BOTHlabels(... hozir = TRUE)

[ape.git] / R / DNA.R

diff --git a/R/DNA.R b/R/DNA.R
index 8b016caad40dc9acb8014c4889bee52fa38c2bf0..1f4f5d6ae78e8367635651d4507a126594a581f6 100644 (file)
--- a/R/DNA.R
+++ b/R/DNA.R
@@ -1,4 +1,4 @@
-## DNA.R (2010-07-13)
+## DNA.R (2010-07-14)
 
 ##   Manipulations and Comparisons of DNA Sequences
 
@@ -313,7 +313,7 @@ dist.dna <- function(x, model = "K80", variance = FALSE, gamma = FALSE,
                      as.matrix = FALSE)
 {
     MODELS <- c("RAW", "JC69", "K80", "F81", "K81", "F84", "T92", "TN93",
-                "GG95", "LOGDET", "BH87", "PARALIN", "N")
+                "GG95", "LOGDET", "BH87", "PARALIN", "N", "TS", "TV")
     imod <- pmatch(toupper(model), MODELS)
     if (is.na(imod))
         stop(paste("'model' must be one of:",
@@ -322,7 +322,7 @@ dist.dna <- function(x, model = "K80", variance = FALSE, gamma = FALSE,
         warning("computing variance temporarily not available for model BH87.")
         variance <- FALSE
     }
-    if (gamma && imod %in% c(1, 5:7, 9:12)) {
+    if (gamma && imod %in% c(1, 5:7, 9:15)) {
         warning(paste("gamma-correction not available for model", model))
         gamma <- FALSE
     }
@@ -331,7 +331,9 @@ dist.dna <- function(x, model = "K80", variance = FALSE, gamma = FALSE,
     n <- dim(x)
     s <- n[2]
     n <- n[1]
-    BF <- if (is.null(base.freq)) base.freq(x) else base.freq
+    if (imod %in% c(4, 6:8)) {
+        BF <- if (is.null(base.freq)) base.freq(x) else base.freq
+    } else BF <- 0
     if (!pairwise.deletion) {
         keep <- .C("GlobalDeletionDNA", x, n, s,
                    rep(1L, s), PACKAGE = "ape")[[4]]