tests/testthat/test-likelihood-list.R

In pedprobr: Probability Computations on Pedigrees

test_that("pedlist with empty markers give likelihood 1", {
  x = list(singleton("NN"), nuclearPed(1)) #|> addMarker(alleles = 1:2, name = "m1")
  x = setMarkers(x, locusAttributes = list(alleles = 1:2, name = "m1"))
  expect_equal(likelihood(x, "m1"), 1)
})

test_that("pedlist with HW markers give correct likelihood", {
  p = 0.9; q= 1-p
  x = nuclearPed(1) |> addMarker('3'= "1/2", alleles = 1:2, afreq = c(p,q))
  y = singleton("nn") |> addMarker(nn = "1/1", alleles = 1:2, afreq = c(p,q))

  skip("likelihood-list tests need modifications")

  liks = likelihood(list(x,y), 1, total=FALSE)
  expect_equal(liks, c(2*p*q, p^2))

  liktot = likelihood(list(x,y), list(mx, my))
  expect_equal(liktot, 2*p*q * p^2)
})