suppressPackageStartupMessages(library(dplyr))
suppressPackageStartupMessages(library(gt))
suppressPackageStartupMessages(library(gtsummary))
suppressPackageStartupMessages(library(readr))
suppressPackageStartupMessages(library(tidyr))

cli::cli_h1("Naive analysis of the simulated ICU cohort")

icu_data <- read_csv("data/icu_septic_shock_base_r.csv", show_col_types = FALSE)

if (!dir.exists("outputs")) {
  dir.create("outputs")
}

eligible_data <- icu_data |>
  filter(eligible == 1)

analysis_summary <- eligible_data |>
  summarize(
    n_eligible = n(),
    n_early = sum(early_vasopressor == 1),
    n_not_early = sum(early_vasopressor == 0),
    risk_early = mean(death_28d[early_vasopressor == 1]),
    risk_not_early = mean(death_28d[early_vasopressor == 0]),
    risk_difference = risk_early - risk_not_early,
    risk_ratio = risk_early / risk_not_early
  )

analysis_results <- analysis_summary |>
  pivot_longer(
    cols = everything(),
    names_to = "measure",
    values_to = "value"
  )

analysis_table <- analysis_results |>
  gt() |>
  tab_header(title = "Naive 28-Day Mortality Comparison") |>
  cols_label(
    measure = "Measure",
    value = "Value"
  ) |>
  fmt_number(columns = value, decimals = 3)

baseline_table <- eligible_data |>
  mutate(
    early_vasopressor = factor(
      early_vasopressor,
      levels = c(0, 1),
      labels = c("No early vasopressor", "Early vasopressor")
    )
  ) |>
  select(early_vasopressor, age, sex, sofa_score, lactate, map, death_28d) |>
  tbl_summary(
    by = early_vasopressor,
    statistic = list(
      all_continuous() ~ "{mean} ({sd})",
      all_categorical() ~ "{n} ({p}%)"
    ),
    missing = "no"
  ) |>
  add_overall()

baseline_console <- eligible_data |>
  group_by(early_vasopressor) |>
  summarize(
    mean_age = mean(age),
    mean_sofa_score = mean(sofa_score),
    mean_lactate = mean(lactate),
    mean_map = mean(map),
    .groups = "drop"
  )

cli::cli_h2("Core causal contrast")
print(analysis_results)

gtsave(
  data = analysis_table,
  filename = "outputs/naive_mortality_comparison.html"
)

cli::cli_alert_success("Wrote {.file outputs/naive_mortality_comparison.html}.")

cli::cli_h2("Baseline comparison by observed treatment")
print(baseline_console)

baseline_table |>
  as_gt() |>
  gtsave(filename = "outputs/baseline_by_treatment.html")

cli::cli_alert_success("Wrote {.file outputs/baseline_by_treatment.html}.")