tests/testthat/test-discord_regression.R

In discord: Functions for Discordant Kinship Modeling

get_p_value <- function(.results) {
  results_df <- summary(.results)
  results_df <- as.data.frame(results_df$coefficients)
  results_df <- cbind(names = rownames(results_df), results_df)
  rownames(results_df) <- NULL
  results_df[which(results_df$names == "y2_diff"), "Pr(>|t|)"]
}

signif_threshold <- 0.05

test_that("monozygotic significant is as expected", {

  set.seed(18)
  results <- discord_regression(mz_signif,
                                outcome = "y1",
                                predictors = "y2",
                                id = "id",
                                sex = NULL,
                                race = NULL,
                                pair_identifiers = c("_1", "_2"))

  expect_lt(object = get_p_value(results), expected = signif_threshold)


})

test_that("monozygotic nonsignificant is as expected", {

  set.seed(18)
  results <- discord_regression(mz_nonsignif,
                                 outcome = "y1",
                                 predictors = "y2",
                                 id = "id",
                                 sex = NULL,
                                 race = NULL,
                                 pair_identifiers = c("_1", "_2"))

  expect_gt(object = get_p_value(results), expected = signif_threshold)

})

test_that("dizygotic significant is as expected", {

  set.seed(18)
  results <- discord_regression(dz_signif,
                                outcome = "y1",
                                predictors = "y2",
                                id = "id",
                                sex = NULL,
                                race = NULL,
                                pair_identifiers = c("_1", "_2"))

  expect_lt(object = get_p_value(results), expected = signif_threshold)


})

test_that("dizygotic nonsignificant is as expected", {

  set.seed(18)
  results <- discord_regression(dz_nonsignif,
                                outcome = "y1",
                                predictors = "y2",
                                id = "id",
                                sex = NULL,
                                race = NULL,
                                pair_identifiers = c("_1", "_2"))

  expect_gt(object = get_p_value(results), expected = signif_threshold)

})


test_that("half siblings significant is as expected", {

  set.seed(18)
  results <- discord_regression(half_sibs_signif,
                                outcome = "y1",
                                predictors = "y2",
                                id = "id",
                                sex = NULL,
                                race = NULL,
                                pair_identifiers = c("_1", "_2"))

  expect_lt(object = get_p_value(results), expected = signif_threshold)


})

test_that("half siblings nonsignificant is as expected", {

  set.seed(18)
  results <- discord_regression(half_sibs_nonsignif,
                                outcome = "y1",
                                predictors = "y2",
                                id = "id",
                                sex = NULL,
                                race = NULL,
                                pair_identifiers = c("_1", "_2"))

  expect_gt(object = get_p_value(results), expected = signif_threshold)

})