tests/testthat/test-mr_ivw_stan.R

In mrbayes: Bayesian Summary Data Models for Mendelian Randomization Studies

# Tests for the mrbayes package

context("Tests for mr_ivw_stan() function")

# Analysis
## IVW stan

test_that("Dataset is formatted",
          {
            dat <- mr_format(rsid = dodata$rsid,
                             xbeta = dodata$ldlcbeta,
                             ybeta = dodata$chdbeta,
                             xse = dodata$ldlcse,
                             yse = dodata$chdse)
            expect_s3_class(dat, "mr_format")
          })

test_that("IVW using default prior method",
          {
            skip_on_cran()
            skip_if_not_installed("rstan")
            dat <- mr_format(rsid = dodata$rsid,
                             xbeta = dodata$ldlcbeta,
                             ybeta = dodata$chdbeta,
                             xse = dodata$ldlcse,
                             yse = dodata$chdse)
            ivwfit <- mr_ivw_stan(dat)
            summfit <- rstan::summary(ivwfit)
            expect_equal(class(ivwfit)[1], "stanfit")
            expect_equal(summfit$summary["estimate","mean"], 0.5, tol = 1e-2)
            expect_equal(summfit$summary["estimate","sd"], 0.04, tol = 1e-2)
            expect_equal(summfit$summary["estimate","2.5%"], 0.43, tol = 1e-2)
            expect_equal(summfit$summary["estimate","50%"], 0.50, tol = 1e-2)
            expect_equal(summfit$summary["estimate","97.5%"], 0.57, tol = 1e-2)
          })

test_that("IVW using weak prior method",
          {
            skip_on_cran()
            skip_if_not_installed("rstan")
            dat <- mr_format(rsid = dodata$rsid,
                             xbeta = dodata$ldlcbeta,
                             ybeta = dodata$chdbeta,
                             xse = dodata$ldlcse,
                             yse = dodata$chdse)

            ivwfit1 <- mr_ivw_stan(dat, prior = 2)
            summfit1 <- rstan::summary(ivwfit1)
            expect_equal(class(ivwfit1)[1], "stanfit")
            expect_equal(summfit1$summary["estimate","mean"], 0.5, tol = 1e-2)
            expect_equal(summfit1$summary["estimate","sd"], 0.037, tol = 1e-2)
            expect_equal(summfit1$summary["estimate","2.5%"], 0.43, tol = 1e-2)
            expect_equal(summfit1$summary["estimate","50%"], 0.5, tol = 1e-2)
            expect_equal(summfit1$summary["estimate","97.5%"], 0.576, tol = 1e-2)
          })

test_that("IVW using pseudo prior method",
          {
            skip_on_cran()
            skip_if_not_installed("rstan")
            dat <- mr_format(rsid = dodata$rsid,
                             xbeta = dodata$ldlcbeta,
                             ybeta = dodata$chdbeta,
                             xse = dodata$ldlcse,
                             yse = dodata$chdse)

            ivwfit2 <- mr_ivw_stan(dat, prior = 3)
            summfit2 <- rstan::summary(ivwfit2)
            expect_equal(class(ivwfit2)[1], "stanfit")
            expect_equal(summfit2$summary["estimate","mean"], 0.5, tol = 1e-2)
            expect_equal(summfit2$summary["estimate","sd"], 0.0379, tol = 1e-2)
            expect_equal(summfit2$summary["estimate","2.5%"], 0.429, tol = 1e-2)
            expect_equal(summfit2$summary["estimate","50%"], 0.50, tol = 1e-2)
            expect_equal(summfit2$summary["estimate","97.5%"], 0.576, tol = 1e-2)
          })