removing files that have moved to pegas

[ape.git] / R / heterozygosity.R

diff --git a/R/heterozygosity.R b/R/heterozygosity.R
deleted file mode 100644 (file)
index 18dd0d3..0000000
--- a/R/heterozygosity.R
+++ /dev/null
@@ -1,35 +0,0 @@
-## heterozygosity.R (2002-08-28)
-
-##   Heterozygosity at a Locus Using Gene Frequencies
-
-## Copyright 2002 Emmanuel Paradis
-
-## This file is part of the R-package `ape'.
-## See the file ../COPYING for licensing issues.
-
-heterozygosity <- function(x, variance = FALSE)
-{
-    if (!is.factor(x)) {
-        if (is.numeric(x)) {
-            n <- sum(x)
-            k <- length(x)
-            freq <- x/n
-        }
-        else x <- factor(x)
-    }
-    if (is.factor(x)) { # ne pas remplacer par `else'...
-        n <- length(x)
-        k <- nlevels(x)
-        freq <- table(x)/n
-    }
-    sp2 <- sum(freq^2)
-    H <- n * (1 - sp2) / (n - 1)
-    if (variance) {
-        sp3 <- sum(freq^3)
-        var.H <- 2 * (2 * (n - 2) * (sp3 - sp2^2) + sp2 - sp2^2) / (n * (n - 1))
-        return(c(H, var.H))
-    }
-    else return(H)
-}
-
-H <- function(x, variance = FALSE) heterozygosity(x, variance)