\method{print}{DNAbin}(x, \dots)
\method{summary}{DNAbin}(object, printlen = 6, digits = 3, \dots)
\method{rbind}{DNAbin}(\dots)
-\method{cbind}{DNAbin}(\dots, check.names = TRUE)
+\method{cbind}{DNAbin}(\dots, check.names = TRUE, fill.with.gaps = FALSE,
+ quiet = FALSE)
\method{[}{DNAbin}(x, i, j, drop = TRUE)
\method{as.matrix}{DNAbin}(x, \dots)
}
\item{digits}{the number of digits to print (3 by default).}
\item{check.names}{a logical specifying whether to check the rownames
before binding the columns (see details).}
+ \item{fill.with.gaps}{a logical indicating whether to keep all
+ possible individuals as indicating by the rownames, and eventually
+ filling the missing data with insertion gaps (ignored if
+ \code{check.names = FALSE}).}
+ \item{quiet}{a logical to switch off warning messages when some rows
+ 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).}
comparisons of sequences, as well as storing them in less memory
compared to the format used before \pkg{ape} 1.10.
- For \code{cbind}, if \code{"check.names = TRUE"}, the rownames of each
- matrix are checked, and the rows are reordered if necessary. If the
- rownames differ among matrices, an error occurs. If
- \code{"check.names = FALSE"}, the matrices are simply binded and the
- rownames of the first matrix are used.
+ For \code{cbind}, the default behaviour is to keep only individuals
+ (as indicated by the rownames) for which there are no missing data. If
+ \code{fill.with.gaps = TRUE}, a `complete' matrix is returned,
+ enventually with insertion gaps as missing data. If \code{check.names
+ = TRUE} (the default), the rownames of each matrix are checked, and
+ the rows are reordered if necessary. If \code{check.names = FALSE},
+ the matrices must all have the same number of rows, and are simply
+ binded; the rownames of the first matrix are used. See the examples.
\code{as.matrix} may be used to convert DNA sequences (of the same
length) stored in a list into a matrix while keeping the names and the
}
\references{
Paradis, E. (2007) A Bit-Level Coding Scheme for Nucleotides.
- \url{http://pbil.univ-lyon1.fr/R/ape/misc/BitLevelCodingScheme_20April2007.pdf}
+ \url{http://ape.mpl.ird.fr/misc/BitLevelCodingScheme_20April2007.pdf}
}
\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
\seealso{
### Just to show how distances could be influenced by sampling:
dist.dna(woodmouse[1:2, ])
dist.dna(woodmouse[1:3, ])
+### cbind and its options:
+x <- woodmouse[1:2, 1:5]
+y <- woodmouse[2:4, 6:10]
+as.character(cbind(x, y)) # gives warning
+as.character(cbind(x, y, fill.with.gaps = TRUE))
+\dontrun{
+as.character(cbind(x, y, check.names = FALSE)) # gives an error
+}
}
\keyword{manip}