tests/testthat/test-sbc.R

In OncoBayes2: Bayesian Logistic Regression for Oncology Dose-Escalation Trials

context("SBC validation")

test_that("blrm_exnex meets SBC requirements wrt to a Chi-Square statistic.", {
    require(dplyr)
    require(tidyr)
    sbc_chisq_test <-  OncoBayes2:::calibration_data %>%
        group_by(data_scenario, param) %>%
        do(as.data.frame(chisq.test(.$count)[c("statistic", "p.value")]))
    num_tests  <- nrow(sbc_chisq_test)
    num_failed <- sum(sbc_chisq_test$p.value < 0.05)
    pv <- pbinom(num_failed, num_tests, 0.05)
    expect_true( pv > 0.025 & pv < 0.975 )
}
)

test_that("blrm_exnex meets SBC requirements per bin.", {
    require(dplyr)
    require(tidyr)
    B <- OncoBayes2:::calibration_meta$B
    S  <- OncoBayes2:::calibration_meta$S
    alpha  <- 0.2
    ptrue  <- 1/B
    crit_low  <- qbinom(alpha/2, S, ptrue)
    crit_high  <- qbinom(1-alpha/2, S, ptrue)
    sbc_binom_test <-  OncoBayes2:::calibration_data %>%
        group_by(data_scenario, param) %>%
        summarise(crit=sum(count < crit_low | count > crit_high)) %>%
        mutate(pvalue=pbinom(crit, B, alpha), extreme=pvalue<0.025|pvalue>0.975)
    num_tests  <- nrow(sbc_binom_test)
    num_failed <- sum(sbc_binom_test$extreme)
    pv <- pbinom(num_failed, num_tests, 0.05)
    expect_true( pv > 0.025 & pv < 0.975 )
}
)

test_that("blrm_exnex data was up to date at package creation.", {
    calibration_datum  <- OncoBayes2:::calibration_meta$created
    package_datum <- OncoBayes2:::pkg_create_date
    delta <- difftime(package_datum, calibration_datum, units="weeks")
    expect_true(delta < 52./2.)
}
)