some changes for ape 3.0-6

[ape.git] / man / njs.Rd

diff --git a/man/njs.Rd b/man/njs.Rd
index 90a3444cca2004d04fe12ab9cfe3610c35610625..b400e26784d851a2e269fc5793c72c5c54af20e9 100644 (file)
--- a/man/njs.Rd
+++ b/man/njs.Rd
@@ -12,15 +12,16 @@ bionjs(X, fs = 15)
 }
 \arguments{
   \item{X}{a distance matrix.}
-  \item{fs}{argument \emph{s} of the agglomerative criterion.}
+  \item{fs}{argument \emph{s} of the agglomerative criterion: it is
+    coerced as an integer and must at least equal to one.}
 }
 \details{
   Missing values represented by either \code{NA} or any negative number.
 
   Basically, the Q* criterion is applied to all the pairs of leaves, and
   the \emph{s} highest scoring ones are chosen for further analysis by
-  the agglomeration criteria that better handle handle missing
-  distances (see references for details).
+  the agglomeration criteria that better handle missing distances (see
+  references for details).
 }
 \value{
   an object of class \code{"phylo"}.
@@ -29,4 +30,16 @@ bionjs(X, fs = 15)
   \url{http://www.biomedcentral.com/1471-2105/9/166}
 }
 \author{Andrei Popescu \email{niteloserpopescu@gmail.com}}
+\seealso{
+  \code{\link{nj}}, \code{\link{bionj}}, \code{\link{triangMtds}}
+}
+\examples{
+data(woodmouse)
+d <- dist.dna(woodmouse)
+dm <- d
+dm[sample(length(dm), size = 3)] <- NA
+dist.topo(njs(dm), nj(d)) # often 0
+dm[sample(length(dm), size = 10)] <- NA
+dist.topo(njs(dm), nj(d)) # sometimes 0
+}
 \keyword{models}