tests/testthat/test-fixParents.R

In sinnweja/kinship2: Pedigree Functions

test_that("fixParents works with number", {
  materdf <- data.frame(id = 1:5, momid = c(0, 1, 1, 2, 2), sex = 2)

  materdf$dadid <- materdf$momid * 100
  expect_error(with(materdf, pedigree(id, dadid, momid, sex)))
  peddf <- with(materdf, fixParents(id, dadid, momid, sex))
  expect_no_error(with(peddf, pedigree(id, dadid, momid, sex)))
})

test_that("fixParrents works with character", {
  test1char <- data.frame(
    id = paste("fam", 101:111, sep = ""),
    sex = c("male", "female")[c(1, 2, 1, 2, 1, 1, 2, 2, 1, 2, 1)],
    father = c(0, 0, "fam101", "fam101", "fam101", 0, 0, "fam106", "fam106", "fam106", "fam109"),
    mother = c(0, 0, "fam102", "fam102", "fam102", 0, 0, "fam107", "fam107", "fam107", "fam112")
  )
  expect_error(with(test1char, pedigree(id, father, mother, sex, missid = "0")))
  test1newmom <- with(test1char, fixParents(id, father, mother, sex, missid = "0"))
  expect_no_error(with(test1newmom, pedigree(id, dadid, momid, sex, missid = "0")))
})

test_that("fixParrents works with sex errors", {
  data(sample.ped)
  datped2 <- sample.ped[sample.ped$ped %in% 2, ]
  datped2[datped2$id %in% 203, "sex"] <- 2
  datped2 <- datped2[-which(datped2$id %in% 209), ]

  ## this gets an error
  expect_error(with(datped2, pedigree(id, father, mother, sex)))

  ## This fix the error
  fixped2 <- with(datped2, fixParents(id, father, mother, sex))
  expect_no_error(with(fixped2, pedigree(id, dadid, momid, sex)))
})