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## dist.gene.R (2012-04-02)
## Pairwise Distances from Genetic Data
## Copyright 2002-2012 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
dist.gene <-
function(x, method = "pairwise", pairwise.deletion = FALSE,
variance = FALSE)
{
if (is.data.frame(x)) x <- as.matrix(x) else { # suggestion by Markus Schlegel
if (!is.matrix(x))
stop("'x' should be a matrix or a data.frame")
}
method <- match.arg(method, c("pairwise", "percentage"))
if (!pairwise.deletion) {
## delete the columns with at least one NA:
del <- apply(x, 2, function(xx) any(is.na(xx)))
x <- x[, !del]
}
n <- dim(x)
L <- n[2]
n <- n[1]
D <- double(n * (n - 1)/2)
if (pairwise.deletion) L <- D
k <- 1L
for (i in 1:(n - 1)) {
for (j in (i + 1):n) {
y <- x[i, ] != x[j, ]
if (pairwise.deletion) L[k] <- sum(!is.na(y))
D[k] <- sum(y, na.rm = TRUE)
k <- k + 1L
}
}
## L is either a single integer value if pairwise.deletion = FALSE,
## or a vector of integers if pairwise.deletion = TRUE
if (method == "percentage") D <- D/L
attr(D, "Size") <- n
attr(D, "Labels") <- dimnames(x)[[1]]
attr(D, "Diag") <- attr(D, "Upper") <- FALSE
attr(D, "call") <- match.call()
attr(D, "method") <- method
class(D) <- "dist"
if (variance) {
y <- if (method == "pairwise") L else 1
attr(D, "variance") <- D * (y - D)/L
}
D
}
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