3 \title{Defines Models of DNA Evolution}
5 DNAmodel(model = "K80", partition = 1,
6 ncat.isv = 1, invar = FALSE,
7 equal.isv = TRUE, equal.invar = 1)
10 \item{model}{a vector of mode character giving the substition model.}
11 \item{partition}{a vector of integers defining the partitions for the
12 substition models (eventually recycled).}
13 \item{ncat.isv}{the number of categories in each partition.}
14 \item{invar}{a logical value specifying whether there are invariants.}
15 \item{equal.isv}{a logical value specifying whether the `alpha'
16 parameter is the same in all partitions; has no effet if \code{ncat
17 = 1} or if \code{partition = 1}.}
18 \item{equal.invar}{similar to the argument above but for the
19 proportion of invariants.}
22 This function defines a model of evolution for a set of DNA sequences
23 with possible partitions.
26 \code{partition} is recycled along the sequence: thus by default there
27 is a single partition. For instance, to partition a sequence of 1000
28 sites into two partitions of equal length, one will use
29 \code{partition = c(rep(1, 500), rep(2, 500))}. The partitions must be
30 numbered with a series of integers (1, 2, 3, ...). To partition the
31 codon positions, one could do \code{partition = c(1, 1, 2)}.
33 The substition models are the same in all partitions. Branch lengths
34 are the same in all partitions up to a multiplying coefficient (the
35 contrast parameter, denoted 'xi').
37 The substitution models must be among the followings: \code{"JC69"}
38 \code{"K80"}, \code{"F81"}, \code{"F84"}, \code{"HKY85"},
39 \code{"T92"}, \code{"TN93"}, and \code{"GTR"}. These models (except
40 HKY85 and GTR) are described in the help page of
41 \code{\link{dist.dna}}.
43 Inter-sites variation in substitution rates (ISV) is allowed by
44 specifying \code{ncat.isv} greater than one.
47 The result of this function is not intended to be used by the user,
48 but rather to be passed to \code{\link{mlphylo}}.
51 an object of class \code{"DNAmodel"} with components defined by the
52 arguments of the function call.
54 \author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
56 \code{\link{mlphylo}}, \code{\link{dist.dna}}
61 ### the simplest substitution model:
62 mod <- DNAmodel("JC69")
63 ### the classical GTR + G4 + I:
64 mod <- DNAmodel("GTR", ncat.isv = 4, invar = TRUE)
65 ### codon-partitioning (with K80):
66 mod <- DNAmodel(partition = c(1, 1, 2))
67 ### the same but adding inter-sites variation (the alpha parameter
68 ### is the same for both partitions):
69 mod <- DNAmodel(partition = c(1, 1, 2), ncat.isv = 4)
70 ### ... and with different `alpha' for each partition:
71 mod <- DNAmodel(partition = c(1, 1, 2), ncat.isv = 4, equal.isv = FALSE)