Created
August 13, 2018 15:16
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Compare bias in Poisson MLE and various Sim methods (10 August)
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library(pacman) | |
p_load(MASS, tidyverse) | |
# set seed | |
set.seed(4321) | |
# set simulation paramters | |
n <- 100 # sample size | |
x <- rnorm(n) # single explanatory variable | |
n_qi <- 100 # number of points at which to calculate the marginal effect | |
x0 <- seq(-3, 3, length.out = n_qi) # points at which to calculate the marginal effect | |
beta <- c(-2, 1) # true coefficients | |
lambda <- exp(beta[1] + beta[2]*x) # implied mean | |
n_sims <- 10000 # number of mc simulations | |
tau_hat_mean_pre <- tau_hat_median_pre <- tau_hat_median <- tau_hat_mle <- tau_hat_avg <- matrix(NA, nrow = n_sims, ncol = n_qi) | |
for (i in 1:n_sims) { | |
y <- rpois(n, lambda = lambda) | |
fit <- glm(y ~ x, family = poisson) | |
beta_hat <- coef(fit) | |
Sigma_hat <- vcov(fit) | |
beta_tilde <- MASS::mvrnorm(1000, mu = beta_hat, Sigma = Sigma_hat) | |
tau_tilde <- t(exp(cbind(1, x0)%*%t(beta_tilde)))*beta_tilde[, 2] | |
tau_hat_avg[i, ] <- apply(tau_tilde, 2, mean) | |
tau_hat_mle[i, ] <- exp(beta_hat[1] + beta_hat[2]*x0)*beta_hat[2] | |
tau_hat_median[i, ] <- apply(tau_tilde, 2, median) | |
tau_hat_median_pre[i, ] <- exp(median(beta_tilde[, 1]) + median(beta_tilde[, 2])*x0)*median(beta_tilde[, 2]) | |
tau_hat_mean_pre[i, ] <- exp(mean(beta_tilde[, 1]) + mean(beta_tilde[, 2])*x0)*mean(beta_tilde[, 2]) | |
} | |
sims_df_sep <- data.frame(true_qi = exp(beta[1] + beta[2]*x0)*beta[2], | |
mle = apply(tau_hat_mle, 2, mean), | |
avg = apply(tau_hat_avg, 2, mean), | |
med = apply(tau_hat_median, 2, mean), | |
med_pre = apply(tau_hat_median_pre, 2, mean), | |
mean_pre = apply(tau_hat_mean_pre, 2, mean)) | |
sims_df <- sims_df_sep %>% | |
gather(method, ev, mle, avg, med, med_pre, mean_pre) | |
par(mfrow = c(1, 3)) | |
plot(sims_df_sep$true_qi, with(sims_df_sep, (med_pre - true_qi) - (mle - true_qi)), | |
ylab = "Bias of Median of Simulated Betas for QI vs. MLE", xlab = "True Value") | |
plot(sims_df_sep$true_qi, with(sims_df_sep, (mean_pre - true_qi) - (mle - true_qi)), | |
ylab = "Bias of Mean of Simulated Betas for QI vs. MLE", xlab = "True Value") | |
plot(sims_df_sep$true_qi, with(sims_df_sep, (med - true_qi) - (mle - true_qi)), | |
ylab = "Bias of Median of Simulated QI vs. MLE", xlab = "True Value") |
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