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).}
\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:
\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