tests/testthat/test_update.R

In thomas-fung/mpcmp: Mean-Parametrized Conway-Maxwell Poisson (COM-Poisson) Regression

context("Test Inference")
library(mpcmp)
data("takeoverbids")
data("sitophilus")
M.sit.full <- glm.cmp(
  formula = ninsect ~ extract,
  formula_nu = ~extract, data = sitophilus
)
M.bids.full <- glm.cmp(numbids ~ leglrest + rearest +
  finrest + whtknght +
  bidprem + insthold + size +
  sizesq + regulatn, data = takeoverbids)
M.attendance <- glm.cmp(daysabs ~ gender + math + prog, data = attendance)
M.bids.null <- update(M.bids.full, . ~ . - whtknght)

test_that("Test updating the mean regression formula", {
  expect_equal(round(M.bids.null$residual_deviance, 3), 131.838)
  expect_equal(length(M.bids.full$coef), 10)
  expect_equal(length(M.bids.null$coef), 9)
})

test_that("Test cmplrtest function", {
  expect_equal(
    capture_output_lines(cmplrtest(M.bids.full, M.bids.null))[5],
    "P-value:  0.000214 "
  )
})

test_that("Test LRTnu", {
  expect_equal(
    capture_output_lines(LRTnu(M.attendance))[8],
    "P-value: < 2e-16"
  )
})

test_that("Test updating the dispersion regression formula", {
  M.sit.null1 <- update(M.sit.full, formula_nu. = ~ . - extract)
  expect_equal(round(M.sit.null1$residual_deviance, 3), 41.408)
  expect_equal(length(M.sit.full$coefficients), 8)
  expect_equal(length(M.sit.null1$coefficients), 5)
  expect_equal(length(M.sit.null1$nu), 40)
  M.sit.null2 <- update(M.sit.full, formula_nu. = NULL)
  expect_equal(length(M.sit.null2$nu), 1)
  data(attendance)
  M.attendance.fix.nu <- glm.cmp(daysabs ~ gender + math + prog,
    data = attendance
  )
  M.attendance.vary.nu <- update(M.attendance.fix.nu,
    formula_nu. = ~ 1 + math
  )
  expect_equal(length(M.attendance.fix.nu$nu), 1)
  expect_equal(length(M.attendance.vary.nu$nu), 314)
})

test_that("Test the confint function", {
  expect_is(confint.cmp(M.attendance), class = "matrix")
  expect_equal(
    colnames(confint.cmp(M.attendance)),
    c("2.5 %", "97.5 %")
  )
  expect_equal(
    colnames(confint.cmp(M.attendance, parm = "math", level = 0.9)),
    c("5 %", "95 %")
  )
  expect_length(confint.cmp(M.attendance, parm = "math", level = 0.9), 2)
})