some big fixes for ape 2.7-1

[ape.git] / man / fastme.Rd

diff --git a/man/fastme.Rd b/man/fastme.Rd
index cd8b4edd8cc755b8e0b975a73ebc1dc5de616aea..d29d305e851e1ebcb9b85b6f1925e0ecda609c7f 100644 (file)
--- a/man/fastme.Rd
+++ b/man/fastme.Rd
@@ -10,12 +10,14 @@
   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"}.
@@ -32,10 +34,9 @@
 \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{
-\dontrun{
 ### From Saitou and Nei (1987, Table 1):
 x <- c(7, 8, 11, 13, 16, 13, 17, 5, 8, 10, 13,
        10, 14, 5, 7, 10, 7, 11, 8, 11, 8, 12,
@@ -51,6 +52,5 @@ data(woodmouse)
 trw <- fastme.bal(dist.dna(woodmouse))
 plot(trw)
 }
-}
 \keyword{models}