Nothing
context("basic HMM functions in 6-way doubled haploids")
test_that("dh6 n_gen, n_alleles work", {
expect_equal(nalleles("dh6"), 6)
expect_equal(test_ngen("dh6", FALSE), 6)
})
test_that("dh6 possible_gen work", {
expect_equal(test_possible_gen("dh6", FALSE, FALSE, 1:6), 1:6)
})
# FIX_ME: test check_geno
test_that("dh6 init work", {
expect_equal( sapply(1:6, function(i) test_init("dh6", i, FALSE, FALSE, 1:6)), log(rep(1/6, 6)) )
})
# FIX_ME: test emit
test_that("dh6 step works", {
for(rf in c(0.01, 0.1, 0.45)) {
for(ngen in c(3, 5)) {
expected <- matrix((5 - (5-6*rf)*(1-rf)^(ngen-2))/30, ncol=6, nrow=6)
diag(expected) <- (1 + (5-6*rf)*(1-rf)^(ngen-2))/6
result <- matrix(ncol=6, nrow=6)
for(i in 1:6) {
for(j in 1:6) {
result[i,j] <- test_step("dh6", i, j, rf, FALSE, FALSE, ngen)
}
}
expect_equal(result, log(expected))
}
}
})
test_that("dh6 geno_names work", {
expect_equal( geno_names("dh6", LETTERS[5:10], FALSE), paste0(LETTERS[5:10], LETTERS[5:10]) )
})
test_that("dh6 nrec work", {
x <- matrix(ncol=6, nrow=6)
x <- matrix(as.numeric(col(x) != row(x)), ncol=6)
res6 <- matrix(ncol=6, nrow=6)
for(i in 1:6) {
for(j in 1:6) {
res6[i,j] <- test_nrec("dh6", i, j, FALSE, FALSE, 3)
}
}
expect_equal( res6, x )
})
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