setwd("C:/Users/irina/Documents/DND/EOHI/eohi1")
options(scipen = 999)
df <- read.csv("ehi1.csv")
library(psych)
library(knitr)
# fixed-decimal formatter (five decimals)
fmt5 <- function(x) formatC(x, format = "f", digits = 5)
# Select the 4 variables for reliability analysis
reliability_data <- df[complete.cases(df[, c("eohiDGEN_mean", "ehi_global_mean")]),
c("eohiDGEN_mean", "ehi_global_mean")]
# Cronbach's Alpha
alpha_result <- alpha(reliability_data)
# Split-half reliability
split_half <- splitHalf(reliability_data)
# Inter-item correlations
cor_matrix <- cor(reliability_data, use = "complete.obs")
# Two-item reliability summary (if applicable)
two_item_section <- ""
if (ncol(reliability_data) == 2) {
n_complete <- sum(complete.cases(reliability_data))
r_pearson <- cor(reliability_data[, 1], reliability_data[, 2], use = "complete.obs", method = "pearson")
r_spearman <- suppressWarnings(cor(reliability_data[, 1], reliability_data[, 2], use = "complete.obs", method = "spearman"))
# Fisher z CI for r
fisher_z <- atanh(r_pearson)
se_z <- 1 / sqrt(n_complete - 3)
z_crit <- qnorm(0.975)
ci_z_lower <- fisher_z - z_crit * se_z
ci_z_upper <- fisher_z + z_crit * se_z
ci_r_lower <- tanh(ci_z_lower)
ci_r_upper <- tanh(ci_z_upper)
# Approximate Fisher z CI for Spearman rho (large-sample approximation)
fisher_z_s <- atanh(r_spearman)
ci_zs_lower <- fisher_z_s - z_crit * se_z
ci_zs_upper <- fisher_z_s + z_crit * se_z
ci_s_lower <- tanh(ci_zs_lower)
ci_s_upper <- tanh(ci_zs_upper)
# Spearman–Brown/Cronbach's alpha for k = 2
alpha_sb <- (2 * r_pearson) / (1 + r_pearson)
alpha_lower <- (2 * ci_r_lower) / (1 + ci_r_lower)
alpha_upper <- (2 * ci_r_upper) / (1 + ci_r_upper)
two_item_section <- paste0(
"Two-Item Reliability Summary
",
"Pearson r: ", fmt5(r_pearson), " (95% CI: [", fmt5(ci_r_lower), ", ", fmt5(ci_r_upper), "])
",
"Spearman r: ", fmt5(r_spearman), " (95% CI: [", fmt5(ci_s_lower), ", ", fmt5(ci_s_upper), "])
",
"Spearman–Brown / Cronbach's ", intToUtf8(945), ": ", fmt5(alpha_sb),
" (95% CI: [", fmt5(alpha_lower), ", ", fmt5(alpha_upper), "])
"
)
}
# Create a summary table
summary_table <- data.frame(
Variable = names(reliability_data),
n = nrow(reliability_data),
Mean = round(colMeans(reliability_data, na.rm = TRUE), 5),
SD = round(apply(reliability_data, 2, sd, na.rm = TRUE), 5),
Min = round(apply(reliability_data, 2, min, na.rm = TRUE), 5),
Max = round(apply(reliability_data, 2, max, na.rm = TRUE), 5),
Median = round(apply(reliability_data, 2, median, na.rm = TRUE), 5)
)
html_output <- paste0(
"EHI Reliability Analysis",
"EHI Reliability Analysis
",
two_item_section,
"Cronbach's Alpha
",
kable(alpha_result$total, format = "html"),
"Split-Half Reliability
",
"Maximum split half reliability: ", fmt5(split_half$maxrb), "
",
"Item-Level Statistics
",
kable(alpha_result$item.stats, format = "html"),
""
)
writeLines(html_output, "EHI reliability.html")