X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Ffastme.Rd;h=9174b48cca957c76676437b2bcd523c65eff33ec;hb=40eeb40e48bccc220826860ce0ada4521cbc0148;hp=794e6c84bc25596e59ccef4dfb4c87a5606a233b;hpb=f3426364b40c7c0e6aadf6ea2690716425abdfc9;p=ape.git

diff --git a/man/fastme.Rd b/man/fastme.Rd
index 794e6c8..9174b48 100644
--- a/man/fastme.Rd
+++ b/man/fastme.Rd
@@ -34,7 +34,7 @@
 \seealso{
   \code{\link{nj}}, \code{\link{bionj}},
   \code{\link{write.tree}}, \code{\link{read.tree}},
-  \code{\link{dist.dna}}, \code{\link{mlphylo}}
+  \code{\link{dist.dna}}
 }
 \examples{
 ### From Saitou and Nei (1987, Table 1):
@@ -42,9 +42,10 @@ x <- c(7, 8, 11, 13, 16, 13, 17, 5, 8, 10, 13,
        10, 14, 5, 7, 10, 7, 11, 8, 11, 8, 12,
        5, 6, 10, 9, 13, 8)
 M <- matrix(0, 8, 8)
-M[row(M) > col(M)] <- x
-M[row(M) < col(M)] <- x
-rownames(M) <- colnames(M) <- 1:8
+M[lower.tri(M)] <- x
+M <- t(M)
+M[lower.tri(M)] <- x
+dimnames(M) <- list(1:8, 1:8)
 tr <- fastme.bal(M)
 plot(tr, "u")
 ### a less theoretical example