## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", eval = TRUE)
library(gtstats)

## ----effect-size--------------------------------------------------------------
to_flextable(effect_size(mtcars, variable = mpg, group = am))

## ----effect-size-rank---------------------------------------------------------
to_flextable(effect_size(
  mtcars,
  variable = mpg,
  group = am,
  method = "rank_biserial"
))

## ----proportion---------------------------------------------------------------
to_flextable(proportion_stats(mtcars, var = vs, by = am))

## ----categorical--------------------------------------------------------------
to_flextable(compare_groups(mtcars, variable = vs, group = am))
to_flextable(crosstabs(mtcars, row = am, col = vs))

## ----mcnemar------------------------------------------------------------------
to_flextable(compare_groups(
  paired_data,
  variable = symptom_present,
  group = visit,
  paired = TRUE,
  id = id
))

## ----variance-diagnostics-----------------------------------------------------
to_flextable(assess_variance(mtcars, vars = mpg, by = am))
to_flextable(assess_variance(mtcars, vars = mpg, by = am, test = "none"))
to_flextable(assess_variance(mtcars, vars = mpg, by = am, test = "bartlett"))

## ----continuous---------------------------------------------------------------
to_flextable(compare_groups(
  mtcars,
  variable = mpg,
  group = am,
  test = "auto"
))

to_flextable(compare_groups(mtcars, variable = mpg, group = cyl))
to_flextable(compare_groups(mtcars, variable = mpg, group = cyl, test = "anova"))

## ----auto-audit---------------------------------------------------------------
result <- compare_groups(mtcars, variable = mpg, group = am)
result$method$selection_rule
result$method$selection_inputs
diagnostics_stats(result)

## ----add-p--------------------------------------------------------------------
summary_table(mtcars, by = am, include = c(mpg, wt, vs), overall = TRUE) |>
  add_p() |>
  to_flextable()

## ----add-p-explicit-----------------------------------------------------------
summary_table(mtcars, by = am, include = c(mpg, wt, vs)) |>
  add_p(
    test = c(
      mpg = "welch_t",
      wt = "wilcox",
      vs = "fisher"
    ),
    distribution_check = FALSE
  ) |>
  to_flextable()

## ----equal-variance-auto------------------------------------------------------
to_flextable(compare_groups(trial_data, change_score, group = arm, var_equal = TRUE))

## ----correlation-matrix-------------------------------------------------------
matrix_result <- correlation(
  mtcars,
  vars = c(mpg, disp, hp, wt),
  display = "estimate_p",
  adjust = "holm"
)

to_flextable(matrix_result)
plot_correlation(matrix_result)

## ----inspect------------------------------------------------------------------
result <- compare_groups(mtcars, variable = vs, group = am)

result$inferential
result$method
result$assumptions
result$diagnostics
result$denominators
result$notes

## ----inspect-helpers----------------------------------------------------------
assumptions_stats(result)
diagnostics_stats(result)
denominators_stats(result)

denominators_stats(result, format = "tibble")