## ----echo = FALSE-------------------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", eval = TRUE)

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library(testflow)
cardio <- make_cardio_data()
test_one_sample(cardio, sbp_3m, mu = 140)

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test_two_groups(sbp_3m ~ sex, data = cardio)

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test_paired(sbp_3m ~ sbp_baseline, data = cardio)

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test_groups(sbp_3m ~ treatment, data = cardio)

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test_factorial(sbp_3m ~ sex * treatment, data = cardio)

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test_repeated(cardio, c(sbp_baseline, sbp_3m, sbp_6m), id = id)

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test_categorical(treatment ~ controlled_3m, data = cardio)

## -----------------------------------------------------------------------------
test_repeated_categorical(cardio, c(controlled_baseline, controlled_3m, controlled_6m))

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test_correlation(sbp_3m ~ age, data = cardio)

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test_linear_regression(sbp_3m ~ age + ldl, data = cardio)

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test_logistic_regression(controlled_3m ~ age + ldl, data = cardio)

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set.seed(1)
n <- 100
survival_dat <- tibble::tibble(
  time = rexp(n, 0.1),
  status = rbinom(n, 1, 0.7),
  arm = rep(c("control", "treatment"), each = n / 2),
  age = rnorm(n, 60, 10)
)
test_survival(Surv(time, status) ~ arm, data = survival_dat)

## -----------------------------------------------------------------------------
test_cox(Surv(time, status) ~ age + arm, data = survival_dat)

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set.seed(1)
diag_dat <- tibble::tibble(
  test = c(rep("positive", 55), rep("negative", 98)),
  reference = c(rep("positive", 45), rep("negative", 10), rep("positive", 8), rep("negative", 90))
)
test_diagnostic(diag_dat, test, reference)

## -----------------------------------------------------------------------------
roc_dat <- tibble::tibble(
  marker = c(rnorm(60, 2, 1), rnorm(50, 0, 1)),
  disease = c(rep("yes", 60), rep("no", 50))
)
test_roc(roc_dat, marker, disease)

## -----------------------------------------------------------------------------
agree_dat <- tibble::tibble(
  rater1 = sample(c("mild", "moderate", "severe"), 100, replace = TRUE),
  rater2 = sample(c("mild", "moderate", "severe"), 100, replace = TRUE)
)
test_agreement(agree_dat, rater1, rater2)

## -----------------------------------------------------------------------------
icc_dat <- tibble::tibble(
  rater1 = rnorm(30, 50, 10),
  rater2 = rnorm(30, 50, 10),
  rater3 = rnorm(30, 50, 10)
)
test_icc(icc_dat, c(rater1, rater2, rater3))

## -----------------------------------------------------------------------------
test_outliers(c(sbp_3m, ldl, crp), data = cardio)