61 lines
2.1 KiB
R
61 lines
2.1 KiB
R
context("Spatial mixture")
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test_that("functions work with basic input", {
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q <- c(1, 3, 0, 2)
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w <- array(c(1, 3, 2, 4, 5, 7, 6, 8), c(2, 2, 2))
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e <- computeCounts(q, 4, 5, w)
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r <- matrix(c(5, 3, 3, 6, 4, 4, 7, 9, 1), 3)
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t <- 1:5
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y <- c(4, 3, 1, 4, 8)
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expect_equal(e$cliqcounts, t(c(1, 1, 1, 0, 0)))
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expect_equal(e$sepcounts, t(c(0, 0, 0, 1, 0)))
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expect_equal(computeDiffInCliqCounts(r, 4), matrix(c(0, 1, 1)))
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expect_equal(computeDiffInCliqCounts(r, 3), matrix(c(0, 1, 1)))
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expect_equal(computeDiffInCliqCounts(r, 5), matrix(c(1, 0, 0)))
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expect_equal(computeDiffInCliqCounts(r, 0), matrix(c(0, 0, 0)))
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expect_equal(mysetdiff(t, y), c(2, 5))
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})
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test_that("testaaKoordinaatit works as expected", {
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m1 <- matrix(c(11.1, 22.2, 33.3, 44.4), 2, byrow = TRUE)
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m2 <- matrix(c(11.1, 22.2, 33.3, 44.4, 55.5, 66.6), byrow = TRUE)
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m3 <- matrix(c(11, 22.2, 11, 44.4, 11, 66.6), ncol = 2, byrow = TRUE)
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expect_equal(
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testaaKoordinaatit(2, m1), list("viallinen" = 0, "coordinates" = m1)
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)
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expect_warning(testaaKoordinaatit(2, m2), "Wrong coordinates dimension!")
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expect_equal(
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{set.seed(5676402); testaaKoordinaatit(3, m3, FALSE)},
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list(
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"viallinen" = 0,
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"coordinates" = matrix(
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c(11.99, 22.2, 11.50, 44.4, 11.00, 66.6), ncol = 2, byrow = TRUE)
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)
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)
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})
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test_that("lakseKlitik() and subfunctions produce expected output", {
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# TODO: test elim_order()
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# TODO: test triangulate()
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# TODO: test neighbors()
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# TODO: test myintersect()
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# TODO: test mysubset()
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# TODO: test findCliques()
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# TODO: test cliques_to_jtree()
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# TODO: test minimum_spanning_tree()
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# TODO: test myunion()
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# TODO: test argmin()
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# TODO: test mysize()
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# TODO: test ind2subv()
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# TODO: test myisvector()
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# TODO: ... and anythin left from findCliques.m
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# TODO: test lakseKlitik()
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})
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test_that("testFastaData() produces same output as on MATLAB", {
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msa <- system.file("ext", "seqs.fa", package = "rBAPS")
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test_msa <- testFastaData(msa)
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expect_equal(test_msa$ninds, 515)
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expect_equal(dim(test_msa$data), c(515, 745))
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expect_named(table(test_msa$data), c("-9", as.character(1:515)))
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})
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