tests/testthat/test_checks.R

In mcmcsae: Markov Chain Monte Carlo Small Area Estimation

context("Input checks")

# for reproducibility, even across platforms:
set.seed(1, kind="Mersenne-Twister", normal.kind="Inversion")

n <- 1000L
dat <- data.frame(
  x = rnorm(n),
  z = runif(n)
)
dat$y <- rnorm(n)

test_that("missing values in y are flagged", {
  dat$y[sample.int(n, 2L)] <- NA
  expect_error(create_sampler(y ~ x + z, data=dat), "2 missing")
  expect_error(create_sampler(y ~ x + z, family="binomial", data=dat), "2 missing")
})

test_that("range for binomial response is checked", {
  dat$y <- rnorm(n)
  expect_error(sampler <- create_sampler(y ~ x + z, data=dat, family="binomial"), "range")
  expect_error(create_sampler(y ~ x + z, data=dat, family="binomial", ny=100), "range")
})

test_that("logistic binomial model works for non-integral data", {
  dat$y <- runif(n)
  sampler <- create_sampler(y ~ 1, data=dat, family="binomial")
  sim <- MCMCsim(sampler, n.chain=2, burnin=100, n.iter=300, verbose=FALSE)
  expect_equal(summary(sim$reg1)[, "Mean"], 0, tolerance=0.2)
})

test_that("for negative binomial and Poisson families negative response values are flagged", {
  dat$y <- rnorm(n)
  expect_error(create_sampler(y ~ x + z, data=dat, family="negbinomial"), "negative")
  expect_error(create_sampler(y ~ x + z, data=dat, family="poisson"), "negative")
})

test_that("response variable for multinomial family is checked", {
  dat$y <- rnorm(n)
  expect_error(create_sampler(y ~ x + z, data=dat, family="multinomial"))
  dat$y <- cbind(rbinom(n, 2, prob=0.2), rbinom(n, 2, prob=0.2), rep(1, n))
  sampler <- create_sampler(y ~ x + z, data=dat, family="multinomial")
  expect_identical(sampler$Km1, 2L)
  dat$y[1, 1] <- -1L
  expect_error(create_sampler(y ~ x + z, data=dat, family="multinomial"), "negative")
})

test_that("zeroes are flagged for gamma family", {
  dat$y <- rgamma(n, shape=1e-4)  # this yields many 0s due to numerical underflow
  expect_error(create_sampler(y ~ 1, data=dat, family="gamma"), "strictly positive")
})