tests/testthat/test2.R

In ratesci: Confidence Intervals for Comparisons of Binomial or Poisson Rates

library(ratesci)
context("p-values")

n1 <- 40
n2 <- 20
xs <- expand.grid(0:n1, 0:n2)
x1 <- xs[, 1]
x2 <- xs[, 2]

for (skew in c(TRUE, FALSE)) {
  test_that("p-values consistent with confidence interval", {
    expect_equal(
      scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
              contrast = "RD", precis = 10)$estimates[, "Lower"] > 0 |
        scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
                contrast = "RD", precis = 10)$estimates[, "Upper"] < 0,
      scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
              contrast = "RD", precis = 10)$pval[, "pval2sided"] < 0.05
    )
    expect_equal(
      scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
              contrast = "RD", precis = 10)$estimates[, "Lower"] > 0,
      scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
              contrast = "RD", precis = 10)$pval[, "pval_right"] < 0.025
    )
    expect_equal(
      scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
              contrast = "RD", precis = 10)$estimates[, "Upper"] < 0,
      scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
              contrast = "RD", precis = 10)$pval[, "pval_left"] < 0.025
    )
    expect_equal(
      scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
              contrast = "RR", distrib = "poi", precis = 10)$estimates[, "Lower"] > 1 |
        scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
                contrast = "RR", distrib = "poi", precis = 10)$estimates[, "Upper"] < 1,
      scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
              contrast = "RR", distrib = "poi", precis = 10)$pval[, "pval2sided"] < 0.05
    )
    expect_equal(
      scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
              contrast = "RR", distrib = "poi", precis = 10, theta0 = 2
              )$estimates[, "Lower"] > 2,
      scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
              contrast = "RR", distrib = "poi", precis = 10, theta0 = 2
              )$pval[, "pval_right"] < 0.025
    )
    expect_equal(
      scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
              contrast = "RR", distrib = "poi", precis = 10, theta0 = 2
              )$estimates[, "Upper"] < 2,
      scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
              contrast = "RR", distrib = "poi", precis = 10, theta0 = 2
              )$pval[, "pval_left"] < 0.025
    )
    expect_equal(
      scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
              contrast = "OR", precis = 10)$estimates[, "Lower"] > 1 |
        scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
                contrast = "OR", precis = 10)$estimates[, "Upper"] < 1,
      scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
              contrast = "OR", precis = 10)$pval[, "pval2sided"] < 0.05
    )
    expect_equal(
      scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
              contrast = "OR", precis = 10)$estimates[, "Lower"] > 1,
      scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
              contrast = "OR", precis = 10)$pval[, "pval_right"] < 0.025
    )
    expect_equal(
      scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
              contrast = "OR", precis = 10)$estimates[, "Upper"] < 1,
      scoreci(x1 = x1, n1 = n1, x2 = x2, n2 = n2, skew = skew,
              contrast = "OR", precis = 10)$pval[, "pval_left"] < 0.025
    )
  })
}


n <- 10
combos <- NULL
for (a in 0:n) {
  for (b in 0:(n - a)) {
    for (c in 0:(n - a - b)) {
      for (d in 0:(n - a - b - c)) {
        combos <- rbind(combos, c(a = a, b = b, c = c, d = d))
      }
    }
  }
}

test_that("p-values consistent with paired confidence interval", {
  expect_equal(
    (sapply(1:dim(combos)[1], function(i) pairbinci(
      x = combos[i, ], contrast = "RD")$estimates[1] > 0)),
    (sapply(1:dim(combos)[1], function(i) pairbinci(
      x = combos[i, ], contrast = "RD")$pval[, "pval_right"] < 0.025))
  )
})
for (contrast in c("RR", "OR")) {
  test_that("p-values consistent with paired confidence interval", {
    expect_equal(
      (sapply(1:dim(combos)[1], function(i) pairbinci(
        x = combos[i, ], contrast = contrast, method_OR = "SCAS"
        )$estimates[1] > 1)),
      (sapply(1:dim(combos)[1], function(i) pairbinci(
        x = combos[i, ], contrast = contrast, method_OR = "SCAS"
        )$pval[, "pval_right"] < 0.025))
    )
  })
}