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

## ----message=FALSE, warning=FALSE---------------------------------------------
library(gsDesign)
library(gsDesignNB)
library(data.table)
library(ggplot2)
library(gt)

## ----sample-size--------------------------------------------------------------
# Sample size calculation
# Enrollment: constant rate over 12 months
# Trial duration: 24 months
event_gap_val <- 20 / 30.4375 # Minimum gap between events is 20 days (approx)

nb_ss <- sample_size_nbinom(
  lambda1 = 1.5 / 12, # Control event rate (per month)
  lambda2 = 1.0 / 12, # Experimental event rate (per month)
  dispersion = 0.5, # Overdispersion parameter
  power = 0.9, # 90% power
  alpha = 0.025, # One-sided alpha
  accrual_rate = 1, # This will be scaled to achieve the target power
  accrual_duration = 12, # 12 months enrollment
  trial_duration = 24, # 24 months trial
  max_followup = 12, # 12 months of follow-up per patient
  dropout_rate = -log(0.95) / 12, # 5% dropout rate at 1 year
  event_gap = event_gap_val
)

# Print key results
message("Fixed design")
nb_ss

## ----gs-design----------------------------------------------------------------
# Analysis times (in months)
analysis_times <- c(10, 18, 24)

# Create group sequential design and round the final sample size
gs_nb_calendar <- gsNBCalendar(
  x = nb_ss, # Input fixed design for negative binomial
  k = 3, # 3 analyses
  test.type = 4, # Two-sided asymmetric, non-binding futility
  sfu = sfLinear, # Linear spending function for upper bound
  sfupar = c(.5, .5), # Identity function
  sfl = sfHSD, # HSD spending for lower bound
  sflpar = -8, # Conservative futility bound
  usTime = c(.1, .18, 1), # Upper spending timing
  lsTime = NULL, # Spending based on information
  analysis_times = analysis_times # Calendar times in months
)
gs_nb <- gsDesignNB::toInteger(gs_nb_calendar)

## -----------------------------------------------------------------------------
summary(gs_nb)

## -----------------------------------------------------------------------------
gs_nb |>
  gsDesign::gsBoundSummary(
    deltaname = "RR",
    logdelta = TRUE,
    Nname = "Information",
    timename = "Month",
    digits = 4,
    ddigits = 2
  ) |>
  gt() |>
  tab_header(
    title = "Group Sequential Design Bounds for Negative Binomial Outcome",
    subtitle = paste0(
      "N = ", ceiling(gs_nb$n_total[gs_nb$k]),
      ", Expected events = ", round(gs_nb$nb_design$total_events, 1)
    )
  )

## ----load-results-------------------------------------------------------------
# Load pre-computed simulation results
results_file <- file.path("inst", "extdata", "gs_simulation_results.rds")

if (!file.exists(results_file) && file.exists("../inst/extdata/gs_simulation_results.rds")) {
  results_file <- "../inst/extdata/gs_simulation_results.rds"
}

if (!file.exists(results_file)) {
  results_file <- system.file("extdata", "gs_simulation_results.rds", package = "gsDesignNB")
}

if (results_file != "") {
  sim_data <- readRDS(results_file)
  results <- sim_data$results
  summary_gs <- summarize_gs_sim(results)
  analysis_summary <- data.table::as.data.table(summary_gs$analysis_summary)
  required_summary_cols <- c(
    "n_ctrl", "n_exp",
    "exposure_total_ctrl", "exposure_total_exp",
    "exposure_at_risk_ctrl", "exposure_at_risk_exp",
    "events_ctrl", "events_exp"
  )
  if (!all(required_summary_cols %in% names(analysis_summary))) {
    result_dt <- data.table::as.data.table(results)
    result_means <- result_dt[, .(
      n_ctrl = mean(n_ctrl, na.rm = TRUE),
      n_exp = mean(n_exp, na.rm = TRUE),
      exposure_total_ctrl = mean(exposure_total_ctrl, na.rm = TRUE),
      exposure_total_exp = mean(exposure_total_exp, na.rm = TRUE),
      exposure_at_risk_ctrl = mean(exposure_at_risk_ctrl, na.rm = TRUE),
      exposure_at_risk_exp = mean(exposure_at_risk_exp, na.rm = TRUE),
      events_ctrl = mean(events_ctrl, na.rm = TRUE),
      events_exp = mean(events_exp, na.rm = TRUE)
    ), by = analysis]
    existing_result_mean_cols <- intersect(required_summary_cols, names(analysis_summary))
    if (length(existing_result_mean_cols) > 0) {
      analysis_summary[, (existing_result_mean_cols) := NULL]
    }
    analysis_summary <- merge(
      analysis_summary,
      result_means,
      by = "analysis",
      all.x = TRUE,
      sort = FALSE
    )
  }
  n_sims <- sim_data$n_sims
  params <- sim_data$params
} else {
  # Fallback if data is not available (e.g. not installed yet)
  warning("Simulation results not found. Skipping simulation analysis.")
  results <- NULL
  summary_gs <- NULL
  analysis_summary <- NULL
  n_sims <- 0
}

## ----summary-table, eval=!is.null(results)------------------------------------
sim_summary <- data.table::copy(analysis_summary)

if (!"events" %in% names(sim_summary) && "events_total" %in% names(sim_summary)) {
  sim_summary[, events := events_total]
}
if (!"info_blinded" %in% names(sim_summary) && "blinded_info" %in% names(sim_summary)) {
  sim_summary[, info_blinded := blinded_info]
}
if (!"info_unblinded" %in% names(sim_summary) && "unblinded_info" %in% names(sim_summary)) {
  sim_summary[, info_unblinded := unblinded_info]
}

planning_comparison <- data.frame(
  Analysis = seq_len(gs_nb$k),
  Month = params$analysis_times,
  Planned_N = gs_nb$n_total,
  Mean_N = sim_summary$n_enrolled,
  Planned_Total_Exposure = gs_nb$n1 * gs_nb$exposure + gs_nb$n2 * gs_nb$exposure,
  Mean_Total_Exposure = sim_summary$exposure_total_ctrl + sim_summary$exposure_total_exp,
  Planned_At_Risk_Exposure =
    gs_nb$n1 * gs_nb$exposure_at_risk1 + gs_nb$n2 * gs_nb$exposure_at_risk2,
  Mean_At_Risk_Exposure =
    sim_summary$exposure_at_risk_ctrl + sim_summary$exposure_at_risk_exp,
  Planned_Events = gs_nb$events,
  Mean_Events = sim_summary$events,
  Planned_Info = gs_nb$n.I,
  Mean_Unblinded_Info = sim_summary$info_unblinded
)

planning_comparison$Event_Diff <- planning_comparison$Mean_Events -
  planning_comparison$Planned_Events
planning_comparison$Info_Diff <- planning_comparison$Mean_Unblinded_Info -
  planning_comparison$Planned_Info

planning_comparison |>
  gt() |>
  tab_header(
    title = "Design Planning Quantities vs Simulation Means",
    subtitle = sprintf("Based on %d simulated trials", n_sims)
  ) |>
  cols_label(
    Analysis = "Analysis",
    Month = "Month",
    Planned_N = "Planned N",
    Mean_N = "Mean N",
    Planned_Total_Exposure = "Planned total exposure",
    Mean_Total_Exposure = "Mean total exposure",
    Planned_At_Risk_Exposure = "Planned at-risk exposure",
    Mean_At_Risk_Exposure = "Mean at-risk exposure",
    Planned_Events = "Planned events",
    Mean_Events = "Mean events",
    Planned_Info = "Planned information",
    Mean_Unblinded_Info = "Mean unblinded information",
    Event_Diff = "Event diff.",
    Info_Diff = "Information diff."
  ) |>
  fmt_number(
    columns = c(
      Planned_N, Mean_N,
      Planned_Total_Exposure, Mean_Total_Exposure,
      Planned_At_Risk_Exposure, Mean_At_Risk_Exposure,
      Planned_Events, Mean_Events,
      Planned_Info, Mean_Unblinded_Info,
      Event_Diff, Info_Diff
    ),
    decimals = 1
  )

## ----overall-summary, eval=!is.null(results)----------------------------------
cat("=== Overall Operating Characteristics ===\n")
cat(sprintf("Number of simulations: %d\n", n_sims))
cat(sprintf("Overall Power (P[reject H0]): %.1f%% (SE: %.1f%%)\n", 
            summary_gs$power * 100, 
            sqrt(summary_gs$power * (1 - summary_gs$power) / n_sims) * 100))
cat(sprintf("Futility Stopping Rate: %.1f%%\n", summary_gs$futility * 100))
cat(sprintf("Design Power (target): %.1f%%\n", (1 - gs_nb$beta) * 100))

## ----power-comparison, eval=!is.null(results)---------------------------------
# Create comparison table
crossing_summary <- data.frame(
  Analysis = 1:3,
  Analysis_Time = params$analysis_times,
  Sim_Power = summary_gs$analysis_summary$prob_cross_upper,
  Sim_Cum_Power = summary_gs$analysis_summary$cum_prob_upper,
  Design_Cum_Power = cumsum(gs_nb$upper$prob[, 2])
)

crossing_summary |>
  gt() |>
  tab_header(
    title = "Power Comparison: Simulation vs Design",
    subtitle = sprintf("Based on %d simulated trials", n_sims)
  ) |>
  cols_label(
    Analysis = "Analysis",
    Analysis_Time = "Month",
    Sim_Power = "Incremental Power (Sim)",
    Sim_Cum_Power = "Cumulative Power (Sim)",
    Design_Cum_Power = "Cumulative Power (Design)"
  ) |>
  fmt_percent(columns = c(Sim_Power, Sim_Cum_Power, Design_Cum_Power), decimals = 1)

## ----plot-z-stats, fig.width=7, fig.height=5, fig.alt="Z-statistics across analyses with group sequential boundaries", eval=!is.null(results)----
# Prepare data for plotting
plot_data <- results
plot_data$z_flipped <- -plot_data$z_stat # Flip for efficacy direction

# Boundary data
bounds_df <- data.frame(
  analysis = 1:gs_nb$k,
  upper = gs_nb$upper$bound,
  lower = gs_nb$lower$bound
)

ggplot(plot_data, aes(x = factor(analysis), y = z_flipped)) +
  geom_violin(fill = "steelblue", alpha = 0.5, color = "steelblue") +
  geom_boxplot(width = 0.1, fill = "white", outlier.shape = NA) +
  # Draw bounds as lines connecting analyses
  geom_line(
    data = bounds_df, aes(x = analysis, y = upper, group = 1),
    linetype = "dashed", color = "darkgreen", linewidth = 1
  ) +
  geom_line(
    data = bounds_df, aes(x = analysis, y = lower, group = 1),
    linetype = "dashed", color = "darkred", linewidth = 1
  ) +
  # Draw points for bounds
  geom_point(data = bounds_df, aes(x = analysis, y = upper), color = "darkgreen") +
  geom_point(data = bounds_df, aes(x = analysis, y = lower), color = "darkred") +
  geom_hline(yintercept = 0, color = "gray50") +
  labs(
    title = "Simulated Z-Statistics by Analysis",
    subtitle = "Green dashed = efficacy bound, Red dashed = futility bound",
    x = "Analysis",
    y = "Z-statistic (positive = favors experimental)"
  ) +
  theme_minimal() +
  ylim(c(-4, 6))