X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2FrTrait.c;h=43dc73ad85f3163b65e49333889a2088d30a06a5;hb=646d8be3497d656d95331e2c7f6bef5d2ff86b2c;hp=2e7371f850f808ec54abcfef8479f2d0629b3778;hpb=2419de65ffb4f7c45eb8c2448bcba3d0df64744f;p=ape.git

diff --git a/src/rTrait.c b/src/rTrait.c
index 2e7371f..43dc73a 100644
--- a/src/rTrait.c
+++ b/src/rTrait.c
@@ -1,6 +1,6 @@
-/* rTrait.c       2010-05-26 */
+/* rTrait.c       2011-06-25 */
 
-/* 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. */
@@ -12,6 +12,7 @@ void rTraitCont(int *model, int *Nedge, int *edge1, int *edge2, double *el,
 {
 /* The tree must be in pruningwise order */
 	int i;
+	double alphaT, M, S;
 
 	switch(*model) {
 	case 1 : for (i = *Nedge - 1; i >= 0; i--) {
@@ -21,8 +22,16 @@ void rTraitCont(int *model, int *Nedge, int *edge1, int *edge2, double *el,
 		}
 		break;
 	case 2 : for (i = *Nedge - 1; i >= 0; i--) {
+			if (alpha[i]) {
+				alphaT = alpha[i] * el[i];
+				M = exp(-alphaT);
+				S = sigma[i] * sqrt((1 - exp(-2 * alphaT))/(2 * alpha[i]));
+			} else { /* same than if (alpha[i] ==0) */
+				M = 1;
+				S = sqrt(el[i]) * sigma[i];
+			}
 			GetRNGstate();
-			x[edge2[i]] = x[edge1[i]] + (sigma[i]*norm_rand() - alpha[i]*(x[edge1[i]] - theta[i])) * el[i]; /* need sqrt(el[i]) ? */
+			x[edge2[i]] = x[edge1[i]] * M +  theta[i] * (1 - M) + S * norm_rand();
 			PutRNGstate();
 		}
 		break;