context("pos1S: 1-Sample Probability of Success") ## test the analytical OC function via brute force simulation set.seed(12354) ## expect results to be 1% exact eps <- 1e-2 ## we test here that the PoS indeed averages over the predictive of an ## informative prior the conditional power. ## Example for Figure 3 s <- 2 theta_ni <- 0.4 theta_a <- 0 alpha <- 0.05 beta <- 0.2 za <- qnorm(1-alpha) n1 <- 155 c1 <- theta_ni - za * s / sqrt(n1) N_samp <- 1E4 thetaA <- c(theta_a, theta_ni) ## standard NI design, tests only statistical significance to be ## smaller than theta_ni with 1-alpha certainty decA <- decision1S(1 - alpha, theta_ni, lower.tail=TRUE) decAU <- decision1S(1 - alpha, theta_ni, lower.tail=FALSE) prior <- mixnorm(c(1,0,100), sigma=s) ## let's say we have 40 events at an interim and a HR of 0.9 ia_dist <- postmix(prior, m=log(0.9), se=s/sqrt(40)) test_pos1S <- function(prior, ia_dist, n, dec, decU) { ## the PoS is the expected value of the condition power integrated ## over the interim density which is what we check here cpo_analytic <- oc1S(prior, n, dec) pos_analytic <- pos1S(prior, n, dec) samp <- rmix(ia_dist, N_samp) pos_mc <- mean(cpo_analytic(samp)) expect_true(all(abs(pos_mc - pos_analytic(ia_dist)) < eps)) lower.tail <- attr(dec,"lower.tail") if(lower.tail) { test_pos1S(prior, ia_dist, n, decU) } } test_that("Normal PoS 1 sample function matches MC integration of CPO", test_pos1S(prior, ia_dist, n1, decA, decAU)) beta_prior <- mixbeta(c(1, 1, 1)) beta_ia <- postmix(beta_prior, r=20, n=50) test_that("Binomial PoS 1 sample function matches MC integration of CPO", test_pos1S(beta_prior, beta_ia, n1, decA, decAU)) gamma_prior <- mixgamma(c(1, 1, 1), param="mn") dec_count <- decision1S(1-alpha, 1, lower.tail=TRUE) dec_countU <- decision1S(1-alpha, 1, lower.tail=FALSE) gamma_ia <- postmix(gamma_prior, m=0.9, n=40) test_that("Poisson PoS 1 sample function matches MC integration of CPO", test_pos1S(gamma_prior, gamma_ia, n1, dec_count, dec_countU)) prior_unit_inf <- mixnorm(c(1, 0, 1), sigma=s, param="mn") post_ia_unit_inf <- postmix(prior_unit_inf, m=-1, n=162) test_pos1S(prior_unit_inf, post_ia_unit_inf, 459-162, decA, decAU) test_that("Normal PoS 1 sample function matches MC integration of CPO (more extreme case)", test_pos1S(prior_unit_inf, post_ia_unit_inf, 459-162, decA, decAU))