# Setup -------------------------------------------------------------------

statistics <- list()

# t.test() ----------------------------------------------------------------

sleep_wide <- reshape(
  sleep,
  direction = "wide",
  idvar = "ID",
  timevar = "group",
  sep = "_"
)

t_test_one_sample <- t.test(extra ~ 1, data = sleep)
t_test_two_sample <- t.test(extra ~ group, data = sleep, var.equal = TRUE)
t_test_welch <- t.test(extra ~ group, data = sleep)
t_test_paired <- t.test(sleep_wide$extra_1, sleep_wide$extra_2, paired = TRUE)

statistics <- statistics |>
  add_stats(t_test_one_sample) |>
  add_stats(t_test_two_sample) |>
  add_stats(t_test_welch) |>
  add_stats(t_test_paired)

t_test_one_sample
t_test_two_sample
t_test_welch
t_test_paired

# cor.test() --------------------------------------------------------------

x <- c(44.4, 45.9, 41.9, 53.3, 44.7, 44.1, 50.7, 45.2, 60.1)
y <- c(2.6, 3.1, 2.5, 5.0, 3.6, 4.0, 5.2, 2.8, 3.8)

correlation_pearson <- cor.test(x, y, method = "pearson")
correlation_kendall <- cor.test(x, y, method = "kendall")
correlation_spearman <- cor.test(x, y, method = "spearman")

statistics <- statistics |>
  add_stats(correlation_pearson) |>
  add_stats(correlation_kendall) |>
  add_stats(correlation_spearman)

correlation_pearson
correlation_kendall
correlation_spearman

# chisq.test() ------------------------------------------------------------

M <- as.table(rbind(c(762, 327, 468), c(484, 239, 477)))
dimnames(M) <- list(gender = c("F", "M"), party = c(
  "Democrat", "Independent",
  "Republican"
))
x <- matrix(c(12, 5, 7, 7), ncol = 2)
y <- c(A = 20, B = 15, C = 25)

chi_squared <- chisq.test(M)
chi_squared_yates <- chisq.test(x)
chi_squared_prob <- chisq.test(y)

statistics <- statistics |>
  add_stats(chi_squared) |>
  add_stats(chi_squared_yates) |>
  add_stats(chi_squared_prob)

chi_squared
chi_squared_yates
chi_squared_prob

# prop.test() -------------------------------------------------------------

set.seed(1)

heads <- rbinom(1, size = 100, prob = .5)
smokers <- c(83, 90, 129, 70)
patients <- c(86, 93, 136, 82)

prop_test <- prop.test(heads, 100)
prop_test_correct <- prop.test(heads, 100, correct = FALSE)
prop_test_smokers <- prop.test(smokers, patients)

statistics <- statistics |>
  add_stats(prop_test) |>
  add_stats(prop_test_correct) |>
  add_stats(prop_test_smokers)

prop_test
prop_test_correct
prop_test_smokers

# prop.trend.test()  ------------------------------------------------------

prop_trend_test <- prop.trend.test(smokers, patients)
prop_trend_test_scores <- prop.trend.test(smokers, patients, c(0, 0, 0, 1))

statistics <- statistics |>
  add_stats(prop_trend_test) |>
  add_stats(prop_trend_test_scores)

prop_trend_test
prop_trend_test_scores

# wilcox.test() -----------------------------------------------------------

x <- c(1.83, 0.50, 1.62, 2.48, 1.68, 1.88, 1.55, 3.06, 1.30)
y <- c(0.878, 0.647, 0.598, 2.05, 1.06, 1.29, 1.06, 3.14, 1.29)

wilcoxon_signed_rank <- wilcox.test(x, y,
  paired = TRUE,
  alternative = "greater"
)
wilcoxon_rank_sum_continuity <- wilcox.test(Ozone ~ Month,
  data = airquality,
  subset = Month %in% c(5, 8)
)

x <- c(0.80, 0.83, 1.89, 1.04, 1.45, 1.38, 1.91, 1.64, 0.73, 1.46)
y <- c(1.15, 0.88, 0.90, 0.74, 1.21)

wilcoxon_rank_sum <- wilcox.test(x, y,
  alternative = "greater", exact = FALSE,
  correct = FALSE
)
wilcoxon_rank_sum_conf <- wilcox.test(x, y, conf.int = TRUE, conf.level = .9)

statistics <- statistics |>
  add_stats(wilcoxon_signed_rank) |>
  add_stats(wilcoxon_rank_sum_continuity) |>
  add_stats(wilcoxon_rank_sum) |>
  add_stats(wilcoxon_rank_sum_conf)

wilcoxon_signed_rank
wilcoxon_rank_sum_continuity
wilcoxon_rank_sum
wilcoxon_rank_sum_conf

# kruskal.test() ----------------------------------------------------------

x <- c(2.9, 3.0, 2.5, 2.6, 3.2)
y <- c(3.8, 2.7, 4.0, 2.4)
z <- c(2.8, 3.4, 3.7, 2.2, 2.0)

kruskal <- kruskal.test(list(x, y, z))
kruskal_formula <- kruskal.test(Ozone ~ Month, data = airquality)

statistics <- statistics |>
  add_stats(kruskal) |>
  add_stats(kruskal_formula)

kruskal
kruskal_formula

# fisher.test() -----------------------------------------------------------

set.seed(2015)

TeaTasting <- matrix(
  data = c(3, 1, 1, 3),
  nrow = 2,
  dimnames = list(Guess = c("Milk", "Tea"), Truth = c("Milk", "Tea"))
)

Convictions <- matrix(
  data = c(2, 10, 15, 3),
  nrow = 2,
  dimnames = list(
    c("Dizygotic", "Monozygotic"),
    c("Convicted", "Not convicted")
  )
)

Job <- matrix(
  data = c(1, 2, 1, 0, 3, 3, 6, 1, 10, 10, 14, 9, 6, 7, 12, 11),
  nrow = 4,
  ncol = 4,
  dimnames = list(
    income = c("< 15k", "15-25k", "25-40k", "> 40k"),
    satisfaction = c("VeryD", "LittleD", "ModerateS", "VeryS")
  )
)

MP6 <- rbind(
  c(1, 2, 2, 1, 1, 0, 1),
  c(2, 0, 0, 2, 3, 0, 0),
  c(0, 1, 1, 1, 2, 7, 3),
  c(1, 1, 2, 0, 0, 0, 1),
  c(0, 1, 1, 1, 1, 0, 0)
)

fisher_test <- fisher.test(TeaTasting, alternative = "greater")
fisher_test_no_CI <- fisher.test(Convictions, conf.int = FALSE)
fisher_test_r_by_c <- fisher.test(Job)
fisher_test_simulated_p <- fisher.test(Job, simulate.p.value = TRUE, B = 1e5)
fisher_test_hybrid <- fisher.test(MP6, hybrid = TRUE)

statistics <- statistics |>
  add_stats(fisher_test) |>
  add_stats(fisher_test_no_CI) |>
  add_stats(fisher_test_r_by_c) |>
  add_stats(fisher_test_simulated_p) |>
  add_stats(fisher_test_hybrid)

fisher_test
fisher_test_no_CI
fisher_test_r_by_c
fisher_test_simulated_p
fisher_test_hybrid

# ks.test() ---------------------------------------------------------------

set.seed(1)

x <- rnorm(50)
y <- runif(30)

ks_test_two <- ks.test(x, y)
ks_test_one <- ks.test(x + 2, "pgamma", 3, 2)
ks_test_inexact <- ks.test(x + 2, "pgamma", 3, 2, exact = FALSE)
ks_test_greater <- ks.test(x + 2, "pgamma", 3, 2, alternative = "greater")

statistics <- statistics |>
  add_stats(ks_test_two) |>
  add_stats(ks_test_one) |>
  add_stats(ks_test_inexact) |>
  add_stats(ks_test_greater)

ks_test_two
ks_test_one
ks_test_inexact
ks_test_greater

# oneway.test() -----------------------------------------------------------

oneway_test <- oneway.test(extra ~ group, data = sleep)
oneway_test_equal_var <- oneway.test(extra ~ group,
  data = sleep,
  var.equal = TRUE
)

statistics <- statistics |>
  add_stats(oneway_test) |>
  add_stats(oneway_test_equal_var)

oneway_test
oneway_test_equal_var

# var.test() --------------------------------------------------------------

set.seed(1)

x <- rnorm(50, mean = 0, sd = 2)
y <- rnorm(30, mean = 1, sd = 1)

var_test <- var.test(x, y)

statistics <- add_stats(statistics, var_test)

var_test

# mauchly.test() ----------------------------------------------------------

example(SSD)

idata <- data.frame(
  deg = gl(3, 1, 6, labels = c(0, 4, 8)),
  noise = gl(2, 3, 6, labels = c("A", "P"))
)

mauchly_test <- mauchly.test(mlmfit, X = ~1)
mauchly_test_orthogonal <- mauchly.test(
  mlmfit,
  X = ~ deg + noise,
  idata = idata
)
mauchly_test_spanned <- mauchly.test(
  mlmfit,
  M = ~ deg + noise, X = ~noise,
  idata = idata
)

statistics <- statistics |>
  add_stats(mauchly_test) |>
  add_stats(mauchly_test_orthogonal) |>
  add_stats(mauchly_test_spanned)

mauchly_test
mauchly_test_orthogonal
mauchly_test_spanned

# mcnemar.test()  ---------------------------------------------------------

Performance <- matrix(
  data = c(794, 86, 150, 570),
  nrow = 2,
  dimnames = list(
    "1st Survey" = c("Approve", "Disapprove"),
    "2nd Survey" = c("Approve", "Disapprove")
  )
)

mcnemar_test <- mcnemar.test(Performance)
mcnemar_test_nocorrect <- mcnemar.test(Performance, correct = FALSE)

statistics <- statistics |>
  add_stats(mcnemar_test) |>
  add_stats(mcnemar_test_nocorrect)

mcnemar_test
mcnemar_test_nocorrect

# binom.test()  -----------------------------------------------------------

binom_test <- binom.test(c(682, 243))
binom_test_params <- binom.test(c(682, 243), p = 3 / 4, alternative = "less")

statistics <- statistics |>
  add_stats(binom_test) |>
  add_stats(binom_test_params)

binom_test
binom_test_params

# PP.test() ---------------------------------------------------------------

set.seed(1)

x <- rnorm(1000)
y <- cumsum(x)

pp_test <- PP.test(x)
pp_test_long <- PP.test(y, lshort = FALSE)

statistics <- statistics |>
  add_stats(pp_test) |>
  add_stats(pp_test_long)

pp_test
pp_test_long

# Box.test() --------------------------------------------------------------

set.seed(1)

x <- rnorm(100)

box_test <- Box.test(x, lag = 1)
box_test_ljung <- Box.test(x, lag = 2, type = "Ljung")

statistics <- statistics |>
  add_stats(box_test) |>
  add_stats(box_test_ljung)

box_test
box_test_ljung

# ansari.test() -----------------------------------------------------------

set.seed(1)

ramsay <- c(
  111, 107, 100, 99, 102, 106, 109, 108, 104, 99, 101, 96, 97, 102, 107, 113,
  116, 113, 110, 98
)
jung_parekh <- c(
  107, 108, 106, 98, 105, 103, 110, 105, 104, 100, 96, 108, 103, 104, 114, 114,
  113, 108, 106, 99
)

ansari_test <- ansari.test(ramsay, jung_parekh)
ansari_test_ci <- ansari.test(rnorm(100), rnorm(100, 0, 2), conf.int = TRUE)

statistics <- statistics |>
  add_stats(ansari_test) |>
  add_stats(ansari_test_ci)

ansari_test
ansari_test_ci

# mood.test() -------------------------------------------------------------

ramsay <- c(
  111, 107, 100, 99, 102, 106, 109, 108, 104, 99,
  101, 96, 97, 102, 107, 113, 116, 113, 110, 98
)
jung_parekh <- c(
  107, 108, 106, 98, 105, 103, 110, 105, 104,
  100, 96, 108, 103, 104, 114, 114, 113, 108, 106, 99
)

mood_test <- mood.test(ramsay, jung_parekh)

statistics <- add_stats(statistics, mood_test)

mood_test

# quade.test() ------------------------------------------------------------

dataFreq <- matrix(
  nrow = 7,
  byrow = TRUE,
  data = c(
    5, 4, 7, 10, 12,
    1, 3, 1, 0, 2,
    16, 12, 22, 22, 35,
    5, 4, 3, 5, 4,
    10, 9, 7, 13, 10,
    19, 18, 28, 37, 58,
    10, 7, 6, 8, 7
  ),
  dimnames = list(Store = as.character(1:7), Brand = LETTERS[1:5])
)

quade_test <- quade.test(dataFreq)

statistics <- add_stats(statistics, quade_test)

quade_test

# bartlett.test() ---------------------------------------------------------

bartlett_test <- bartlett.test(InsectSprays$count, InsectSprays$spray)

statistics <- add_stats(statistics, bartlett_test)

bartlett_test

# fligner.test() ----------------------------------------------------------

fligner_test <- fligner.test(InsectSprays$count, InsectSprays$spray)

statistics <- add_stats(statistics, fligner_test)

fligner_test

# poisson.test() ----------------------------------------------------------

poisson_test <- poisson.test(137, 24.19893)
poisson_test_comparison <- poisson.test(
  x = c(11, 6 + 8 + 7),
  T = c(800, 1083 + 1050 + 878)
)

statistics <- statistics |>
  add_stats(poisson_test) |>
  add_stats(poisson_test_comparison)

poisson_test
poisson_test_comparison

# shapiro.test() ----------------------------------------------------------

set.seed(1)

shapiro_test <- shapiro.test(runif(100, min = 2, max = 4))

statistics <- add_stats(statistics, shapiro_test)

shapiro_test

# friedman.test() ---------------------------------------------------------

rounding_times <- matrix(
  nrow = 22,
  byrow = TRUE,
  data = c(
    5.40, 5.50, 5.55,
    5.85, 5.70, 5.75,
    5.20, 5.60, 5.50,
    5.55, 5.50, 5.40,
    5.90, 5.85, 5.70,
    5.45, 5.55, 5.60,
    5.40, 5.40, 5.35,
    5.45, 5.50, 5.35,
    5.25, 5.15, 5.00,
    5.85, 5.80, 5.70,
    5.25, 5.20, 5.10,
    5.65, 5.55, 5.45,
    5.60, 5.35, 5.45,
    5.05, 5.00, 4.95,
    5.50, 5.50, 5.40,
    5.45, 5.55, 5.50,
    5.55, 5.55, 5.35,
    5.45, 5.50, 5.55,
    5.50, 5.45, 5.25,
    5.65, 5.60, 5.40,
    5.70, 5.65, 5.55,
    6.30, 6.30, 6.25
  ),
  dimnames = list(1:22, c("Round Out", "Narrow Angle", "Wide Angle"))
)

friedman_test <- friedman.test(rounding_times)

statistics <- add_stats(statistics, friedman_test)

friedman_test

# mantelhaen.test() -------------------------------------------------------

Satisfaction <- as.table(
  array(
    dim = c(4, 4, 2),
    data = c(
      1, 2, 0, 0, 3, 3, 1, 2,
      11, 17, 8, 4, 2, 3, 5, 2,
      1, 0, 0, 0, 1, 3, 0, 1,
      2, 5, 7, 9, 1, 1, 3, 6
    ),
    dimnames = list(
      Income = c("<5000", "5000-15000", "15000-25000", ">25000"),
      `Job Satisfaction` = c("V_D", "L_S", "M_S", "V_S"),
      Gender = c("Female", "Male")
    )
  )
)

Rabbits <- array(
  dim = c(2, 2, 5),
  data = c(
    0, 0, 6, 5,
    3, 0, 3, 6,
    6, 2, 0, 4,
    5, 6, 1, 0,
    2, 5, 0, 0
  ),
  dimnames = list(
    Delay = c("None", "1.5h"),
    Response = c("Cured", "Died"),
    Penicillin.Level = c("1/8", "1/4", "1/2", "1", "4")
  )
)

mantelhaen_test <- mantelhaen.test(Satisfaction)
mantelhaen_test_2by2 <- mantelhaen.test(Rabbits)
mantelhaen_test_2by2_exact <- mantelhaen.test(Rabbits, exact = TRUE)

statistics <- statistics |>
  add_stats(mantelhaen_test) |>
  add_stats(mantelhaen_test_2by2) |>
  add_stats(mantelhaen_test_2by2_exact)

mantelhaen_test
mantelhaen_test_2by2
mantelhaen_test_2by2_exact

# tidy_stats_to_data_frame() ----------------------------------------------

df <- tidy_stats_to_data_frame(statistics)

# write_stats() -----------------------------------------------------------

write_test_stats(statistics, "tests/data/htest.json")

# Cleanup -----------------------------------------------------------------

rm(
  ansari_test, ansari_test_ci, bartlett_test, binom_test, binom_test_params,
  box_test, box_test_ljung, chi_squared, chi_squared_prob, chi_squared_yates,
  Convictions, correlation_kendall, correlation_pearson, correlation_spearman,
  dataFreq, df, fisher_test, fisher_test_hybrid, fisher_test_no_CI,
  fisher_test_r_by_c, fisher_test_simulated_p, fligner_test, friedman_test,
  idata, Job, kruskal, kruskal_formula, ks_test_greater, ks_test_inexact,
  ks_test_one, ks_test_two, mantelhaen_test, mantelhaen_test_2by2,
  mantelhaen_test_2by2_exact, mauchly_test, mauchly_test_orthogonal,
  mauchly_test_spanned, mcnemar_test, mcnemar_test_nocorrect, mlmfit,
  mood_test, MP6, oneway_test, oneway_test_equal_var, Performance, poisson_test,
  poisson_test_comparison, pp_test, pp_test_long, prop_test, prop_test_correct,
  prop_test_smokers, prop_trend_test, prop_trend_test_scores, quade_test,
  reacttime, rounding_times, shapiro_test, statistics, t_test_one_sample,
  t_test_paired, t_test_two_sample, t_test_welch, TeaTasting, var_test,
  wilcoxon_rank_sum, wilcoxon_rank_sum_conf, wilcoxon_rank_sum_continuity,
  wilcoxon_signed_rank, heads, jung_parekh, M, patients, Rabbits, ramsay,
  Satisfaction, smokers, x, y, z, sleep_wide
)