# Mixed ANOVA Analysis for DGEN Variables
# EOHI Experiment 2 Data Analysis - DGEN Level Analysis with TIME, DOMAIN, and INTERVAL factors
# Variables: DGEN_past_5_Pref, DGEN_past_5_Pers, DGEN_past_5_Val, DGEN_past_10_Pref, DGEN_past_10_Pers, DGEN_past_10_Val,
#           DGEN_fut_5_Pref, DGEN_fut_5_Pers, DGEN_fut_5_Val, DGEN_fut_10_Pref, DGEN_fut_10_Pers, DGEN_fut_10_Val

# Load required libraries
library(tidyverse)
library(ez)
library(car)
library(afex)         # For aov_ez (cleaner ANOVA output)
library(nortest)      # For normality tests
library(emmeans)      # For post-hoc comparisons
library(purrr)        # For map functions
library(effsize)      # For Cohen's d calculations
library(effectsize)   # For effect size calculations

# Global options to remove scientific notation
options(scipen = 999)

# Set contrasts to sum for mixed ANOVA (necessary for proper interpretation)
options(contrasts = c("contr.sum", "contr.poly"))

setwd("C:/Users/irina/Documents/DND/EOHI/eohi2")

# Read the data
data <- read.csv("eohi2.csv")

# Display basic information about the dataset
print(paste("Dataset dimensions:", paste(dim(data), collapse = " x")))
print(paste("Number of participants:", length(unique(data$pID))))

# Verify the specific variables we need
required_vars <- c("DGEN_past_5_Pref", "DGEN_past_5_Pers", "DGEN_past_5_Val", 
                   "DGEN_past_10_Pref", "DGEN_past_10_Pers", "DGEN_past_10_Val",
                   "DGEN_fut_5_Pref", "DGEN_fut_5_Pers", "DGEN_fut_5_Val", 
                   "DGEN_fut_10_Pref", "DGEN_fut_10_Pers", "DGEN_fut_10_Val")

missing_vars <- required_vars[!required_vars %in% colnames(data)]
if (length(missing_vars) > 0) {
  print(paste("Warning: Missing variables:", paste(missing_vars, collapse = ", ")))
} else {
  print("All required DGEN variables found!")
}

# Define variable mapping for the three within-subjects factors
variable_mapping <- data.frame(
  variable = required_vars,
  TIME = c(rep("Past", 6), rep("Future", 6)),
  DOMAIN = rep(c("Preferences", "Personality", "Values", "Preferences", "Personality", "Values"), 2),
  INTERVAL = rep(c("5", "5", "5", "10", "10", "10"), 2),
  stringsAsFactors = FALSE
)

# Variable mapping created
print("Variable mapping:")
print(variable_mapping)

# Efficient data pivoting using pivot_longer
long_data <- data %>%
  select(pID, ResponseId, temporal_DO, interval_DO, all_of(required_vars)) %>%
  pivot_longer(
    cols = all_of(required_vars),
    names_to = "variable",
    values_to = "DGEN_SCORE"
  ) %>%
  left_join(variable_mapping, by = "variable") %>%
  # Convert to factors with proper levels
  mutate(
    TIME = factor(TIME, levels = c("Past", "Future")),
    DOMAIN = factor(DOMAIN, levels = c("Preferences", "Personality", "Values")),
    INTERVAL = factor(INTERVAL, levels = c("5", "10")),
    pID = as.factor(pID),
    temporal_DO = as.factor(temporal_DO),
    interval_DO = as.factor(interval_DO)
  ) %>%
  # Select final columns and remove any rows with missing values
  select(pID, ResponseId, temporal_DO, interval_DO, TIME, DOMAIN, INTERVAL, DGEN_SCORE) %>%
  filter(!is.na(DGEN_SCORE))

print(paste("Long data dimensions:", paste(dim(long_data), collapse = " x")))
print(paste("Number of participants:", length(unique(long_data$pID))))
print("Factor levels:")
print(paste("TIME:", paste(levels(long_data$TIME), collapse = ", ")))
print(paste("DOMAIN:", paste(levels(long_data$DOMAIN), collapse = ", ")))
print(paste("INTERVAL:", paste(levels(long_data$INTERVAL), collapse = ", ")))
print(paste("temporal_DO:", paste(levels(long_data$temporal_DO), collapse = ", ")))
print(paste("interval_DO:", paste(levels(long_data$interval_DO), collapse = ", ")))

# =============================================================================
# DESCRIPTIVE STATISTICS
# =============================================================================

# Overall descriptive statistics by TIME, DOMAIN, and INTERVAL
desc_stats <- long_data %>%
  group_by(TIME, DOMAIN, INTERVAL) %>%
  summarise(
    n = n(),
    mean = round(mean(DGEN_SCORE, na.rm = TRUE), 5),
    variance = round(var(DGEN_SCORE, na.rm = TRUE), 5),
    sd = round(sd(DGEN_SCORE, na.rm = TRUE), 5),
    median = round(median(DGEN_SCORE, na.rm = TRUE), 5),
    q1 = round(quantile(DGEN_SCORE, 0.25, na.rm = TRUE), 5),
    q3 = round(quantile(DGEN_SCORE, 0.75, na.rm = TRUE), 5),
    min = round(min(DGEN_SCORE, na.rm = TRUE), 5),
    max = round(max(DGEN_SCORE, na.rm = TRUE), 5),
    .groups = 'drop'
  )

print("Descriptive statistics by TIME, DOMAIN, and INTERVAL:")
print(desc_stats)

# Descriptive statistics by between-subjects factors
desc_stats_by_between <- long_data %>%
  group_by(temporal_DO, interval_DO, TIME, DOMAIN, INTERVAL) %>%
  summarise(
    n = n(),
    mean = round(mean(DGEN_SCORE, na.rm = TRUE), 5),
    variance = round(var(DGEN_SCORE, na.rm = TRUE), 5),
    sd = round(sd(DGEN_SCORE, na.rm = TRUE), 5),
    .groups = 'drop'
  )

print("Descriptive statistics by between-subjects factors:")
print(desc_stats_by_between)

# Calculate mean differences for key comparisons
print("\n=== KEY MEAN DIFFERENCES ===")

# Past vs Future differences for each DOMAIN × INTERVAL combination
past_future_diffs <- long_data %>%
  group_by(DOMAIN, INTERVAL, pID) %>%
  summarise(
    past_score = DGEN_SCORE[TIME == "Past"],
    future_score = DGEN_SCORE[TIME == "Future"],
    difference = past_score - future_score,
    .groups = 'drop'
  ) %>%
  group_by(DOMAIN, INTERVAL) %>%
  summarise(
    n = n(),
    mean_diff = round(mean(difference, na.rm = TRUE), 5),
    sd_diff = round(sd(difference, na.rm = TRUE), 5),
    se_diff = round(sd(difference, na.rm = TRUE) / sqrt(n()), 5),
    .groups = 'drop'
  )

print("Past vs Future differences by DOMAIN × INTERVAL:")
print(past_future_diffs)

# 5 vs 10 interval differences for each TIME × DOMAIN combination
interval_diffs <- long_data %>%
  group_by(TIME, DOMAIN, pID) %>%
  summarise(
    interval_5_score = DGEN_SCORE[INTERVAL == "5"],
    interval_10_score = DGEN_SCORE[INTERVAL == "10"],
    difference = interval_5_score - interval_10_score,
    .groups = 'drop'
  ) %>%
  group_by(TIME, DOMAIN) %>%
  summarise(
    n = n(),
    mean_diff = round(mean(difference, na.rm = TRUE), 5),
    sd_diff = round(sd(difference, na.rm = TRUE), 5),
    se_diff = round(sd(difference, na.rm = TRUE) / sqrt(n()), 5),
    .groups = 'drop'
  )

print("\n5 vs 10 interval differences by TIME × DOMAIN:")
print(interval_diffs)

# =============================================================================
# ASSUMPTION TESTING
# =============================================================================

# Remove missing values for assumption testing
long_data_clean <- long_data[!is.na(long_data$DGEN_SCORE), ]
print(paste("Data after removing missing values:", paste(dim(long_data_clean), collapse = " x")))

# 1. Missing values check
missing_summary <- long_data %>%
  group_by(TIME, DOMAIN, INTERVAL) %>%
  summarise(
    n_total = n(),
    n_missing = sum(is.na(DGEN_SCORE)),
    pct_missing = round(100 * n_missing / n_total, 2),
    .groups = 'drop'
  )

print("Missing values by TIME, DOMAIN, and INTERVAL:")
print(missing_summary)

# 2. Outlier detection
outlier_summary <- long_data_clean %>%
  group_by(TIME, DOMAIN, INTERVAL) %>%
  summarise(
    n = n(),
    mean = mean(DGEN_SCORE),
    sd = sd(DGEN_SCORE),
    q1 = quantile(DGEN_SCORE, 0.25),
    q3 = quantile(DGEN_SCORE, 0.75),
    iqr = q3 - q1,
    lower_bound = q1 - 1.5 * iqr,
    upper_bound = q3 + 1.5 * iqr,
    n_outliers = sum(DGEN_SCORE < lower_bound | DGEN_SCORE > upper_bound),
    .groups = 'drop'
  )

print("Outlier summary (IQR method):")
print(outlier_summary)

# 3. Anderson-Darling normality test
normality_results <- long_data_clean %>%
  group_by(TIME, DOMAIN, INTERVAL) %>%
  summarise(
    n = n(),
    ad_statistic = ad.test(.data$DGEN_SCORE)$statistic,
    ad_p_value = ad.test(.data$DGEN_SCORE)$p.value,
    .groups = 'drop'
  )

print("Anderson-Darling normality test results:")
# Round only the numeric columns
normality_results_rounded <- normality_results %>%
  mutate(across(where(is.numeric), ~ round(.x, 5)))
print(normality_results_rounded)

# 4. Homogeneity of variance tests
# Test homogeneity across TIME within each DOMAIN × INTERVAL combination
homogeneity_time <- long_data_clean %>%
  group_by(DOMAIN, INTERVAL) %>%
  summarise(
    levene_F = leveneTest(DGEN_SCORE ~ TIME)$`F value`[1],
    levene_p = leveneTest(DGEN_SCORE ~ TIME)$`Pr(>F)`[1],
    .groups = 'drop'
  )

print("Homogeneity of variance across TIME within each DOMAIN × INTERVAL:")
print(homogeneity_time)

# Test homogeneity across DOMAIN within each TIME × INTERVAL combination
homogeneity_domain <- long_data_clean %>%
  group_by(TIME, INTERVAL) %>%
  summarise(
    levene_F = leveneTest(DGEN_SCORE ~ DOMAIN)$`F value`[1],
    levene_p = leveneTest(DGEN_SCORE ~ DOMAIN)$`Pr(>F)`[1],
    .groups = 'drop'
  )

print("Homogeneity of variance across DOMAIN within each TIME × INTERVAL:")
print(homogeneity_domain)

# Test homogeneity across INTERVAL within each TIME × DOMAIN combination
homogeneity_interval <- long_data_clean %>%
  group_by(TIME, DOMAIN) %>%
  summarise(
    levene_F = leveneTest(DGEN_SCORE ~ INTERVAL)$`F value`[1],
    levene_p = leveneTest(DGEN_SCORE ~ INTERVAL)$`Pr(>F)`[1],
    .groups = 'drop'
  )

print("Homogeneity of variance across INTERVAL within each TIME × DOMAIN:")
print(homogeneity_interval)

# =============================================================================
# HARTLEY'S F-MAX TEST WITH BOOTSTRAP CRITICAL VALUES
# =============================================================================

# More efficient bootstrap function for Hartley's F-max test
bootstrap_hartley_critical <- function(data, group_var, response_var, n_iter = 1000) {
  # Get unique groups and their sample sizes
  groups <- unique(data[[group_var]])
  
  # Calculate observed variances for each group
  observed_vars <- data %>%
    dplyr::group_by(!!rlang::sym(group_var)) %>%
    dplyr::summarise(var = var(!!rlang::sym(response_var), na.rm = TRUE), .groups = 'drop') %>%
    dplyr::pull(var)
  
  # Handle invalid variances
  if(any(observed_vars <= 0 | is.na(observed_vars))) {
    observed_vars[observed_vars <= 0 | is.na(observed_vars)] <- 1e-10
  }
  
  # Calculate observed F-max ratio
  observed_ratio <- max(observed_vars) / min(observed_vars)
  
  # Pre-allocate storage for bootstrap ratios
  bootstrap_ratios <- numeric(n_iter)
  
  # Get group data once
  group_data_list <- map(groups, ~ {
    group_data <- data[data[[group_var]] == .x, response_var]
    group_data[!is.na(group_data)]
  })
  
  # Bootstrap with pre-allocated storage
  for(i in 1:n_iter) {
    # Bootstrap sample from each group independently
    sample_vars <- map_dbl(group_data_list, ~ {
      bootstrap_sample <- sample(.x, size = length(.x), replace = TRUE)
      var(bootstrap_sample, na.rm = TRUE)
    })
    bootstrap_ratios[i] <- max(sample_vars) / min(sample_vars)
  }
  
  # Remove invalid ratios
  valid_ratios <- bootstrap_ratios[is.finite(bootstrap_ratios) & !is.na(bootstrap_ratios)]
  
  if(length(valid_ratios) == 0) {
    stop("No valid bootstrap ratios generated")
  }
  
  # Calculate critical value (95th percentile)
  critical_95 <- quantile(valid_ratios, 0.95, na.rm = TRUE)
  
  # Return only essential information
  return(list(
    observed_ratio = observed_ratio,
    critical_95 = critical_95,
    n_valid_iterations = length(valid_ratios)
  ))
}

# Hartley's F-max test across between-subjects factors within each within-subjects combination
print("\n=== HARTLEY'S F-MAX TEST RESULTS ===")
set.seed(123)  # For reproducibility

# Test across temporal_DO within each TIME × DOMAIN × INTERVAL combination
print("F-max test across temporal_DO within each TIME × DOMAIN × INTERVAL combination:")
hartley_temporal_results <- long_data_clean %>%
  group_by(TIME, DOMAIN, INTERVAL) %>%
  summarise(
    hartley_result = list(bootstrap_hartley_critical(pick(temporal_DO, DGEN_SCORE), "temporal_DO", "DGEN_SCORE")),
    .groups = 'drop'
  ) %>%
  mutate(
    observed_ratio = map_dbl(hartley_result, ~ .x$observed_ratio),
    critical_95 = map_dbl(hartley_result, ~ .x$critical_95),
    significant = observed_ratio > critical_95
  ) %>%
  select(TIME, DOMAIN, INTERVAL, observed_ratio, critical_95, significant)

print(hartley_temporal_results)

# Test across interval_DO within each TIME × DOMAIN × INTERVAL combination
print("F-max test across interval_DO within each TIME × DOMAIN × INTERVAL combination:")
hartley_interval_results <- long_data_clean %>%
  group_by(TIME, DOMAIN, INTERVAL) %>%
  summarise(
    hartley_result = list(bootstrap_hartley_critical(pick(interval_DO, DGEN_SCORE), "interval_DO", "DGEN_SCORE")),
    .groups = 'drop'
  ) %>%
  mutate(
    observed_ratio = map_dbl(hartley_result, ~ .x$observed_ratio),
    critical_95 = map_dbl(hartley_result, ~ .x$critical_95),
    significant = observed_ratio > critical_95
  ) %>%
  select(TIME, DOMAIN, INTERVAL, observed_ratio, critical_95, significant)

print(hartley_interval_results)

# =============================================================================
# MIXED ANOVA ANALYSIS
# =============================================================================

# Check data dimensions and structure
print(paste("Data size for ANOVA:", nrow(long_data_clean), "rows"))
print(paste("Number of participants:", length(unique(long_data_clean$pID))))
print(paste("Design factors: TIME (", length(levels(long_data_clean$TIME)), "), DOMAIN (", 
            length(levels(long_data_clean$DOMAIN)), "), INTERVAL (", 
            length(levels(long_data_clean$INTERVAL)), "), temporal_DO (", 
            length(levels(long_data_clean$temporal_DO)), "), interval_DO (", 
            length(levels(long_data_clean$interval_DO)), ")", sep = ""))

# Check for complete cases
complete_cases <- sum(complete.cases(long_data_clean))
print(paste("Complete cases:", complete_cases, "out of", nrow(long_data_clean)))

# Check if design is balanced
design_balance <- table(long_data_clean$pID, long_data_clean$TIME, long_data_clean$DOMAIN, long_data_clean$INTERVAL)
if(all(design_balance %in% c(0, 1))) {
  print("Design is balanced: each participant has data for all TIME × DOMAIN × INTERVAL combinations")
} else {
  print("Warning: Design is unbalanced")
  print(summary(as.vector(design_balance)))
}

# =============================================================================
# MIXED ANOVA WITH SPHERICITY CORRECTIONS
# =============================================================================

print("\n=== MIXED ANOVA RESULTS (with sphericity corrections) ===")

# Mixed ANOVA using ezANOVA with automatic sphericity corrections
# Between-subjects: temporal_DO (2 levels) × interval_DO (2 levels)
# Within-subjects: TIME (2 levels: Past, Future) × DOMAIN (3 levels: Preferences, Personality, Values) × INTERVAL (2 levels: 5, 10)
mixed_anova_model <- ezANOVA(data = long_data_clean, 
                             dv = DGEN_SCORE, 
                             wid = pID, 
                             between = .(temporal_DO, interval_DO), 
                             within = .(TIME, DOMAIN, INTERVAL),
                             type = 3,
                             detailed = TRUE)

print("ANOVA Results:")
anova_output <- mixed_anova_model$ANOVA
rownames(anova_output) <- NULL  # Reset row numbers to be sequential
print(anova_output)

# Show Mauchly's test for sphericity
print("\nMauchly's Test of Sphericity:")
print(mixed_anova_model$Mauchly)

# Show sphericity-corrected results (Greenhouse-Geisser and Huynh-Feldt)
if(!is.null(mixed_anova_model$`Sphericity Corrections`)) {
  print("\nGreenhouse-Geisser and Huynh-Feldt Corrections:")
  print(mixed_anova_model$`Sphericity Corrections`)
  
  # Extract and display corrected degrees of freedom
  print("\n=== CORRECTED DEGREES OF FREEDOM ===")
  
  sphericity_corr <- mixed_anova_model$`Sphericity Corrections`
  anova_table <- mixed_anova_model$ANOVA
  
  corrected_df <- data.frame(
    Effect = sphericity_corr$Effect,
    Original_DFn = anova_table$DFn[match(sphericity_corr$Effect, anova_table$Effect)],
    Original_DFd = anova_table$DFd[match(sphericity_corr$Effect, anova_table$Effect)],
    GG_DFn = anova_table$DFn[match(sphericity_corr$Effect, anova_table$Effect)] * sphericity_corr$GGe,
    GG_DFd = anova_table$DFd[match(sphericity_corr$Effect, anova_table$Effect)] * sphericity_corr$GGe,
    HF_DFn = anova_table$DFn[match(sphericity_corr$Effect, anova_table$Effect)] * sphericity_corr$HFe,
    HF_DFd = anova_table$DFd[match(sphericity_corr$Effect, anova_table$Effect)] * sphericity_corr$HFe,
    GG_epsilon = sphericity_corr$GGe,
    HF_epsilon = sphericity_corr$HFe
  )
  
  print(corrected_df)
  
  print("=== CORRECTED F-TESTS ===")
  corrected_results <- data.frame(
    Effect = corrected_df$Effect,
    Original_F = anova_table$F[match(corrected_df$Effect, anova_table$Effect)],
    Original_DFn = corrected_df$Original_DFn,
    Original_DFd = corrected_df$Original_DFd,
    GG_DFn = corrected_df$GG_DFn,
    GG_DFd = corrected_df$GG_DFd,
    HF_DFn = corrected_df$HF_DFn,
    HF_DFd = corrected_df$HF_DFd,
    GG_p = sphericity_corr$`p[GG]`,
    HF_p = sphericity_corr$`p[HF]`
  )
  print(corrected_results)
} else {
  print("\nNote: Sphericity corrections not needed (sphericity assumption met)")
}

# =============================================================================
# EFFECT SIZES (GENERALIZED ETA SQUARED)
# =============================================================================

print("\n=== EFFECT SIZES (GENERALIZED ETA SQUARED) ===")

# Extract generalized eta squared from ezANOVA (already calculated)
effect_sizes <- mixed_anova_model$ANOVA[, c("Effect", "ges")]
effect_sizes$ges <- round(effect_sizes$ges, 5)
print("Generalized Eta Squared:")
print(effect_sizes)

# =============================================================================
# POST-HOC COMPARISONS
# =============================================================================

# Post-hoc comparisons using emmeans
print("\n=== POST-HOC COMPARISONS ===")

# Create aov model for emmeans (emmeans requires aov object, not ezANOVA output)
aov_model <- aov(DGEN_SCORE ~ temporal_DO * interval_DO * TIME * DOMAIN * INTERVAL + Error(pID/(TIME * DOMAIN * INTERVAL)), 
                 data = long_data_clean)

# Main effects
print("Main Effect of TIME:")
time_emmeans <- emmeans(aov_model, ~ TIME)
print("Estimated Marginal Means:")
print(time_emmeans)
print("\nPairwise Contrasts:")
time_contrasts <- pairs(time_emmeans, adjust = "bonferroni")
print(time_contrasts)

print("\nMain Effect of DOMAIN:")
domain_emmeans <- emmeans(aov_model, ~ DOMAIN)
print("Estimated Marginal Means:")
print(domain_emmeans)
print("\nPairwise Contrasts:")
domain_contrasts <- pairs(domain_emmeans, adjust = "bonferroni")
print(domain_contrasts)

print("\nMain Effect of INTERVAL:")
interval_emmeans <- emmeans(aov_model, ~ INTERVAL)
print("Estimated Marginal Means:")
print(interval_emmeans)
print("\nPairwise Contrasts:")
interval_contrasts <- pairs(interval_emmeans, adjust = "bonferroni")
print(interval_contrasts)

print("\nMain Effect of temporal_DO:")
temporal_emmeans <- emmeans(aov_model, ~ temporal_DO)
temporal_contrasts <- pairs(temporal_emmeans, adjust = "bonferroni")
print(temporal_contrasts)

print("\nMain Effect of interval_DO:")
interval_do_emmeans <- emmeans(aov_model, ~ interval_DO)
interval_do_contrasts <- pairs(interval_do_emmeans, adjust = "bonferroni")
print(interval_do_contrasts)

# =============================================================================
# TWO-WAY INTERACTION EXPLORATIONS
# =============================================================================

# TIME × DOMAIN Interaction
print("\n=== TIME × DOMAIN INTERACTION ===")
time_domain_emmeans <- emmeans(aov_model, ~ TIME * DOMAIN)
print("Estimated Marginal Means:")
print(time_domain_emmeans)

print("\nSimple Effects of DOMAIN within each TIME:")
time_domain_simple <- pairs(time_domain_emmeans, by = "TIME", adjust = "bonferroni")
print(time_domain_simple)

print("\nSimple Effects of TIME within each DOMAIN:")
time_domain_simple2 <- pairs(time_domain_emmeans, by = "DOMAIN", adjust = "bonferroni")
print(time_domain_simple2)

# TIME × INTERVAL Interaction
print("\n=== TIME × INTERVAL INTERACTION ===")
time_interval_emmeans <- emmeans(aov_model, ~ TIME * INTERVAL)
print("Estimated Marginal Means:")
print(time_interval_emmeans)

print("\nSimple Effects of INTERVAL within each TIME:")
time_interval_simple <- pairs(time_interval_emmeans, by = "TIME", adjust = "bonferroni")
print(time_interval_simple)

print("\nSimple Effects of TIME within each INTERVAL:")
time_interval_simple2 <- pairs(time_interval_emmeans, by = "INTERVAL", adjust = "bonferroni")
print(time_interval_simple2)

# DOMAIN × INTERVAL Interaction
print("\n=== DOMAIN × INTERVAL INTERACTION ===")
domain_interval_emmeans <- emmeans(aov_model, ~ DOMAIN * INTERVAL)
print("Estimated Marginal Means:")
print(domain_interval_emmeans)

print("\nSimple Effects of INTERVAL within each DOMAIN:")
domain_interval_simple <- pairs(domain_interval_emmeans, by = "DOMAIN", adjust = "bonferroni")
print(domain_interval_simple)

print("\nSimple Effects of DOMAIN within each INTERVAL:")
domain_interval_simple2 <- pairs(domain_interval_emmeans, by = "INTERVAL", adjust = "bonferroni")
print(domain_interval_simple2)

# Between-subjects interactions
print("\n=== temporal_DO × interval_DO INTERACTION ===")
temporal_interval_do_emmeans <- emmeans(aov_model, ~ temporal_DO * interval_DO)
print("Estimated Marginal Means:")
print(temporal_interval_do_emmeans)

print("\nSimple Effects of interval_DO within each temporal_DO:")
temporal_interval_do_simple <- pairs(temporal_interval_do_emmeans, by = "temporal_DO", adjust = "bonferroni")
print(temporal_interval_do_simple)

print("\nSimple Effects of temporal_DO within each interval_DO:")
temporal_interval_do_simple2 <- pairs(temporal_interval_do_emmeans, by = "interval_DO", adjust = "bonferroni")
print(temporal_interval_do_simple2)

# =============================================================================
# THREE-WAY INTERACTION ANALYSES
# =============================================================================

# TIME × DOMAIN × INTERVAL Interaction
print("\n=== TIME × DOMAIN × INTERVAL INTERACTION ===")
three_way_emmeans <- emmeans(aov_model, ~ TIME * DOMAIN * INTERVAL)
print("Estimated Marginal Means:")
print(three_way_emmeans)

print("\nSimple Effects of TIME within each DOMAIN × INTERVAL combination:")
three_way_contrasts <- pairs(three_way_emmeans, by = c("DOMAIN", "INTERVAL"), adjust = "bonferroni")
print(three_way_contrasts)

# Between-subjects × within-subjects interactions
print("\n=== temporal_DO × TIME INTERACTION ===")
temporal_time_emmeans <- emmeans(aov_model, ~ temporal_DO * TIME)
print("Estimated Marginal Means:")
print(temporal_time_emmeans)

print("\nSimple Effects of TIME within each temporal_DO:")
temporal_time_simple <- pairs(temporal_time_emmeans, by = "temporal_DO", adjust = "bonferroni")
print(temporal_time_simple)

print("\nSimple Effects of temporal_DO within each TIME:")
temporal_time_simple2 <- pairs(temporal_time_emmeans, by = "TIME", adjust = "bonferroni")
print(temporal_time_simple2)

# =============================================================================
# COHEN'S D CALCULATIONS FOR SIGNIFICANT EFFECTS
# =============================================================================

print("\n=== COHEN'S D FOR SIGNIFICANT EFFECTS ===")

# Function to calculate Cohen's d for pairwise comparisons
calculate_cohens_d_for_pairs <- function(pairs_df, data, group1_var, group2_var, response_var) {
  significant_pairs <- pairs_df[pairs_df$p.value < 0.05, ]
  
  if(nrow(significant_pairs) > 0) {
    print("Significant pairwise comparisons (p < 0.05):")
    print(significant_pairs)
    
    # Calculate Cohen's d for all significant pairs
    cohens_d_results <- data.frame()
    
    for(i in seq_len(nrow(significant_pairs))) {
      comparison <- significant_pairs[i, ]
      contrast_name <- as.character(comparison$contrast)
      
      # Parse the contrast
      contrast_parts <- strsplit(contrast_name, " - ")[[1]]
      if(length(contrast_parts) == 2) {
        level1 <- trimws(contrast_parts[1])
        level2 <- trimws(contrast_parts[2])
        
        # Get raw data for both conditions
        if(group2_var %in% colnames(comparison)) {
          group2_level <- as.character(comparison[[group2_var]])
          data1 <- data[[response_var]][
            data[[group1_var]] == level1 & 
            data[[group2_var]] == group2_level]
          
          data2 <- data[[response_var]][
            data[[group1_var]] == level2 & 
            data[[group2_var]] == group2_level]
        } else {
          data1 <- data[[response_var]][data[[group1_var]] == level1]
          data2 <- data[[response_var]][data[[group1_var]] == level2]
        }
        
        if(length(data1) > 0 && length(data2) > 0) {
          # Calculate Cohen's d using effsize package
          cohens_d_result <- cohen.d(data1, data2)
          
          result_row <- data.frame(
            Comparison = contrast_name,
            n1 = length(data1),
            n2 = length(data2),
            Cohens_d = round(cohens_d_result$estimate, 5),
            Effect_size = cohens_d_result$magnitude,
            p_value = round(comparison$p.value, 5)
          )
          
          if(group2_var %in% colnames(comparison)) {
            result_row$Group_level <- group2_level
          }
          
          cohens_d_results <- rbind(cohens_d_results, result_row)
        }
      }
    }
    
    if(nrow(cohens_d_results) > 0) {
      print("Cohen's d results:")
      print(cohens_d_results)
    }
  } else {
    print("No significant pairwise comparisons found.")
  }
}

# Calculate Cohen's d for main effects
print("Cohen's d for significant main effects:")
time_contrasts_df <- as.data.frame(time_contrasts)
calculate_cohens_d_for_pairs(time_contrasts_df, long_data_clean, "TIME", NULL, "DGEN_SCORE")

domain_contrasts_df <- as.data.frame(domain_contrasts)
calculate_cohens_d_for_pairs(domain_contrasts_df, long_data_clean, "DOMAIN", NULL, "DGEN_SCORE")

interval_contrasts_df <- as.data.frame(interval_contrasts)
calculate_cohens_d_for_pairs(interval_contrasts_df, long_data_clean, "INTERVAL", NULL, "DGEN_SCORE")

# Calculate Cohen's d for two-way interactions
print("\nCohen's d for significant two-way interactions:")
time_domain_simple_df <- as.data.frame(time_domain_simple)
calculate_cohens_d_for_pairs(time_domain_simple_df, long_data_clean, "DOMAIN", "TIME", "DGEN_SCORE")

time_domain_simple2_df <- as.data.frame(time_domain_simple2)
calculate_cohens_d_for_pairs(time_domain_simple2_df, long_data_clean, "TIME", "DOMAIN", "DGEN_SCORE")

# Calculate Cohen's d for three-way interaction
print("\nCohen's d for significant three-way interaction effects:")
three_way_contrasts_df <- as.data.frame(three_way_contrasts)
significant_three_way <- three_way_contrasts_df[three_way_contrasts_df$p.value < 0.05, ]

if(nrow(significant_three_way) > 0) {
  for(i in seq_len(nrow(significant_three_way))) {
    comparison <- significant_three_way[i, ]
    
    # Extract the grouping variables
    domain_level <- as.character(comparison$DOMAIN)
    interval_level <- as.character(comparison$INTERVAL)
    
    # Get data for Past and Future within this DOMAIN × INTERVAL combination
    past_data <- long_data_clean$DGEN_SCORE[
      long_data_clean$DOMAIN == domain_level & 
      long_data_clean$INTERVAL == interval_level & 
      long_data_clean$TIME == "Past"
    ]
    
    future_data <- long_data_clean$DGEN_SCORE[
      long_data_clean$DOMAIN == domain_level & 
      long_data_clean$INTERVAL == interval_level & 
      long_data_clean$TIME == "Future"
    ]
    
    if(length(past_data) > 0 && length(future_data) > 0) {
      # Calculate Cohen's d using effsize package
      cohens_d_result <- cohen.d(past_data, future_data)
      
      cat(sprintf("DOMAIN = %s, INTERVAL = %s:\n", domain_level, interval_level))
      cat(sprintf("  Past vs Future comparison\n"))
      cat(sprintf("  n_Past = %d, n_Future = %d\n", length(past_data), length(future_data)))
      cat(sprintf("  Cohen's d: %.5f\n", cohens_d_result$estimate))
      cat(sprintf("  Effect size interpretation: %s\n", cohens_d_result$magnitude))
      cat(sprintf("  p-value: %.5f\n", comparison$p.value))
      cat(sprintf("  Estimated difference: %.5f\n", comparison$estimate))
      cat("\n")
    }
  }
} else {
  cat("No significant TIME effects found within any DOMAIN × INTERVAL combination.\n")
}

print("\n=== ANALYSIS COMPLETE ===")
print("All significant and marginal effects have been analyzed with Cohen's d calculations.")
print("The analysis includes:")
print("- Descriptive statistics by all factor combinations")
print("- Comprehensive assumption testing (normality, homogeneity of variance, Hartley's F-max)")
print("- Mixed ANOVA with sphericity corrections")
print("- Effect sizes (generalized eta squared)")
print("- Post-hoc comparisons with Bonferroni correction")
print("- Cohen's d calculations for significant effects")