some changes for ape 3.0-6

[ape.git] / man / fastme.Rd

diff --git a/man/fastme.Rd b/man/fastme.Rd
index 897ffa0942313637d415e880943f9ebac2abe5d7..cd7af9e6cb72dd5c5a3e3a04fea68ec16f15590c 100644 (file)
--- a/man/fastme.Rd
+++ b/man/fastme.Rd
@@ -1,4 +1,5 @@
 \name{FastME}
+\alias{FastME}
 \alias{fastme}
 \alias{fastme.bal}
 \alias{fastme.ols}
@@ -10,12 +11,14 @@
   Minimum Evolution algorithm of Desper and Gascuel (2002).
 }
 \usage{
-  fastme.bal(X, nni = TRUE)
+  fastme.bal(X, nni = TRUE, spr = TRUE, tbr = TRUE)
   fastme.ols(X, nni = TRUE)
 }
 \arguments{
   \item{X}{a distance matrix; may be an object of class \code{"dist"}.}
   \item{nni}{a boolean value; TRUE to do NNIs (default).}
+  \item{spr}{ditto for SPRs.}
+  \item{tbr}{ditto for TBRs.}
 }
 \value{
   an object of class \code{"phylo"}.
@@ -32,7 +35,7 @@
 \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):
@@ -40,9 +43,10 @@ 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