test_that("equal model is station/revers only for equal freqs", {
mutmat = mutationMatrix(alleles = 1:3, model = "equal", rate = 0.1)
expect_false(isStationary(mutmat, c(0.2, 0.3, 0.5)))
expect_false(isReversible(mutmat, c(0.2, 0.3, 0.5)))
expect_true(isStationary(mutmat, c(1,1,1)/3))
expect_true(isReversible(mutmat, c(1,1,1)/3))
})
test_that("proportial model is stationary and reversible", {
afreq = c(0.2, 0.3, 0.5)
mutmat = mutationMatrix(alleles = 1:3, model = "prop", rate = 0.1, afreq = afreq)
expect_true(isStationary(mutmat, afreq))
expect_true(isReversible(mutmat, afreq))
})
test_that("random model 3*3 is not stationary (nor reversible)", {
afreq = c(0.2, 0.3, 0.5)
mutmat = mutationMatrix(alleles = 1:3, model = "random", rate = 0.1)
expect_false(isStationary(mutmat, afreq))
expect_false(isReversible(mutmat, afreq))
})
test_that("equal model is always lumpable", {
mutmat = mutationMatrix(alleles = 1:4, model = "equal", rate = 0.1)
expect_true(isLumpable(mutmat, lump = 1:2))
expect_true(isLumpable(mutmat, lump = c(2,4)))
expect_true(isLumpable(mutmat, lump = c(1:2,4)))
})
test_that("proportional model is always lumpable", {
afreq = c(0.2, 0.3, 0.5)
mutmat = mutationMatrix(alleles = 1:3, model = "prop", rate = 0.1, afreq = afreq)
expect_true(isLumpable(mutmat, lump = 1:2))
expect_true(isLumpable(mutmat, lump = c(1,3)))
})
test_that("isStationary and isReversible works with full models", {
afreq = c(0.5, 0.5)
m1 = mutationMatrix("eq", alleles = 1:2, rate = 0.1, afreq = afreq)
m2 = mutationMatrix("random", alleles = 1:2, afreq = afreq)
expect_true(isStationary(mutationModel(list(female = m1, male = m1))))
expect_false(isStationary(mutationModel(list(female = m1, male = m2))))
expect_false(isStationary(mutationModel(list(female = m2, male = m2))))
expect_true(isReversible(mutationModel(list(female = m1, male = m1))))
expect_false(isReversible(mutationModel(list(female = m1, male = m2))))
expect_false(isReversible(mutationModel(list(female = m2, male = m2))))
stb = stabilize(mutationModel(list(female = m1, male = m2)))
expect_true(isStationary(stb))
})
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