# \donttest{
## Example 1: Basic Hessian Evaluation
# Generate sample data
set.seed(123)
n <- 1000
true_params <- c(alpha = 2.5, beta = 3.5, lambda = 2.0)
data <- rekw(n, alpha = true_params[1], beta = true_params[2],
lambda = true_params[3])
# Evaluate Hessian at true parameters
hess_true <- hsekw(par = true_params, data = data)
cat("Hessian matrix at true parameters:\n")
print(hess_true, digits = 4)
# Check symmetry
cat("\nSymmetry check (max |H - H^T|):",
max(abs(hess_true - t(hess_true))), "\n")
## Example 2: Hessian Properties at MLE
# Fit model
fit <- optim(
par = c(2, 3, 1.5),
fn = llekw,
gr = grekw,
data = data,
method = "BFGS",
hessian = TRUE
)
mle <- fit$par
names(mle) <- c("alpha", "beta", "lambda")
# Hessian at MLE
hessian_at_mle <- hsekw(par = mle, data = data)
cat("\nHessian at MLE:\n")
print(hessian_at_mle, digits = 4)
# Compare with optim's numerical Hessian
cat("\nComparison with optim Hessian:\n")
cat("Max absolute difference:",
max(abs(hessian_at_mle - fit$hessian)), "\n")
# Eigenvalue analysis
eigenvals <- eigen(hessian_at_mle, only.values = TRUE)$values
cat("\nEigenvalues:\n")
print(eigenvals)
cat("\nPositive definite:", all(eigenvals > 0), "\n")
cat("Condition number:", max(eigenvals) / min(eigenvals), "\n")
## Example 3: Standard Errors and Confidence Intervals
# Observed information matrix
obs_info <- hessian_at_mle
# Variance-covariance matrix
vcov_matrix <- solve(obs_info)
cat("\nVariance-Covariance Matrix:\n")
print(vcov_matrix, digits = 6)
# Standard errors
se <- sqrt(diag(vcov_matrix))
names(se) <- c("alpha", "beta", "lambda")
# Correlation matrix
corr_matrix <- cov2cor(vcov_matrix)
cat("\nCorrelation Matrix:\n")
print(corr_matrix, digits = 4)
# Confidence intervals
z_crit <- qnorm(0.975)
results <- data.frame(
Parameter = c("alpha", "beta", "lambda"),
True = true_params,
MLE = mle,
SE = se,
CI_Lower = mle - z_crit * se,
CI_Upper = mle + z_crit * se
)
print(results, digits = 4)
## Example 4: Determinant and Trace Analysis
# Compute at different points
test_params <- rbind(
c(2.0, 3.0, 1.5),
c(2.5, 3.5, 2.0),
mle,
c(3.0, 4.0, 2.5)
)
hess_properties <- data.frame(
Alpha = numeric(),
Beta = numeric(),
Lambda = numeric(),
Determinant = numeric(),
Trace = numeric(),
Min_Eigenval = numeric(),
Max_Eigenval = numeric(),
Cond_Number = numeric(),
stringsAsFactors = FALSE
)
for (i in 1:nrow(test_params)) {
H <- hsekw(par = test_params[i, ], data = data)
eigs <- eigen(H, only.values = TRUE)$values
hess_properties <- rbind(hess_properties, data.frame(
Alpha = test_params[i, 1],
Beta = test_params[i, 2],
Lambda = test_params[i, 3],
Determinant = det(H),
Trace = sum(diag(H)),
Min_Eigenval = min(eigs),
Max_Eigenval = max(eigs),
Cond_Number = max(eigs) / min(eigs)
))
}
cat("\nHessian Properties at Different Points:\n")
print(hess_properties, digits = 4, row.names = FALSE)
## Example 5: Curvature Visualization (Alpha vs Beta)
# Create grid around MLE
alpha_grid <- seq(mle[1] - 0.5, mle[1] + 0.5, length.out = 25)
beta_grid <- seq(mle[2] - 0.5, mle[2] + 0.5, length.out = 25)
alpha_grid <- alpha_grid[alpha_grid > 0]
beta_grid <- beta_grid[beta_grid > 0]
# Compute curvature measures
determinant_surface <- matrix(NA, nrow = length(alpha_grid),
ncol = length(beta_grid))
trace_surface <- matrix(NA, nrow = length(alpha_grid),
ncol = length(beta_grid))
for (i in seq_along(alpha_grid)) {
for (j in seq_along(beta_grid)) {
H <- hsekw(c(alpha_grid[i], beta_grid[j], mle[3]), data)
determinant_surface[i, j] <- det(H)
trace_surface[i, j] <- sum(diag(H))
}
}
# Plot
contour(alpha_grid, beta_grid, determinant_surface,
xlab = expression(alpha), ylab = expression(beta),
main = "Hessian Determinant", las = 1,
col = "#2E4057", lwd = 1.5, nlevels = 15)
points(mle[1], mle[2], pch = 19, col = "#8B0000", cex = 1.5)
points(true_params[1], true_params[2], pch = 17, col = "#006400", cex = 1.5)
grid(col = "gray90")
contour(alpha_grid, beta_grid, trace_surface,
xlab = expression(alpha), ylab = expression(beta),
main = "Hessian Trace", las = 1,
col = "#2E4057", lwd = 1.5, nlevels = 15)
points(mle[1], mle[2], pch = 19, col = "#8B0000", cex = 1.5)
points(true_params[1], true_params[2], pch = 17, col = "#006400", cex = 1.5)
grid(col = "gray90")
## Example 6: Confidence Ellipse (Alpha vs Beta)
# Extract 2x2 submatrix for alpha and beta
vcov_2d <- vcov_matrix[1:2, 1:2]
# Create confidence ellipse
theta <- seq(0, 2 * pi, length.out = 100)
chi2_val <- qchisq(0.95, df = 2)
eig_decomp <- eigen(vcov_2d)
ellipse <- matrix(NA, nrow = 100, ncol = 2)
for (i in 1:100) {
v <- c(cos(theta[i]), sin(theta[i]))
ellipse[i, ] <- mle[1:2] + sqrt(chi2_val) *
(eig_decomp$vectors %*% diag(sqrt(eig_decomp$values)) %*% v)
}
# Marginal confidence intervals
se_2d <- sqrt(diag(vcov_2d))
ci_alpha <- mle[1] + c(-1, 1) * 1.96 * se_2d[1]
ci_beta <- mle[2] + c(-1, 1) * 1.96 * se_2d[2]
# Plot
plot(ellipse[, 1], ellipse[, 2], type = "l", lwd = 2, col = "#2E4057",
xlab = expression(alpha), ylab = expression(beta),
main = "95% Confidence Ellipse (Alpha vs Beta)", las = 1)
# Add marginal CIs
abline(v = ci_alpha, col = "#808080", lty = 3, lwd = 1.5)
abline(h = ci_beta, col = "#808080", lty = 3, lwd = 1.5)
points(mle[1], mle[2], pch = 19, col = "#8B0000", cex = 1.5)
points(true_params[1], true_params[2], pch = 17, col = "#006400", cex = 1.5)
legend("topright",
legend = c("MLE", "True", "95% CR", "Marginal 95% CI"),
col = c("#8B0000", "#006400", "#2E4057", "#808080"),
pch = c(19, 17, NA, NA),
lty = c(NA, NA, 1, 3),
lwd = c(NA, NA, 2, 1.5),
bty = "n")
grid(col = "gray90")
## Example 7: Confidence Ellipse (Alpha vs Lambda)
# Extract 2x2 submatrix for alpha and lambda
vcov_2d_al <- vcov_matrix[c(1, 3), c(1, 3)]
# Create confidence ellipse
eig_decomp_al <- eigen(vcov_2d_al)
ellipse_al <- matrix(NA, nrow = 100, ncol = 2)
for (i in 1:100) {
v <- c(cos(theta[i]), sin(theta[i]))
ellipse_al[i, ] <- mle[c(1, 3)] + sqrt(chi2_val) *
(eig_decomp_al$vectors %*% diag(sqrt(eig_decomp_al$values)) %*% v)
}
# Marginal confidence intervals
se_2d_al <- sqrt(diag(vcov_2d_al))
ci_alpha_2 <- mle[1] + c(-1, 1) * 1.96 * se_2d_al[1]
ci_lambda <- mle[3] + c(-1, 1) * 1.96 * se_2d_al[2]
# Plot
plot(ellipse_al[, 1], ellipse_al[, 2], type = "l", lwd = 2, col = "#2E4057",
xlab = expression(alpha), ylab = expression(lambda),
main = "95% Confidence Ellipse (Alpha vs Lambda)", las = 1)
# Add marginal CIs
abline(v = ci_alpha_2, col = "#808080", lty = 3, lwd = 1.5)
abline(h = ci_lambda, col = "#808080", lty = 3, lwd = 1.5)
points(mle[1], mle[3], pch = 19, col = "#8B0000", cex = 1.5)
points(true_params[1], true_params[3], pch = 17, col = "#006400", cex = 1.5)
legend("topright",
legend = c("MLE", "True", "95% CR", "Marginal 95% CI"),
col = c("#8B0000", "#006400", "#2E4057", "#808080"),
pch = c(19, 17, NA, NA),
lty = c(NA, NA, 1, 3),
lwd = c(NA, NA, 2, 1.5),
bty = "n")
grid(col = "gray90")
## Example 8: Confidence Ellipse (Beta vs Lambda)
# Extract 2x2 submatrix for beta and lambda
vcov_2d_bl <- vcov_matrix[2:3, 2:3]
# Create confidence ellipse
eig_decomp_bl <- eigen(vcov_2d_bl)
ellipse_bl <- matrix(NA, nrow = 100, ncol = 2)
for (i in 1:100) {
v <- c(cos(theta[i]), sin(theta[i]))
ellipse_bl[i, ] <- mle[2:3] + sqrt(chi2_val) *
(eig_decomp_bl$vectors %*% diag(sqrt(eig_decomp_bl$values)) %*% v)
}
# Marginal confidence intervals
se_2d_bl <- sqrt(diag(vcov_2d_bl))
ci_beta_2 <- mle[2] + c(-1, 1) * 1.96 * se_2d_bl[1]
ci_lambda_2 <- mle[3] + c(-1, 1) * 1.96 * se_2d_bl[2]
# Plot
plot(ellipse_bl[, 1], ellipse_bl[, 2], type = "l", lwd = 2, col = "#2E4057",
xlab = expression(beta), ylab = expression(lambda),
main = "95% Confidence Ellipse (Beta vs Lambda)", las = 1)
# Add marginal CIs
abline(v = ci_beta_2, col = "#808080", lty = 3, lwd = 1.5)
abline(h = ci_lambda_2, col = "#808080", lty = 3, lwd = 1.5)
points(mle[2], mle[3], pch = 19, col = "#8B0000", cex = 1.5)
points(true_params[2], true_params[3], pch = 17, col = "#006400", cex = 1.5)
legend("topright",
legend = c("MLE", "True", "95% CR", "Marginal 95% CI"),
col = c("#8B0000", "#006400", "#2E4057", "#808080"),
pch = c(19, 17, NA, NA),
lty = c(NA, NA, 1, 3),
lwd = c(NA, NA, 2, 1.5),
bty = "n")
grid(col = "gray90")
# }
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