tests/testthat/test-boot.R

In broom: Convert Statistical Objects into Tidy Tibbles

skip_on_cran()

skip_if_not_installed("modeltests")
library(modeltests)

skip_if_not_installed("boot")
suppressPackageStartupMessages(library(boot))

test_that("boot tidier arguments", {
  check_arguments(tidy.boot)
})

test_that("tidy.boot for glms", {
  clotting <- data.frame(
    u = c(5, 10, 15, 20, 30, 40, 60, 80, 100),
    lot1 = c(118, 58, 42, 35, 27, 25, 21, 19, 18),
    lot2 = c(69, 35, 26, 21, 18, 16, 13, 12, 12)
  )

  g1 <- glm(lot2 ~ log(u), data = clotting, family = Gamma)

  boot_fun <- function(d, i) {
    stats::coef(stats::update(g1, data = d[i, ]))
  }

  bootres <- boot::boot(clotting, boot_fun, R = 100)
  td <- tidy(bootres, conf.int = TRUE)

  tdnorm <- tidy(bootres, conf.int = TRUE, conf.method = "norm")
  expect_false(any(is.na(tdnorm[[4]])))

  bootresw <- boot::boot(clotting, boot_fun, R = 100, weights = rep(1 / 9, 9))
  tdw <- tidy(bootresw, conf.int = TRUE)
  tdwe <- tidy(bootresw, conf.int = TRUE, exponentiate = TRUE)

  check_tidy_output(td)
  check_tidy_output(tdw)
  check_tidy_output(tdwe)

  check_dims(td, 2, 6)
  check_dims(tdw, 2, 7)
  check_dims(tdwe, 2, 7)

  expect_equal(exp(tdw$statistic), tdwe$statistic)
  expect_equal(exp(tdw$conf.low), tdwe$conf.low)
})

test_that("tidy.boot for time series", {
  lynx.fun <- function(tsb) {
    ar.fit <- ar(tsb, order.max = 25)
    c(ar.fit$order, mean(tsb), tsb)
  }

  lynx <- boot::tsboot(log(lynx), lynx.fun, R = 99, l = 20, orig.t = FALSE)
  td <- tidy(lynx)

  check_tidy_output(td)
  check_dims(td, expected_cols = 2)
})

test_that("dimensionality of CIs is correct (#1212)", {
  set.seed(123)
  d = data.frame(v1 = rnorm(100), v2 = rnorm(100))
  boot1 <- function(d, i) {
    d = d[i, ]
    c(mean(d$v1), mean(d$v2), cor(d$v1, d$v2))
  }
  boot2 <- function(d, i) {
    d = d[i, ]
    c(mean(d$v1), mean(d$v2))
  }
  boot3 <- function(d, i) {
    d = d[i, ]
    c(mean(d$v1))
  }

  r1 <- boot(d, boot1, 100)
  r2 <- boot(d, boot2, 100)
  r3 <- boot(d, boot3, 100)

  td1 <- tidy(r1, conf.int = T, conf.method = "norm")
  td2 <- tidy(r2, conf.int = T, conf.method = "norm")
  td3 <- tidy(r3, conf.int = T, conf.method = "norm")

  check_tidy_output(td1)
  check_tidy_output(td2)
  check_tidy_output(td3)
})