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

## -----------------------------------------------------------------------------
# library(gp3tools)
# 
# data("gazepoint_example_master")
# data("gazepoint_example_pupil_windows")
# 
# master <- gazepoint_example_master
# pupil_windows <- gazepoint_example_pupil_windows

## -----------------------------------------------------------------------------
# export_dir <- system.file(
#   "extdata",
#   "gazepoint_realistic_demo_exports",
#   package = "gp3tools"
# )
# output_dir <- "C:/Users/YourName/Desktop/gp3_outputs"
# 
# results <- run_gazepoint_workflow(
#   export_dir = export_dir,
#   output_dir = output_dir,
#   prefix = "study1",
#   save_plots = TRUE,
#   create_report = TRUE
# )
# 
# all_gaze <- results$all_gaze
# master <- create_gazepoint_master(all_gaze)

## -----------------------------------------------------------------------------
# master_audit <- audit_gazepoint_master(master)
# 
# validation <- validate_gazepoint_master(master)
# 
# master_audit$overview
# validation$summary
# validation$checks

## -----------------------------------------------------------------------------
# pupil_summary <- summarise_gazepoint_pupil(master)
# 
# flagged_pupil <- flag_gazepoint_pupil(
#   master,
#   pupil_col = "pupil"
# )
# 
# interpolated_pupil <- interpolate_gazepoint_pupil(
#   flagged_pupil,
#   pupil_col = "pupil_for_preprocessing",
#   time_col = "time",
#   group_cols = c("subject", "MEDIA_ID", "trial_global")
# )
# 
# baseline_corrected <- baseline_correct_gazepoint_pupil(
#   interpolated_pupil,
#   pupil_col = "pupil_interpolated",
#   time_col = "time",
#   group_cols = c("subject", "MEDIA_ID", "trial_global"),
#   baseline_window = c(0, 200),
#   min_baseline_samples = 1
# )
# 
# smoothed_pupil <- smooth_gazepoint_pupil(
#   baseline_corrected,
#   pupil_col = "pupil_baseline_corrected",
#   time_col = "time",
#   group_cols = c("subject", "MEDIA_ID", "trial_global"),
#   window_samples = 5,
#   method = "mean",
#   align = "center",
#   min_points = 2
# )

## -----------------------------------------------------------------------------
# pupil_windows <- summarise_gazepoint_pupil_windows(
#   smoothed_pupil,
#   pupil_col = "pupil_smoothed",
#   time_col = "time",
#   windows = c(0, 500, 1000, 2000, 5000),
#   group_cols = c("subject", "MEDIA_ID", "trial_global", "condition"),
#   min_valid_samples = 1
# )
# 
# pupil_windows

## -----------------------------------------------------------------------------
# registry <- create_gazepoint_preprocessing_registry(
#   blink_padding_ms = 50,
#   interpolation_max_gap_ms = 150,
#   smoothing_window_samples = 5,
#   baseline_window = c(0, 200)
# )
# 
# artifact_pupil <- flag_gazepoint_pupil_artifacts(
#   master,
#   registry = registry,
#   pupil_col = "pupil",
#   time_col = "time",
#   group_cols = c("subject", "MEDIA_ID", "trial_global")
# )
# 
# interpolated_artifact_pupil <- interpolate_gazepoint_pupil(
#   artifact_pupil,
#   pupil_col = "pupil_clean",
#   time_col = "time",
#   group_cols = c("subject", "MEDIA_ID", "trial_global")
# )
# 
# baseline_artifact_pupil <- baseline_correct_gazepoint_pupil(
#   interpolated_artifact_pupil,
#   pupil_col = "pupil_interpolated",
#   time_col = "time",
#   group_cols = c("subject", "MEDIA_ID", "trial_global"),
#   baseline_window = c(0, 200),
#   min_baseline_samples = 1
# )
# 
# smoothed_artifact_pupil <- smooth_gazepoint_pupil(
#   baseline_artifact_pupil,
#   pupil_col = "pupil_baseline_corrected",
#   time_col = "time",
#   group_cols = c("subject", "MEDIA_ID", "trial_global"),
#   window_samples = 5,
#   method = "mean",
#   align = "center",
#   min_points = 2
# )
# 
# pupil_windows_conservative <- summarise_gazepoint_pupil_windows(
#   smoothed_artifact_pupil,
#   pupil_col = "pupil_smoothed",
#   time_col = "time",
#   windows = c(0, 500, 1000, 2000, 5000),
#   group_cols = c("subject", "MEDIA_ID", "trial_global", "condition"),
#   min_valid_samples = 1
# )

## -----------------------------------------------------------------------------
# gap_audit <- audit_gazepoint_pupil_gaps(
#   interpolated_artifact_pupil,
#   group_cols = c("subject", "MEDIA_ID", "trial_global")
# )
# 
# baseline_audit <- audit_gazepoint_pupil_baseline(
#   baseline_artifact_pupil,
#   group_cols = c("subject", "MEDIA_ID", "trial_global")
# )
# 
# imbalance_audit <- audit_gazepoint_pupil_imbalance(
#   smoothed_artifact_pupil,
#   group_cols = "condition"
# )
# 
# drift_audit <- audit_gazepoint_pupil_drift(
#   smoothed_artifact_pupil,
#   pupil_col = "pupil_smoothed",
#   time_col = "time",
#   group_cols = c("subject", "MEDIA_ID", "trial_global")
# )
# 
# overlap_audit <- audit_gazepoint_pupil_overlap_risk(
#   master,
#   time_col = "time",
#   event_col = "event_label",
#   group_cols = c("subject", "MEDIA_ID", "trial_global")
# )
# 
# gap_audit$overview
# baseline_audit$overview
# imbalance_audit$overview
# drift_audit$overview
# overlap_audit$overview

## -----------------------------------------------------------------------------
# pupil_reliability <- audit_gazepoint_pupil_reliability(
#   pupil_windows_conservative,
#   subject_col = "subject",
#   outcome_col = "mean_pupil",
#   condition_col = "condition"
# )
# 
# pchip_pupil <- interpolate_gazepoint_pupil_pchip(
#   artifact_pupil,
#   pupil_col = "pupil_clean",
#   time_col = "time",
#   group_cols = c("subject", "MEDIA_ID", "trial_global")
# )
# 
# hampel_pupil <- flag_gazepoint_pupil_hampel(
#   smoothed_artifact_pupil,
#   pupil_col = "pupil_smoothed",
#   time_col = "time",
#   grouping_cols = c("subject", "MEDIA_ID", "trial_global"),
#   window_size_samples = 7,
#   k = 3,
#   min_valid_samples = 3,
#   corrected_col = "pupil_hampel_corrected"
# )
# 
# pupil_reliability$overview
# attr(pchip_pupil, "gp3_pchip_overview")
# attr(hampel_pupil, "gp3_hampel_overview")

## -----------------------------------------------------------------------------
# pupil_window_model_data <- prepare_gazepoint_pupil_window_model_data(
#   pupil_windows_conservative,
#   outcome_col = "mean_pupil",
#   subject_col = "subject",
#   condition_col = "condition",
#   window_col = "window_label",
#   trial_col = "trial_global",
#   valid_samples_col = "n_valid_samples",
#   total_samples_col = "n_samples",
#   min_valid_samples = 1
# )
# 
# dplyr::count(
#   pupil_window_model_data,
#   pupil_window_condition,
#   pupil_window_label,
#   pupil_window_model_status
# )

## -----------------------------------------------------------------------------
# pupil_window_lmm <- fit_gazepoint_pupil_window_lmm(
#   pupil_window_model_data,
#   random_window_slopes = FALSE,
#   use_weights = TRUE,
#   REML = FALSE
# )
# 
# pupil_window_lmm$model_status
# pupil_window_lmm$formula
# pupil_window_lmm$fixed_effects
# pupil_window_lmm$comparison

## -----------------------------------------------------------------------------
# pupil_window_sensitivity <- fit_gazepoint_pupil_window_sensitivity(
#   pupil_window_model_data,
#   model_types = c(
#     "unweighted_lmm",
#     "weighted_lmm",
#     "fixed_lm",
#     "weighted_lm"
#   ),
#   include_condition = TRUE,
#   include_window = TRUE,
#   include_interaction = TRUE
# )
# 
# pupil_window_sensitivity$comparison
# pupil_window_sensitivity$fixed_effects

## -----------------------------------------------------------------------------
# pupil_gamm_data <- prepare_gazepoint_pupil_gamm_data(
#   smoothed_artifact_pupil,
#   pupil_col = "pupil_smoothed",
#   time_col = "time",
#   subject_col = "subject",
#   condition_col = "condition",
#   trial_col = "trial_global",
#   bin_width_ms = 50,
#   min_valid_samples = 1
# )

## -----------------------------------------------------------------------------
# pupil_gamm_fit <- fit_gazepoint_pupil_gamm(
#   pupil_gamm_data,
#   n_time_basis = 10,
#   discrete = TRUE
# )
# 
# pupil_gamm_fit$model_status
# pupil_gamm_fit$formula

## -----------------------------------------------------------------------------
# pupil_pfe_fit <- fit_gazepoint_pupil_pfe_gamm(
#   pupil_gamm_data,
#   n_time_basis = 10,
#   n_position_basis = 8,
#   discrete = TRUE
# )
# 
# pupil_pfe_fit$sensitivity_status
# pupil_pfe_fit$comparison

## -----------------------------------------------------------------------------
# pupil_gca_data <- prepare_gazepoint_gca_data(
#   pupil_gamm_data,
#   pupil_col = "mean_pupil",
#   time_col = "time_bin_center_ms",
#   subject_col = "subject",
#   condition_col = "condition",
#   degree = 3,
#   orthogonal = TRUE,
#   valid_samples_col = "n_valid_samples",
#   min_valid_samples = 1
# )
# 
# pupil_gca_fit <- fit_gazepoint_gca(
#   pupil_gca_data,
#   REML = FALSE
# )
# 
# pupil_gca_fit$model_status
# pupil_gca_fit$comparison

## -----------------------------------------------------------------------------
# cluster_data <- prepare_gazepoint_cluster_data(
#   pupil_gamm_data,
#   outcome_col = "mean_pupil",
#   time_col = "time_bin_center_ms",
#   subject_col = "subject",
#   condition_col = "condition"
# )
# 
# cluster_results <- run_gazepoint_cluster_permutation(
#   cluster_data,
#   condition_levels = c("control", "treatment"),
#   n_permutations = 1000,
#   seed = 123
# )
# 
# cluster_summary <- summarise_gazepoint_clusters(cluster_results)
# 
# cluster_summary$overview
# cluster_summary$significant_clusters

## -----------------------------------------------------------------------------
# divergence <- estimate_gazepoint_divergence_point(
#   data = pupil_gamm_data,
#   outcome_col = "mean_pupil",
#   time_col = "time_bin_center_ms",
#   condition_col = "condition",
#   participant_col = "subject",
#   comparison = c("control", "treatment"),
#   bootstrap_unit = "participant",
#   n_boot = 1000,
#   consecutive_points = 2,
#   seed = 123
# )
# 
# divergence$overview
# divergence$divergence_point

## -----------------------------------------------------------------------------
# pupil_diagnostics <- diagnose_gazepoint_glmm(
#   pupil_window_lmm,
#   model_name = "pupil_window_lmm",
#   use_dharma = FALSE
# )
# 
# pupil_model_summary <- tidy_gazepoint_model_summary(
#   pupil_window_lmm,
#   model_name = "pupil_window_lmm"
# )
# 
# pupil_diagnostics$overview
# pupil_model_summary$fixed_effects

## -----------------------------------------------------------------------------
# reporting <- create_gazepoint_reporting_checklist(
#   data = master,
#   objects = list(
#     validation = validation,
#     gap_audit = gap_audit,
#     baseline_audit = baseline_audit,
#     pupil_model = pupil_window_lmm,
#     diagnostics = pupil_diagnostics
#   ),
#   analysis_type = "pupil",
#   study_title = "Gazepoint pupil study"
# )
# 
# reporting$overview
# reporting$checklist

