Nothing
library(sped)
library(pooh)
data(thompson)
individuals <- sort(unique(thompson))
foo <- kinship(individuals, thompson)
individuals.too <- rownames(foo)
setequal(individuals, individuals.too)
founders <- setdiff(individuals, thompson[ , "ind"])
bar <- foo
for (i in 1:nrow(bar))
for (j in 1:ncol(bar)) {
baz <- double(length(founders))
for (k in seq(along = founders)) {
g <- 1
names(g) <- founders[k]
baz[k] <- descent(individuals.too[c(i, j)], thompson, g)
}
bar[i, j] <- bar[j, i] <- 2 * sum(baz)
}
all.equal(foo, bar)
qux <- kinship(c("U", "V", "Q", "R", "W"), thompson)
idx <- match(rownames(qux), rownames(foo))
all.equal(foo[idx, idx], qux)
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