final changes for ape 2.4 including removing mlphylo!

[ape.git] / man / DNAmodel.Rd

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-\name{DNAmodel}
-\alias{DNAmodel}
-\title{Defines Models of DNA Evolution}
-\usage{
-DNAmodel(model = "K80", partition = 1,
-         ncat.isv = 1, invar = FALSE,
-         equal.isv = TRUE, equal.invar = 1)
-}
-\arguments{
-  \item{model}{a vector of mode character giving the substition model.}
-  \item{partition}{a vector of integers defining the partitions for the
-    substition models (eventually recycled).}
-  \item{ncat.isv}{the number of categories in each partition.}
-  \item{invar}{a logical value specifying whether there are invariants.}
-  \item{equal.isv}{a logical value specifying whether the `alpha'
-    parameter is the same in all partitions; has no effet if \code{ncat
-      = 1} or if \code{partition = 1}.}
-  \item{equal.invar}{similar to the argument above but for the
-    proportion of invariants.}
-}
-\description{
-  This function defines a model of evolution for a set of DNA sequences
-  with possible partitions.
-}
-\details{
-  \code{partition} is recycled along the sequence: thus by default there
-  is a single partition. For instance, to partition a sequence of 1000
-  sites into two partitions of equal length, one will use
-  \code{partition = c(rep(1, 500), rep(2, 500))}. The partitions must be
-  numbered with a series of integers (1, 2, 3, ...). To partition the
-  codon positions, one could do \code{partition = c(1, 1, 2)}.
-
-  The substition models are the same in all partitions. Branch lengths
-  are the same in all partitions up to a multiplying coefficient (the
-  contrast parameter, denoted 'xi').
-
-  The substitution models must be among the followings: \code{"JC69"}
-  \code{"K80"}, \code{"F81"}, \code{"F84"}, \code{"HKY85"},
-  \code{"T92"}, \code{"TN93"}, and \code{"GTR"}. These models (except
-  HKY85 and GTR) are described in the help page of
-  \code{\link{dist.dna}}.
-
-  Inter-sites variation in substitution rates (ISV) is allowed by
-  specifying \code{ncat.isv} greater than one.
-}
-\note{
-  The result of this function is not intended to be used by the user,
-  but rather to be passed to \code{\link{mlphylo}}.
-}
-\value{
-  an object of class \code{"DNAmodel"} with components defined by the
-  arguments of the function call.
-}
-\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
-\seealso{
-  \code{\link{mlphylo}}, \code{\link{dist.dna}}
-}
-\examples{
-### the K80 model:
-mod <- DNAmodel()
-### the simplest substitution model:
-mod <- DNAmodel("JC69")
-### the classical GTR + G4 + I:
-mod <- DNAmodel("GTR", ncat.isv = 4, invar = TRUE)
-### codon-partitioning (with K80):
-mod <- DNAmodel(partition = c(1, 1, 2))
-### the same but adding inter-sites variation (the alpha parameter
-### is the same for both partitions):
-mod <- DNAmodel(partition = c(1, 1, 2), ncat.isv = 4)
-### ... and with different `alpha' for each partition:
-mod <- DNAmodel(partition = c(1, 1, 2), ncat.isv = 4, equal.isv = FALSE)
-}
-\keyword{models}