new option 'rotate.tree' in plot.phylo()

[ape.git] / man / DNAbin.Rd

diff --git a/man/DNAbin.Rd b/man/DNAbin.Rd
index bce0df2da8998c237f3a22dc7c78bd19627e1669..eb6983ea48e8a6c669d662ffffd0cdba4387b871 100644 (file)
--- a/man/DNAbin.Rd
+++ b/man/DNAbin.Rd
@@ -42,7 +42,7 @@
     are dropped.}
   \item{i, j}{indices of the rows and/or columns to select or to drop.
     They may be numeric, logical, or character (in the same way than for
-    standard R objects).}
+    standard \R objects).}
   \item{drop}{logical; if \code{TRUE}, the returned object is of the
     lowest possible dimension.}
   \item{recursive}{for compatibility with the generic (unused).}
@@ -50,7 +50,7 @@
 \details{
   These are all `methods' of generic functions which are here applied to
   DNA sequences stored as objects of class \code{"DNAbin"}. They are
-  used in the same way than the standard R functions to manipulate
+  used in the same way than the standard \R functions to manipulate
   vectors, matrices, and lists. Additionally, the operators \code{[[}
   and \code{$} may be used to extract a vector from a list. Note that
   the default of \code{drop} is not the same than the generic operator:
@@ -81,11 +81,15 @@
 \references{
   Paradis, E. (2007) A Bit-Level Coding Scheme for Nucleotides.
   \url{http://ape.mpl.ird.fr/misc/BitLevelCodingScheme_20April2007.pdf}
+
+  Paradis, E. (2012) \emph{Analysis of Phylogenetics and Evolution with
+  R (Second Edition)}. New York: Springer.
 }
 \author{Emmanuel Paradis}
 \seealso{
   \code{\link{as.DNAbin}}, \code{\link{read.dna}},
-  \code{\link{read.GenBank}}, \code{\link{write.dna}}
+  \code{\link{read.GenBank}}, \code{\link{write.dna}}, ,
+  \code{\link{image.DNAbin}}
 
   The corresponding generic functions are documented in the package
   \pkg{base}.
@@ -93,9 +97,8 @@
 \examples{
 data(woodmouse)
 woodmouse
-summary(woodmouse)
-summary(woodmouse, 15, 6)
-summary(woodmouse[1:5, 1:300], 15, 6)
+print(woodmouse, 15, 6)
+print(woodmouse[1:5, 1:300], 15, 6)
 ### Just to show how distances could be influenced by sampling:
 dist.dna(woodmouse[1:2, ])
 dist.dna(woodmouse[1:3, ])