bug fix in seg.sites + new option in base.freq

[ape.git] / R / DNA.R

diff --git a/R/DNA.R b/R/DNA.R
index dd9c60bb63ace9abfe1350c73664e365ed91ac36..919f0ecd88912e69ff85b2ee04181d122936eb7b 100644 (file)
--- a/R/DNA.R
+++ b/R/DNA.R
@@ -259,11 +259,11 @@ as.character.DNAbin <- function(x, ...)
     if (is.list(x)) lapply(x, f) else f(x)
 }
 
-base.freq <- function(x)
+base.freq <- function(x, freq = FALSE)
 {
     if (is.list(x)) x <- unlist(x)
     n <- length(x)
-    BF <- .C("BaseProportion", x, n, double(4),
+    BF <- .C("BaseProportion", x, n, double(4), freq,
              DUP = FALSE, NAOK = TRUE, PACKAGE = "ape")[[3]]
     names(BF) <- letters[c(1, 3, 7, 20)]
     BF