875 lines
33 KiB
R
875 lines
33 KiB
R
# Mixed ANOVA Analysis for DGEN Variables
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# EOHI Experiment Data Analysis - DGEN Level Analysis
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# Variables: pastPref_DGEN, pastPers_DGEN, pastVal_DGEN, pastLife_DGEN
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# futPref_DGEN, futPers_DGEN, futVal_DGEN, futLife_DGEN
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# Load required libraries
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library(tidyverse)
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library(ez)
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library(car)
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library(afex) # For aov_ez (cleaner ANOVA output)
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library(nortest) # For normality tests
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library(emmeans) # For post-hoc comparisons
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library(purrr) # For map functions
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library(effsize) # For Cohen's d calculations
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library(effectsize) # For effect size calculations
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# Global options to remove scientific notation
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options(scipen = 999)
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# Set contrasts to sum for mixed ANOVA (necessary for proper interpretation)
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options(contrasts = c("contr.sum", "contr.poly"))
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setwd("C:/Users/irina/Documents/DND/EOHI/eohi1")
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# Read the data
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data <- read.csv("exp1.csv")
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# Verify the specific variables we need
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required_vars <- c("pastPref_DGEN", "pastPers_DGEN", "pastVal_DGEN", "pastLife_DGEN",
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"futPref_DGEN", "futPers_DGEN", "futVal_DGEN", "futLife_DGEN")
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missing_vars <- required_vars[!required_vars %in% colnames(data)]
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if (length(missing_vars) > 0) {
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print(paste("Warning: Missing variables:", paste(missing_vars, collapse = ", ")))
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}
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# Define domain mapping
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domain_mapping <- data.frame(
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variable = c("pastPref_DGEN", "pastPers_DGEN", "pastVal_DGEN", "pastLife_DGEN",
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"futPref_DGEN", "futPers_DGEN", "futVal_DGEN", "futLife_DGEN"),
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time = c(rep("Past", 4), rep("Future", 4)),
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domain = rep(c("Preferences", "Personality", "Values", "Life"), 2),
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stringsAsFactors = FALSE
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)
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# Efficient data pivoting using pivot_longer
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long_data <- data %>%
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select(pID, ResponseId, TEMPORAL_DO, all_of(required_vars)) %>%
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pivot_longer(
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cols = all_of(required_vars),
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names_to = "variable",
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values_to = "DGEN_SCORE"
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) %>%
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left_join(domain_mapping, by = "variable") %>%
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# Convert to factors with proper levels (note: columns are 'time' and 'domain' from mapping)
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mutate(
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TIME = factor(time, levels = c("Past", "Future")),
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DOMAIN = factor(domain, levels = c("Preferences", "Personality", "Values", "Life")),
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pID = as.factor(pID),
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TEMPORAL_DO = as.factor(TEMPORAL_DO)
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) %>%
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# Select final columns and remove any rows with missing values
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select(pID, ResponseId, TEMPORAL_DO, TIME, DOMAIN, DGEN_SCORE) %>%
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filter(!is.na(DGEN_SCORE))
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# =============================================================================
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# DESCRIPTIVE STATISTICS
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# =============================================================================
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# Overall descriptive statistics by TIME and DOMAIN
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desc_stats <- long_data %>%
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group_by(TIME, DOMAIN) %>%
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summarise(
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n = n(),
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mean = round(mean(DGEN_SCORE, na.rm = TRUE), 5),
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variance = round(var(DGEN_SCORE, na.rm = TRUE), 5),
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sd = round(sd(DGEN_SCORE, na.rm = TRUE), 5),
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median = round(median(DGEN_SCORE, na.rm = TRUE), 5),
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q1 = round(quantile(DGEN_SCORE, 0.25, na.rm = TRUE), 5),
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q3 = round(quantile(DGEN_SCORE, 0.75, na.rm = TRUE), 5),
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min = round(min(DGEN_SCORE, na.rm = TRUE), 5),
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max = round(max(DGEN_SCORE, na.rm = TRUE), 5),
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.groups = 'drop'
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)
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print("Descriptive statistics by TIME and DOMAIN:")
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print(desc_stats)
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# Descriptive statistics by between-subjects factors
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desc_stats_by_temporal <- long_data %>%
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group_by(TEMPORAL_DO, TIME, DOMAIN) %>%
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summarise(
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n = n(),
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mean = round(mean(DGEN_SCORE, na.rm = TRUE), 5),
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variance = round(var(DGEN_SCORE, na.rm = TRUE), 5),
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sd = round(sd(DGEN_SCORE, na.rm = TRUE), 5),
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.groups = 'drop'
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)
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print("Descriptive statistics by TEMPORAL_DO, TIME, and DOMAIN:")
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print(desc_stats_by_temporal)
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# =============================================================================
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# ASSUMPTION TESTING
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# =============================================================================
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# Remove missing values for assumption testing
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long_data_clean <- long_data[!is.na(long_data$DGEN_SCORE), ]
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# 1. Missing values check
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missing_summary <- long_data %>%
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group_by(TIME, DOMAIN) %>%
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summarise(
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n_total = n(),
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n_missing = sum(is.na(DGEN_SCORE)),
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pct_missing = round(100 * n_missing / n_total, 2),
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.groups = 'drop'
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)
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print("Missing values by TIME and DOMAIN:")
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print(missing_summary)
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# 2. Outlier detection
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outlier_summary <- long_data_clean %>%
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group_by(TIME, DOMAIN) %>%
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summarise(
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n = n(),
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mean = mean(DGEN_SCORE),
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sd = sd(DGEN_SCORE),
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q1 = quantile(DGEN_SCORE, 0.25),
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q3 = quantile(DGEN_SCORE, 0.75),
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iqr = q3 - q1,
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lower_bound = q1 - 1.5 * iqr,
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upper_bound = q3 + 1.5 * iqr,
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n_outliers = sum(DGEN_SCORE < lower_bound | DGEN_SCORE > upper_bound),
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.groups = 'drop'
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)
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print("Outlier summary (IQR method):")
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print(outlier_summary)
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# 3. Anderson-Darling normality test (streamlined)
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normality_results <- long_data_clean %>%
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group_by(TIME, DOMAIN) %>%
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summarise(
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n = n(),
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ad_statistic = ad.test(.data$DGEN_SCORE)$statistic,
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ad_p_value = ad.test(.data$DGEN_SCORE)$p.value,
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.groups = 'drop'
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)
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print("Anderson-Darling normality test results:")
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# Round only the numeric columns
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normality_results_rounded <- normality_results %>%
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mutate(across(where(is.numeric), ~ round(.x, 5)))
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print(normality_results_rounded)
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# 4. Homogeneity of variance (Levene's test)
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# Test homogeneity across TIME within each DOMAIN
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homogeneity_time <- long_data_clean %>%
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group_by(DOMAIN) %>%
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summarise(
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levene_F = leveneTest(DGEN_SCORE ~ TIME)$`F value`[1],
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levene_p = leveneTest(DGEN_SCORE ~ TIME)$`Pr(>F)`[1],
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.groups = 'drop'
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)
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print("Homogeneity of variance across TIME within each DOMAIN:")
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print(homogeneity_time)
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# Test homogeneity across DOMAIN within each TIME
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homogeneity_domain <- long_data_clean %>%
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group_by(TIME) %>%
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summarise(
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levene_F = leveneTest(DGEN_SCORE ~ DOMAIN)$`F value`[1],
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levene_p = leveneTest(DGEN_SCORE ~ DOMAIN)$`Pr(>F)`[1],
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.groups = 'drop'
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)
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print("Homogeneity of variance across DOMAIN within each TIME:")
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print(homogeneity_domain)
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# =============================================================================
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# HARTLEY'S F-MAX TEST WITH BOOTSTRAP CRITICAL VALUES
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# =============================================================================
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# Function to calculate Hartley's F-max ratio
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calculate_hartley_ratio <- function(variances) {
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max(variances, na.rm = TRUE) / min(variances, na.rm = TRUE)
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}
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# =============================================================================
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# CALCULATE OBSERVED F-MAX RATIOS FOR MIXED ANOVA
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# =============================================================================
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# For mixed ANOVA: Test homogeneity across BETWEEN-SUBJECTS factor (TEMPORAL_DO)
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# within each combination of within-subjects factors (TIME × DOMAIN)
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print("=== OBSERVED F-MAX RATIOS: TEMPORAL_DO within each TIME × DOMAIN combination ===")
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observed_temporal_ratios <- long_data_clean %>%
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group_by(TIME, DOMAIN) %>%
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summarise(
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# Calculate variances for each TEMPORAL_DO level within this TIME × DOMAIN combination
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past_var = var(DGEN_SCORE[TEMPORAL_DO == "01PAST"], na.rm = TRUE),
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fut_var = var(DGEN_SCORE[TEMPORAL_DO == "02FUT"], na.rm = TRUE),
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# Calculate F-max ratio
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f_max_ratio = max(past_var, fut_var) / min(past_var, fut_var),
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.groups = 'drop'
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) %>%
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select(TIME, DOMAIN, past_var, fut_var, f_max_ratio)
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print(observed_temporal_ratios)
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# More efficient bootstrap function for Hartley's F-max test
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bootstrap_hartley_critical <- function(data, group_var, response_var, n_iter = 1000) {
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# Get unique groups and their sample sizes
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groups <- unique(data[[group_var]])
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# Calculate observed variances for each group
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observed_vars <- data %>%
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dplyr::group_by(!!rlang::sym(group_var)) %>%
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dplyr::summarise(var = var(!!rlang::sym(response_var), na.rm = TRUE), .groups = 'drop') %>%
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dplyr::pull(var)
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# Handle invalid variances
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if(any(observed_vars <= 0 | is.na(observed_vars))) {
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observed_vars[observed_vars <= 0 | is.na(observed_vars)] <- 1e-10
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}
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# Calculate observed F-max ratio
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observed_ratio <- max(observed_vars) / min(observed_vars)
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# Pre-allocate storage for bootstrap ratios
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bootstrap_ratios <- numeric(n_iter)
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# Get group data once
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group_data_list <- map(groups, ~ {
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group_data <- data[data[[group_var]] == .x, response_var]
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group_data[!is.na(group_data)]
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})
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# Bootstrap with pre-allocated storage
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for(i in 1:n_iter) {
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# Bootstrap sample from each group independently
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sample_vars <- map_dbl(group_data_list, ~ {
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bootstrap_sample <- sample(.x, size = length(.x), replace = TRUE)
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var(bootstrap_sample, na.rm = TRUE)
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})
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bootstrap_ratios[i] <- max(sample_vars) / min(sample_vars)
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}
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# Remove invalid ratios
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valid_ratios <- bootstrap_ratios[is.finite(bootstrap_ratios) & !is.na(bootstrap_ratios)]
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if(length(valid_ratios) == 0) {
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stop("No valid bootstrap ratios generated")
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}
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# Calculate critical value (95th percentile)
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critical_95 <- quantile(valid_ratios, 0.95, na.rm = TRUE)
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# Return only essential information
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return(list(
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observed_ratio = observed_ratio,
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critical_95 = critical_95,
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n_valid_iterations = length(valid_ratios)
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))
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}
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# Hartley's F-max test across TEMPORAL_DO within each TIME × DOMAIN combination
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print("=== HARTLEY'S F-MAX TEST RESULTS ===")
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set.seed(123) # For reproducibility
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hartley_temporal_results <- long_data_clean %>%
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group_by(TIME, DOMAIN) %>%
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summarise(
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hartley_result = list(bootstrap_hartley_critical(pick(TEMPORAL_DO, DGEN_SCORE), "TEMPORAL_DO", "DGEN_SCORE")),
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.groups = 'drop'
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) %>%
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mutate(
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observed_ratio = map_dbl(hartley_result, ~ .x$observed_ratio),
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critical_95 = map_dbl(hartley_result, ~ .x$critical_95),
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significant = observed_ratio > critical_95
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) %>%
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select(TIME, DOMAIN, observed_ratio, critical_95, significant)
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print(hartley_temporal_results)
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# =============================================================================
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# MIXED ANOVA ANALYSIS
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# =============================================================================
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# Check if design is balanced
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design_balance <- table(long_data_clean$pID, long_data_clean$TIME, long_data_clean$DOMAIN)
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if(all(design_balance %in% c(0, 1))) {
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print("Design is balanced: each participant has data for all TIME × DOMAIN combinations")
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} else {
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print("Warning: Design is unbalanced")
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print(summary(as.vector(design_balance)))
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}
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# =============================================================================
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# MIXED ANOVA WITH SPHERICITY CORRECTIONS
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# =============================================================================
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print("=== MIXED ANOVA RESULTS (with sphericity corrections) ===")
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# Mixed ANOVA using ezANOVA with automatic sphericity corrections
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# Between-subjects: TEMPORAL_DO (2 levels: 01PAST, 02FUT)
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# Within-subjects: TIME (2 levels: Past, Future) × DOMAIN (4 levels: Preferences, Personality, Values, Life)
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mixed_anova_model <- ezANOVA(data = long_data_clean,
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dv = DGEN_SCORE,
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wid = pID,
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between = TEMPORAL_DO,
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within = .(TIME, DOMAIN),
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type = 3,
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detailed = TRUE)
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anova_output <- mixed_anova_model$ANOVA
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rownames(anova_output) <- NULL # Reset row numbers to be sequential
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print(anova_output)
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# Show Mauchly's test for sphericity
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print("Mauchly's Test of Sphericity:")
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print(mixed_anova_model$Mauchly)
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# Show sphericity-corrected results (Greenhouse-Geisser and Huynh-Feldt)
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if(!is.null(mixed_anova_model$`Sphericity Corrections`)) {
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print("Greenhouse-Geisser and Huynh-Feldt Corrections:")
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print(mixed_anova_model$`Sphericity Corrections`)
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# Extract and display corrected degrees of freedom
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cat("\n=== CORRECTED DEGREES OF FREEDOM ===\n")
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sphericity_corr <- mixed_anova_model$`Sphericity Corrections`
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anova_table <- mixed_anova_model$ANOVA
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corrected_df <- data.frame(
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Effect = sphericity_corr$Effect,
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Original_DFn = anova_table$DFn[match(sphericity_corr$Effect, anova_table$Effect)],
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Original_DFd = anova_table$DFd[match(sphericity_corr$Effect, anova_table$Effect)],
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GG_DFn = anova_table$DFn[match(sphericity_corr$Effect, anova_table$Effect)] * sphericity_corr$GGe,
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GG_DFd = anova_table$DFd[match(sphericity_corr$Effect, anova_table$Effect)] * sphericity_corr$GGe,
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HF_DFn = anova_table$DFn[match(sphericity_corr$Effect, anova_table$Effect)] * sphericity_corr$HFe,
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HF_DFd = anova_table$DFd[match(sphericity_corr$Effect, anova_table$Effect)] * sphericity_corr$HFe,
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GG_epsilon = sphericity_corr$GGe,
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HF_epsilon = sphericity_corr$HFe
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)
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print(corrected_df)
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cat("\n=== CORRECTED F-TESTS ===\n")
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for(i in seq_len(nrow(corrected_df))) {
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effect <- corrected_df$Effect[i]
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f_value <- anova_table$F[match(effect, anova_table$Effect)]
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cat(sprintf("\n%s:\n", effect))
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cat(sprintf(" Original: F(%d, %d) = %.3f\n",
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corrected_df$Original_DFn[i], corrected_df$Original_DFd[i], f_value))
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cat(sprintf(" GG-corrected: F(%.2f, %.2f) = %.3f, p = %.6f\n",
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corrected_df$GG_DFn[i], corrected_df$GG_DFd[i], f_value, sphericity_corr$`p[GG]`[i]))
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cat(sprintf(" HF-corrected: F(%.2f, %.2f) = %.3f, p = %.6f\n",
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corrected_df$HF_DFn[i], corrected_df$HF_DFd[i], f_value, sphericity_corr$`p[HF]`[i]))
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}
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} else {
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print("\nNote: Sphericity corrections not needed (sphericity assumption met)")
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}
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# =============================================================================
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# EFFECT SIZES (GENERALIZED ETA SQUARED)
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# =============================================================================
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print("\n=== EFFECT SIZES (GENERALIZED ETA SQUARED) ===")
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# Extract generalized eta squared from ezANOVA (already calculated)
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effect_sizes <- mixed_anova_model$ANOVA[, c("Effect", "ges")]
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effect_sizes$ges <- round(effect_sizes$ges, 5)
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print("Generalized Eta Squared:")
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print(effect_sizes)
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# =============================================================================
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# POST-HOC COMPARISONS
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# =============================================================================
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# Post-hoc comparisons using emmeans
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print("\n=== POST-HOC COMPARISONS ===")
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# Create aov model for emmeans (emmeans requires aov object, not ezANOVA output)
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aov_model <- aov(DGEN_SCORE ~ TEMPORAL_DO * TIME * DOMAIN + Error(pID/(TIME * DOMAIN)),
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data = long_data_clean)
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# Main effect of TIME
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print("Main Effect of TIME:")
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time_emmeans <- emmeans(aov_model, ~ TIME)
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print("Estimated Marginal Means:")
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print(time_emmeans)
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print("\nPairwise Contrasts:")
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time_contrasts <- pairs(time_emmeans, adjust = "bonferroni")
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print(time_contrasts)
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# Main effect of DOMAIN
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print("\nMain Effect of DOMAIN:")
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domain_emmeans <- emmeans(aov_model, ~ DOMAIN)
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print("Estimated Marginal Means:")
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print(domain_emmeans)
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print("\nPairwise Contrasts:")
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domain_contrasts <- pairs(domain_emmeans, adjust = "bonferroni")
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print(domain_contrasts)
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# Main effect of TEMPORAL_DO
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print("\nMain Effect of TEMPORAL_DO:")
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temporal_emmeans <- emmeans(aov_model, ~ TEMPORAL_DO)
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temporal_contrasts <- pairs(temporal_emmeans, adjust = "bonferroni")
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print(temporal_contrasts)
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# =============================================================================
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# INTERACTION EXPLORATIONS
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# =============================================================================
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# TEMPORAL_DO × TIME Interaction
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print("\n=== TEMPORAL_DO × TIME INTERACTION ===")
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temporal_time_emmeans <- emmeans(aov_model, ~ TEMPORAL_DO * TIME)
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print("Estimated Marginal Means:")
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print(temporal_time_emmeans)
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print("\nSimple Effects of TIME within each TEMPORAL_DO:")
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temporal_time_simple <- pairs(temporal_time_emmeans, by = "TEMPORAL_DO", adjust = "bonferroni")
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print(temporal_time_simple)
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print("\nSimple Effects of TEMPORAL_DO within each TIME:")
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temporal_time_simple2 <- pairs(temporal_time_emmeans, by = "TIME", adjust = "bonferroni")
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print(temporal_time_simple2)
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# TIME × DOMAIN Interaction
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print("\n=== TIME × DOMAIN INTERACTION ===")
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time_domain_emmeans <- emmeans(aov_model, ~ TIME * DOMAIN)
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print("Estimated Marginal Means:")
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print(time_domain_emmeans)
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print("\nSimple Effects of DOMAIN within each TIME:")
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time_domain_simple <- pairs(time_domain_emmeans, by = "TIME", adjust = "bonferroni")
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print(time_domain_simple)
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print("\nSimple Effects of TIME within each DOMAIN:")
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time_domain_simple2 <- pairs(time_domain_emmeans, by = "DOMAIN", adjust = "bonferroni")
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print(time_domain_simple2)
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# TEMPORAL_DO × DOMAIN Interaction
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print("\n=== TEMPORAL_DO × DOMAIN INTERACTION ===")
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temporal_domain_emmeans <- emmeans(aov_model, ~ TEMPORAL_DO * DOMAIN)
|
||
print("Estimated Marginal Means:")
|
||
print(temporal_domain_emmeans)
|
||
|
||
print("\nSimple Effects of DOMAIN within each TEMPORAL_DO:")
|
||
temporal_domain_simple <- pairs(temporal_domain_emmeans, by = "TEMPORAL_DO", adjust = "bonferroni")
|
||
print(temporal_domain_simple)
|
||
|
||
print("\nSimple Effects of TEMPORAL_DO within each DOMAIN:")
|
||
temporal_domain_simple2 <- pairs(temporal_domain_emmeans, by = "DOMAIN", adjust = "bonferroni")
|
||
print(temporal_domain_simple2)
|
||
|
||
# =============================================================================
|
||
# THREE-WAY INTERACTION ANALYSIS
|
||
# =============================================================================
|
||
|
||
print("\n=== THREE-WAY INTERACTION ANALYSIS ===")
|
||
three_way_emmeans <- emmeans(aov_model, ~ TEMPORAL_DO * TIME * DOMAIN)
|
||
print("Estimated Marginal Means:")
|
||
print(three_way_emmeans)
|
||
|
||
print("\nSimple Effects of TIME within each TEMPORAL_DO × DOMAIN combination:")
|
||
three_way_contrasts <- pairs(three_way_emmeans, by = c("TEMPORAL_DO", "DOMAIN"), adjust = "bonferroni")
|
||
print(three_way_contrasts)
|
||
|
||
# =============================================================================
|
||
# COHEN'S D FOR SIGNIFICANT TWO-WAY INTERACTIONS
|
||
# =============================================================================
|
||
|
||
# Cohen's d calculations (library already loaded)
|
||
|
||
print("\n=== COHEN'S D FOR SIGNIFICANT TWO-WAY INTERACTIONS ===")
|
||
|
||
# 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) {
|
||
cat("Significant pairwise comparisons (p < 0.05):\n")
|
||
print(significant_pairs)
|
||
|
||
cat("\nCohen's d calculated from raw data:\n")
|
||
|
||
for(i in seq_len(nrow(significant_pairs))) {
|
||
comparison <- significant_pairs[i, ]
|
||
contrast_name <- as.character(comparison$contrast)
|
||
|
||
# Parse the contrast
|
||
contrast_parts <- strsplit(contrast_name, " - ")[[1]]
|
||
if(length(contrast_parts) == 2) {
|
||
level1 <- trimws(contrast_parts[1])
|
||
level2 <- trimws(contrast_parts[2])
|
||
|
||
# Get raw data for both conditions
|
||
if(group2_var %in% colnames(comparison)) {
|
||
group2_level <- as.character(comparison[[group2_var]])
|
||
data1 <- data[[response_var]][
|
||
data[[group1_var]] == level1 &
|
||
data[[group2_var]] == group2_level]
|
||
|
||
data2 <- data[[response_var]][
|
||
data[[group1_var]] == level2 &
|
||
data[[group2_var]] == group2_level]
|
||
} else {
|
||
data1 <- data[[response_var]][data[[group1_var]] == level1]
|
||
data2 <- data[[response_var]][data[[group1_var]] == level2]
|
||
}
|
||
|
||
if(length(data1) > 0 && length(data2) > 0) {
|
||
# Calculate Cohen's d using effsize package
|
||
cohens_d_result <- cohen.d(data1, data2)
|
||
|
||
cat(sprintf("Comparison: %s", contrast_name))
|
||
if(group2_var %in% colnames(comparison)) {
|
||
cat(sprintf(" | %s", group2_level))
|
||
}
|
||
cat(sprintf("\n n1 = %d, n2 = %d\n", length(data1), length(data2)))
|
||
cat(sprintf(" Cohen's d: %.5f\n", cohens_d_result$estimate))
|
||
cat(sprintf(" Effect size interpretation: %s\n", cohens_d_result$magnitude))
|
||
cat(sprintf(" p-value: %.5f\n", comparison$p.value))
|
||
cat("\n")
|
||
}
|
||
}
|
||
}
|
||
} else {
|
||
cat("No significant pairwise comparisons found.\n")
|
||
}
|
||
}
|
||
|
||
# =============================================================================
|
||
# 1. TEMPORAL_DO × TIME INTERACTION
|
||
# =============================================================================
|
||
|
||
print("\n=== COHEN'S D FOR TEMPORAL_DO × TIME INTERACTION ===")
|
||
|
||
# Get simple effects of TIME within each TEMPORAL_DO
|
||
temporal_time_simple_df <- as.data.frame(temporal_time_simple)
|
||
calculate_cohens_d_for_pairs(temporal_time_simple_df, long_data_clean, "TIME", "TEMPORAL_DO", "DGEN_SCORE")
|
||
|
||
# Get simple effects of TEMPORAL_DO within each TIME
|
||
temporal_time_simple2_df <- as.data.frame(temporal_time_simple2)
|
||
calculate_cohens_d_for_pairs(temporal_time_simple2_df, long_data_clean, "TEMPORAL_DO", "TIME", "DGEN_SCORE")
|
||
|
||
# =============================================================================
|
||
# 2. TIME × DOMAIN INTERACTION
|
||
# =============================================================================
|
||
|
||
print("\n=== COHEN'S D FOR TIME × DOMAIN INTERACTION ===")
|
||
|
||
# Get simple effects of TIME within each DOMAIN
|
||
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")
|
||
|
||
# Get simple effects of DOMAIN within each TIME
|
||
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")
|
||
|
||
# =============================================================================
|
||
# 3. TEMPORAL_DO × DOMAIN INTERACTION
|
||
# =============================================================================
|
||
|
||
print("\n=== COHEN'S D FOR TEMPORAL_DO × DOMAIN INTERACTION ===")
|
||
|
||
# Get simple effects of TEMPORAL_DO within each DOMAIN
|
||
temporal_domain_simple2_df <- as.data.frame(temporal_domain_simple2)
|
||
calculate_cohens_d_for_pairs(temporal_domain_simple2_df, long_data_clean, "TEMPORAL_DO", "DOMAIN", "DGEN_SCORE")
|
||
|
||
# Get simple effects of DOMAIN within each TEMPORAL_DO
|
||
temporal_domain_simple_df <- as.data.frame(temporal_domain_simple)
|
||
calculate_cohens_d_for_pairs(temporal_domain_simple_df, long_data_clean, "DOMAIN", "TEMPORAL_DO", "DGEN_SCORE")
|
||
|
||
# =============================================================================
|
||
# 4. THREE-WAY INTERACTION COHEN'S D
|
||
# =============================================================================
|
||
|
||
print("\n=== COHEN'S D FOR THREE-WAY INTERACTION ===")
|
||
|
||
# Get pairwise comparisons for the three-way interaction
|
||
three_way_contrasts_df <- as.data.frame(three_way_contrasts)
|
||
print("The pairwise comparisons show the TIME effects within each TEMPORAL_DO × DOMAIN combination:")
|
||
print(three_way_contrasts_df)
|
||
|
||
# Calculate Cohen's d for significant three-way interaction effects
|
||
print("\nCohen's d calculations for significant TIME effects within each TEMPORAL_DO × DOMAIN combination:")
|
||
|
||
# Extract significant comparisons (p < 0.05)
|
||
significant_three_way <- three_way_contrasts_df[three_way_contrasts_df$p.value < 0.05, ]
|
||
|
||
if(nrow(significant_three_way) > 0) {
|
||
for(i in seq_len(nrow(significant_three_way))) {
|
||
comparison <- significant_three_way[i, ]
|
||
|
||
# Extract the grouping variables
|
||
temporal_do_level <- as.character(comparison$TEMPORAL_DO)
|
||
domain_level <- as.character(comparison$DOMAIN)
|
||
|
||
# Get data for Past and Future within this TEMPORAL_DO × DOMAIN combination
|
||
past_data <- long_data_clean$DGEN_SCORE[
|
||
long_data_clean$TEMPORAL_DO == temporal_do_level &
|
||
long_data_clean$DOMAIN == domain_level &
|
||
long_data_clean$TIME == "Past"
|
||
]
|
||
|
||
future_data <- long_data_clean$DGEN_SCORE[
|
||
long_data_clean$TEMPORAL_DO == temporal_do_level &
|
||
long_data_clean$DOMAIN == domain_level &
|
||
long_data_clean$TIME == "Future"
|
||
]
|
||
|
||
if(length(past_data) > 0 && length(future_data) > 0) {
|
||
# Calculate Cohen's d using effsize package
|
||
cohens_d_result <- cohen.d(past_data, future_data)
|
||
|
||
cat(sprintf("TEMPORAL_DO = %s, DOMAIN = %s:\n", temporal_do_level, domain_level))
|
||
cat(sprintf(" Past vs Future comparison\n"))
|
||
cat(sprintf(" n_Past = %d, n_Future = %d\n", length(past_data), length(future_data)))
|
||
cat(sprintf(" Cohen's d: %.5f\n", cohens_d_result$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 TEMPORAL_DO × DOMAIN combination.\n")
|
||
}
|
||
|
||
# =============================================================================
|
||
# INTERACTION PLOTS
|
||
# =============================================================================
|
||
|
||
print("=== INTERACTION PLOTS ===")
|
||
|
||
# Define color palette for DOMAIN (4 levels)
|
||
domain_colors <- c("Preferences" = "#648FFF", "Personality" = "#DC267F",
|
||
"Values" = "#FFB000", "Life" = "#FE6100")
|
||
|
||
# TEMPORAL_DO × DOMAIN INTERACTION PLOT
|
||
# Create estimated marginal means for TEMPORAL_DO × DOMAIN
|
||
emm_temporal_domain <- emmeans(aov_model, ~ TEMPORAL_DO * DOMAIN)
|
||
|
||
# Prepare emmeans data frame
|
||
emmeans_temporal_domain <- emm_temporal_domain %>%
|
||
as.data.frame() %>%
|
||
filter(!is.na(lower.CL) & !is.na(upper.CL) & !is.na(emmean)) %>%
|
||
rename(
|
||
ci_lower = lower.CL,
|
||
ci_upper = upper.CL,
|
||
plot_mean = emmean
|
||
) %>%
|
||
mutate(
|
||
TEMPORAL_DO = factor(TEMPORAL_DO, levels = c("01PAST", "02FUT")),
|
||
DOMAIN = factor(DOMAIN, levels = c("Preferences", "Personality", "Values", "Life"))
|
||
)
|
||
|
||
# Prepare raw data for plotting
|
||
iPlot_temporal_domain <- long_data_clean %>%
|
||
dplyr::select(pID, TEMPORAL_DO, DOMAIN, DGEN_SCORE) %>%
|
||
mutate(
|
||
TEMPORAL_DO = factor(TEMPORAL_DO, levels = c("01PAST", "02FUT")),
|
||
DOMAIN = factor(DOMAIN, levels = c("Preferences", "Personality", "Values", "Life"))
|
||
)
|
||
|
||
# Create TEMPORAL_DO × DOMAIN interaction plot - clean line plot with distribution
|
||
# Convert to numeric x-axis and add position offsets for dodging
|
||
dodge_width <- 0.6
|
||
iPlot_temporal_domain <- iPlot_temporal_domain %>%
|
||
mutate(
|
||
x_pos = as.numeric(TEMPORAL_DO),
|
||
domain_offset = (as.numeric(DOMAIN) - 2.5) * (dodge_width / 4),
|
||
x_dodged = x_pos + domain_offset
|
||
)
|
||
|
||
emmeans_temporal_domain <- emmeans_temporal_domain %>%
|
||
mutate(
|
||
x_pos = as.numeric(TEMPORAL_DO),
|
||
domain_offset = (as.numeric(DOMAIN) - 2.5) * (dodge_width / 4),
|
||
x_dodged = x_pos + domain_offset
|
||
)
|
||
|
||
interaction_plot_temporal_domain <- ggplot() +
|
||
# Distribution layer - violins (completely separated)
|
||
geom_violin(
|
||
data = iPlot_temporal_domain,
|
||
aes(x = x_dodged, y = DGEN_SCORE, fill = DOMAIN, group = interaction(x_pos, DOMAIN)),
|
||
alpha = 0.4,
|
||
color = NA,
|
||
trim = FALSE,
|
||
scale = "width",
|
||
width = dodge_width / 4
|
||
) +
|
||
# Emmeans error bars
|
||
geom_errorbar(
|
||
data = emmeans_temporal_domain,
|
||
aes(x = x_dodged, ymin = ci_lower, ymax = ci_upper),
|
||
width = 0.08,
|
||
linewidth = 0.8,
|
||
color = "black"
|
||
) +
|
||
# Emmeans points
|
||
geom_point(
|
||
data = emmeans_temporal_domain,
|
||
aes(x = x_dodged, y = plot_mean, fill = DOMAIN, shape = DOMAIN),
|
||
size = 4,
|
||
stroke = 1,
|
||
color = "black"
|
||
) +
|
||
labs(
|
||
x = "Order",
|
||
y = "Mean absolute difference from present",
|
||
title = "TEMPORAL_DO × DOMAIN Interaction"
|
||
) +
|
||
scale_x_continuous(
|
||
breaks = c(1, 2),
|
||
labels = c("Past First", "Future First"),
|
||
limits = c(0.4, 2.6)
|
||
) +
|
||
scale_y_continuous(
|
||
limits = c(0, 10),
|
||
breaks = seq(0, 10, 2)
|
||
) +
|
||
scale_color_manual(name = "Domain", values = domain_colors) +
|
||
scale_fill_manual(name = "Domain", values = domain_colors) +
|
||
scale_shape_manual(name = "Domain", values = c(21, 22, 23, 24)) +
|
||
theme_minimal(base_size = 13) +
|
||
theme(
|
||
axis.text = element_text(size = 11),
|
||
axis.title = element_text(size = 12),
|
||
plot.title = element_text(size = 14, hjust = 0.5),
|
||
legend.position = "right",
|
||
legend.title = element_text(size = 11),
|
||
legend.text = element_text(size = 10),
|
||
panel.grid.major.x = element_blank(),
|
||
panel.grid.minor = element_blank(),
|
||
panel.border = element_rect(color = "gray80", fill = NA, linewidth = 0.5)
|
||
)
|
||
|
||
print(interaction_plot_temporal_domain)
|
||
|
||
# =============================================================================
|
||
# EMMEANS-ONLY PLOT: TEMPORAL_DO × DOMAIN INTERACTION
|
||
# =============================================================================
|
||
|
||
# Create fresh emmeans data for emmeans-only plot
|
||
emm_temporal_domain_simple <- emmeans(aov_model, ~ TEMPORAL_DO * DOMAIN)
|
||
|
||
emmeans_temporal_domain_simple <- emm_temporal_domain_simple %>%
|
||
as.data.frame() %>%
|
||
filter(!is.na(lower.CL) & !is.na(upper.CL) & !is.na(emmean)) %>%
|
||
rename(
|
||
ci_lower = lower.CL,
|
||
ci_upper = upper.CL,
|
||
plot_mean = emmean
|
||
) %>%
|
||
mutate(
|
||
TEMPORAL_DO = factor(TEMPORAL_DO, levels = c("01PAST", "02FUT")),
|
||
DOMAIN = factor(DOMAIN, levels = c("Preferences", "Personality", "Values", "Life")),
|
||
x_pos = as.numeric(TEMPORAL_DO),
|
||
domain_offset = (as.numeric(DOMAIN) - 2.5) * (dodge_width / 4),
|
||
x_dodged = x_pos + domain_offset
|
||
)
|
||
|
||
# Create emmeans-only plot
|
||
interaction_plot_emmeans_only <- ggplot(emmeans_temporal_domain_simple) +
|
||
geom_errorbar(
|
||
aes(x = x_dodged, ymin = ci_lower, ymax = ci_upper, color = DOMAIN),
|
||
width = 0.1,
|
||
linewidth = 1,
|
||
alpha = 0.8
|
||
) +
|
||
geom_point(
|
||
aes(x = x_dodged, y = plot_mean, fill = DOMAIN, shape = DOMAIN),
|
||
size = 5,
|
||
stroke = 1.2,
|
||
color = "black"
|
||
) +
|
||
labs(
|
||
x = "Order",
|
||
y = "Absolute difference from the present",
|
||
title = "TEMPORAL_DO × DOMAIN Interaction (Estimated Marginal Means)"
|
||
) +
|
||
scale_x_continuous(
|
||
breaks = c(1, 2),
|
||
labels = c("Past First", "Future First"),
|
||
limits = c(0.4, 2.6)
|
||
) +
|
||
scale_y_continuous(
|
||
limits = c(3, 6),
|
||
breaks = seq(0, 10, 1)
|
||
) +
|
||
scale_color_manual(name = "Domain", values = domain_colors) +
|
||
scale_fill_manual(name = "Domain", values = domain_colors) +
|
||
scale_shape_manual(name = "Domain", values = c(21, 22, 23, 24)) +
|
||
theme_minimal(base_size = 13) +
|
||
theme(
|
||
axis.text = element_text(size = 11),
|
||
axis.title = element_text(size = 12),
|
||
plot.title = element_text(size = 14, hjust = 0.5),
|
||
legend.position = "right",
|
||
legend.title = element_text(size = 11),
|
||
legend.text = element_text(size = 10),
|
||
panel.grid.major.x = element_blank(),
|
||
panel.grid.minor = element_blank(),
|
||
panel.border = element_rect(color = "gray80", fill = NA, linewidth = 0.5)
|
||
)
|
||
|
||
print(interaction_plot_emmeans_only)
|
||
|
||
# =============================================================================
|
||
# MAIN EFFECT PLOT: TIME (Emmeans + Error Bars Only)
|
||
# =============================================================================
|
||
|
||
# Prepare emmeans data frame for TIME main effect
|
||
time_main_emm_df <- time_emmeans %>%
|
||
as.data.frame() %>%
|
||
filter(!is.na(lower.CL) & !is.na(upper.CL) & !is.na(emmean)) %>%
|
||
rename(
|
||
ci_lower = lower.CL,
|
||
ci_upper = upper.CL,
|
||
plot_mean = emmean
|
||
) %>%
|
||
mutate(
|
||
TIME = factor(TIME, levels = c("Past", "Future"))
|
||
)
|
||
|
||
# Define color palette for TIME
|
||
time_colors <- c("Past" = "#648FFF", "Future" = "#DC267F")
|
||
|
||
# Create TIME main-effect plot (style aligned with existing emmeans-only plot)
|
||
time_main_plot <- ggplot(time_main_emm_df) +
|
||
geom_errorbar(
|
||
aes(x = TIME, ymin = ci_lower, ymax = ci_upper, color = TIME),
|
||
width = 0.15,
|
||
linewidth = 1,
|
||
alpha = 0.8
|
||
) +
|
||
geom_point(
|
||
aes(x = TIME, y = plot_mean, fill = TIME, shape = TIME),
|
||
size = 5,
|
||
stroke = 1.2,
|
||
color = "black"
|
||
) +
|
||
labs(
|
||
x = "Time",
|
||
y = "Absolute difference from the present",
|
||
title = "Main Effect of TIME (Estimated Marginal Means)"
|
||
) +
|
||
scale_color_manual(name = "Temporal Direction", values = time_colors) +
|
||
scale_fill_manual(name = "Temporal Direction", values = time_colors) +
|
||
scale_shape_manual(name = "Temporal Direction", values = c(21, 22)) +
|
||
theme_minimal(base_size = 13) +
|
||
theme(
|
||
axis.text = element_text(size = 11),
|
||
axis.title = element_text(size = 12),
|
||
plot.title = element_text(size = 14, hjust = 0.5),
|
||
legend.position = "right",
|
||
legend.title = element_text(size = 11),
|
||
legend.text = element_text(size = 10),
|
||
panel.grid.major.x = element_blank(),
|
||
panel.grid.minor = element_blank(),
|
||
panel.border = element_rect(color = "gray80", fill = NA, linewidth = 0.5)
|
||
)
|
||
|
||
print(time_main_plot) |