-## DNA.R (2012-06-19)
+## DNA.R (2012-09-13)
## Manipulations and Comparisons of DNA Sequences
{
if (is.list(x)) x <- unlist(x)
n <- length(x)
- BF <-.C("BaseProportion", x, n, double(17),
+ BF <-.C("BaseProportion", x, as.integer(n), double(17),
DUP = FALSE, NAOK = TRUE, PACKAGE = "ape")[[3]]
names(BF) <- c("a", "c", "g", "t", "r", "m", "w", "s",
"k", "y", "v", "h", "d", "b", "n", "-", "?")
n <- n[1]
}
if (n == 1) return(integer(0))
- ans <- .C("SegSites", x, n, s, integer(s),
- DUP = FALSE, NAOK = TRUE, PACKAGE = "ape")
+ ans <- .C("SegSites", x, as.integer(n), as.integer(s),
+ integer(s), DUP = FALSE, NAOK = TRUE, PACKAGE = "ape")
which(as.logical(ans[[4]]))
}
var <- if (variance) double(Ndist) else 0
if (!gamma) gamma <- alpha <- 0
else alpha <- gamma <- 1
- d <- .C("dist_dna", x, n, s, imod, double(Ndist), BF,
- as.integer(pairwise.deletion), as.integer(variance),
- var, as.integer(gamma), alpha, DUP = FALSE, NAOK = TRUE,
- PACKAGE = "ape")
+ d <- .C("dist_dna", x, as.integer(n), as.integer(s), imod,
+ double(Ndist), BF, as.integer(pairwise.deletion),
+ as.integer(variance), var, as.integer(gamma),
+ alpha, DUP = FALSE, NAOK = TRUE, PACKAGE = "ape")
if (variance) var <- d[[9]]
d <- d[[5]]
if (imod == 11) {