modified ace( method = ...)

[ape.git] / man / bionj.Rd

diff --git a/man/bionj.Rd b/man/bionj.Rd
index 261542a382e5295615b794992c85609f04a0991d..3fe1a7918ec07b997d24770b81743112826af85f 100644 (file)
--- a/man/bionj.Rd
+++ b/man/bionj.Rd
@@ -25,9 +25,8 @@ bionj(X)
   ported to \R by Vincent Lefort \email{vincent.lefort@lirmm.fr}
 }
 \seealso{
-  \code{\link{nj}}, \code{\link{fastme}},
-  \code{\link{write.tree}}, \code{\link{read.tree}},
-  \code{\link{dist.dna}}
+  \code{\link{nj}}, \code{\link{fastme}}, \code{\link{mvr}},
+  \code{\link{bionjs}}, \code{\link{SDM}}, \code{\link{dist.dna}}
 }
 \examples{
 ### From Saitou and Nei (1987, Table 1):
@@ -35,9 +34,10 @@ 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 <- bionj(M)
 plot(tr, "u")
 ### a less theoretical example