-## DNA.R (2011-03-21)
+## DNA.R (2012-02-14)
## Manipulations and Comparisons of DNA Sequences
-## Copyright 2002-2011 Emmanuel Paradis
+## Copyright 2002-2012 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
as.DNAbin <- function(x, ...) UseMethod("as.DNAbin")
._cs_ <- c("a", "g", "c", "t", "r", "m", "w", "s", "k",
- "y", "v", "h", "d", "b", "n", "-", "?")
+ "y", "v", "h", "d", "b", "n", "-", "?")
._bs_ <- c(136, 72, 40, 24, 192, 160, 144, 96, 80,
48, 224, 176, 208, 112, 240, 4, 2)
as.matrix = FALSE)
{
MODELS <- c("RAW", "JC69", "K80", "F81", "K81", "F84", "T92", "TN93",
- "GG95", "LOGDET", "BH87", "PARALIN", "N", "TS", "TV")
+ "GG95", "LOGDET", "BH87", "PARALIN", "N", "TS", "TV",
+ "INDEL", "INDELBLOCK")
imod <- pmatch(toupper(model), MODELS)
if (is.na(imod))
stop(paste("'model' must be one of:",
paste("\"", MODELS, "\"", sep = "", collapse = " ")))
if (imod == 11 && variance) {
- warning("computing variance temporarily not available for model BH87.")
+ warning("computing variance not available for model BH87")
variance <- FALSE
}
- if (gamma && imod %in% c(1, 5:7, 9:15)) {
+ if (gamma && imod %in% c(1, 5:7, 9:17)) {
warning(paste("gamma-correction not available for model", model))
gamma <- FALSE
}
n <- dim(x)
s <- n[2]
n <- n[1]
+
if (imod %in% c(4, 6:8)) {
BF <- if (is.null(base.freq)) base.freq(x) else base.freq
} else BF <- 0
+
+ if (imod %in% 16:17) pairwise.deletion <- TRUE
+
if (!pairwise.deletion) {
keep <- .C("GlobalDeletionDNA", x, n, s,
rep(1L, s), PACKAGE = "ape")[[4]]