X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Fbionj.Rd;h=18b06b488754cbfd3131798ee458d46771203b2c;hb=fab4946bb5d41cd408dffd4b66aae8a697690cfa;hp=faa7a80bb6e9377cedaea426625766494e7fdc95;hpb=c827059eeafc8cbe41c812b26979543ab287803e;p=ape.git

diff --git a/man/bionj.Rd b/man/bionj.Rd
index faa7a80..18b06b4 100644
--- a/man/bionj.Rd
+++ b/man/bionj.Rd
@@ -22,12 +22,12 @@ bionj(X)
 }
 \author{
   original C code by Hoa Sien Cuong and Olivier Gascuel; adapted and
-  ported to R by Vincent Lefort \email{vincent.lefort@lirmm.fr}
+  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{mlphylo}}
+  \code{\link{dist.dna}}
 }
 \examples{
 ### From Saitou and Nei (1987, Table 1):
@@ -35,9 +35,10 @@ 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