ -58,9 +58,12 @@ rTraitDisc <-
         environment(model) <- environment() # to find 'k'
         for (i in N:1) x[des[i]] <- model(x[anc[i]], el[i])
     } else {
+        freq <- rep(freq, each = k)
+        Q <- Q * freq
+        diag(Q) <- 0
         diag(Q) <- -rowSums(Q)
         for (i in N:1) {
-            p <- matexpo(Q * freq * el[i])[x[anc[i]], ]
+            p <- matexpo(Q * el[i])[x[anc[i]], ]
             x[des[i]] <- .Internal(sample(k, size = 1, FALSE, prob = p))
         }
     }