Nothing
library("TreeTools", quietly = TRUE)
test_that("MappingQuality() fails gracefully", {
expect_error(ProjectionQuality(dist(1:10), dist(1:5)),
"have the same dimensions")
})
test_that("Trustworthiness range", {
for (N in c(5, 16, 50)) {
k <- floor(seq(1, (N - 1) / 2, length.out = 5))
UkMax <- pmin(k, N - k)
maxVal <- N * ((UkMax * (N - k - 1)) - .Triangle(UkMax - 1))
expect_equal(maxVal, (N * k * (2 * N - 3 * k - 1)) / 2)
}
trees <- as.phylo(1:12, 10)
dists <- ClusteringInfoDist(trees)
mapped <- dist(cmdscale(dists, k = 6))
r <- apply(as.matrix(dists), 2, .Bercow) - 1
diag(r) <- NA
rHat <- apply(as.matrix(mapped), 2, .Bercow) - 1
diag(r) <- NA
rPrime <- 12 - r
.Trustworthiness <- function (x, y, k) {
MappingQuality(x, y, k)[["Trustworthiness"]]
}
expect_warning(expect_equal(.Trustworthiness(r, r, k = 12), NaN),
"All points are nearest neighbours")
expect_equal(.Trustworthiness(r, r, k = 1), 1)
expect_equal(.Trustworthiness(r, r, k = 5), 1)
expect_equal(.Trustworthiness(r, r, k = 10), 1)
expect_lte(.Trustworthiness(r, rHat, k = 1), 1)
expect_lte(.Trustworthiness(r, rHat, k = 5), 1)
expect_lte(.Trustworthiness(r, rHat, k = 10), 1)
expect_gt(.Trustworthiness(r, rHat, k = 1), 0)
expect_gt(.Trustworthiness(r, rHat, k = 5), 0)
expect_gt(.Trustworthiness(r, rHat, k = 10), 0)
expect_equal(.TrustSum(r, rPrime, 12, k = 1), .MMax(12, 1))
expect_equal(.TrustSum(r, rPrime, 12, k = 5), .MMax(12, 5))
expect_equal(.TrustSum(r, rPrime, 12, k = 10), .MMax(12, 10))
})
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