Nothing
context("basic HMM functions in riself")
test_that("riself nalleles works", {
expect_equal(nalleles("riself"), 2)
})
test_that("riself check_geno works", {
expect_true(test_check_geno("riself", 0, TRUE, FALSE, FALSE, integer(0)))
expect_true(test_check_geno("riself", 1, TRUE, FALSE, FALSE, integer(0)))
expect_true(test_check_geno("riself", 2, TRUE, FALSE, FALSE, integer(0)))
expect_true(test_check_geno("riself", 1, FALSE, FALSE, FALSE, integer(0)))
expect_true(test_check_geno("riself", 2, FALSE, FALSE, FALSE, integer(0)))
expect_false(test_check_geno("riself", 3, TRUE, FALSE, FALSE, integer(0)))
expect_false(test_check_geno("riself", 0, FALSE, FALSE, FALSE, integer(0)))
expect_false(test_check_geno("riself", 3, FALSE, FALSE, FALSE, integer(0)))
})
test_that("riself ngen works", {
expect_equal(test_ngen("riself", FALSE), 2)
})
test_that("riself possible_gen works", {
expect_equal(test_possible_gen("riself", FALSE, FALSE, integer(0)), 1:2)
})
test_that("riself nrec works", {
expect_equal(test_nrec("riself", 1, 1, FALSE, FALSE, integer(0)), 0)
expect_equal(test_nrec("riself", 1, 2, FALSE, FALSE, integer(0)), 1)
expect_equal(test_nrec("riself", 2, 1, FALSE, FALSE, integer(0)), 1)
expect_equal(test_nrec("riself", 2, 2, FALSE, FALSE, integer(0)), 0)
})
test_that("riself init works", {
expect_equal(test_init("riself", 1, FALSE, FALSE, integer(0)), log(0.5))
expect_equal(test_init("riself", 2, FALSE, FALSE, integer(0)), log(0.5))
})
test_that("riself emit works", {
eps <- 0.01
expect_equal(test_emit("riself", 0, 1, eps, integer(0), FALSE, FALSE, integer(0)), 0)
expect_equal(test_emit("riself", 0, 2, eps, integer(0), FALSE, FALSE, integer(0)), 0)
expect_equal(test_emit("riself", 1, 1, eps, integer(0), FALSE, FALSE, integer(0)), log(1-eps))
expect_equal(test_emit("riself", 1, 2, eps, integer(0), FALSE, FALSE, integer(0)), log(eps))
expect_equal(test_emit("riself", 2, 1, eps, integer(0), FALSE, FALSE, integer(0)), log(eps))
expect_equal(test_emit("riself", 2, 2, eps, integer(0), FALSE, FALSE, integer(0)), log(1-eps))
# errors
expect_equal(test_emit("riself", 0, 0, eps, integer(0), FALSE, FALSE, integer(0)), 0)
expect_equal(test_emit("riself", 0, 3, eps, integer(0), FALSE, FALSE, integer(0)), 0)
expect_equal(test_emit("riself", 3, 1, eps, integer(0), FALSE, FALSE, integer(0)), 0)
})
test_that("riself step works", {
rf <- 0.01
RF <- 2*rf/(1+2*rf)
expect_equal(test_step("riself", 1, 1, rf, FALSE, FALSE, integer(0)), log(1-RF))
expect_equal(test_step("riself", 1, 2, rf, FALSE, FALSE, integer(0)), log(RF))
expect_equal(test_step("riself", 2, 1, rf, FALSE, FALSE, integer(0)), log(RF))
expect_equal(test_step("riself", 2, 2, rf, FALSE, FALSE, integer(0)), log(1-RF))
})
test_that("geno_names works", {
expect_equal(geno_names("riself", c("B", "R"), FALSE), c("BB", "RR"))
expect_equal(geno_names("riself", c("B", "R"), TRUE), c("BB", "RR"))
})
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