testthat::test_that("Testing nSurv vs nSurvival and nEvents", { # consider a trial with 2 year maximum follow-up, # 6 month uniform enrollment # Treatment/placebo hazards = 0.14/0.2 per 1 person-year # HR = 0.7 # drop out hazard 0.1 per 1 person-year # alpha = 0.025 (1-sided) # power = 0.9 (default beta=.1) ss <- nSurvival( lambda1 = .2, lambda2 = .14, eta = .1, Ts = 2, Tr = .5, sided = 1, alpha = .025 ) ns <- nSurv(lambdaC = .2, hr = .7, eta = .1, T=2, minfup=1.5) nsg <- nSurv(lambdaC = .2, hr = .7, eta = .1, R = 0.5, gamma = ns$gamma) ne <- nEvents(hr=.7) testthat::expect_equal(ss$n, ns$n, info = "Checking sample size") testthat::expect_equal(round(ns$n,3), round(nsg$n,3), info = "Checking sample size") testthat::expect_equal(ss$nEvents, ns$d, info = "Checking event count") testthat::expect_lt(abs(ns$d - ne),3) }) testthat::test_that("Checking consistency of Schoenfeld approximations", { z <- hrn2z(hr = .7, n = 100, ratio = 1.5) hr <- zn2hr(z = -z, n = 100, ratio = 1.5) n <- hrz2n(z = -z, hr = .7, ratio = 1.5) testthat::expect_equal(hr, .7, info = "Checking zn2hr vs hrn2z") testthat::expect_equal(n, 100, info = "Checking hrz2n vs hrn2z") }) testthat::test_that("Checking consistency nEvents power vs sample size", { ss <- nEvents(hr = .7, tbl = TRUE) ne <- nEvents(hr = .7) pwr <- nEvents(hr = .7, n = ne, tbl = TRUE) testthat::expect_equal(ss$n, ceiling(ne), info = "Checking tabular output") testthat::expect_equal(pwr$Power, .9, info = "Checking power calculation") }) ################################################################################ ## ADDITIONAL TEST SCENARIOs ## We use nSurvival() from the gsDesign package to validate the nSurv(). ## This is done keeping in mind that nSurvival has been programmed ## independently and can be used for limited validations of nSurv() testthat::test_that( desc = "Test nSurv() using nSurvival() from the gsDesign package : ", code = { ss2 <- nSurv( lambdaC = log(2) / 6, hr = .5, eta = log(2) / 40, T = 36, minfup = 12 ) ss1 <- nSurvival( lambda1 = log(2) / 6, lambda2 = log(2) / 12, eta = log(2) / 40, Ts = 36, Tr = 24 ) ## Compare ss2$n with ss1$n with tolerance of 1e-6 testthat::expect_lte( object = abs(ss2$n - ss1$n), expected = 1e-6 ) ## Compare ss2$d with ss1$nEvents with tolerance of 1e-6 testthat::expect_lte( object = abs(ss2$d - ss1$nEvents), expected = 1e-6 ) } ) # vary accrual rate to obtain expected events and sample size # The benchmark values have been obtained by creating an # equivalent design in SAS 9.4 - Proc Seqdesign : SAS_nsurv_01.html test_that( desc = "check expected # of events and expected sample size", code = { x <- nSurv( lambdaC = log(2) / 20, hr = .5, gamma = 1, T = 36, minfup = 12 ) # check expected # of events expect_lte(abs(x$d - 87.4793), 2) # check expected sample size expect_lte(abs(x$n - 197.1152), 2) } ) # vary accrual duration to obtain expected events and sample size # The benchmark values have been obtained by creating an # equivalent design in SAS 9.4 - Proc Seqdesign : SAS_nsurv_01.html test_that( desc = "check expected # of events and expected sample size", code = { x <- nSurv( lambdaC = log(2) / 20, hr = .5, gamma = 6, minfup = 12 ) # check expected # of events expect_lte(abs(x$d - 87.4793), 2) # check expected sample size expect_lte(abs(x$n - 182.1759), 2) } ) # vary follow-up duration to obtain expected events and sample size # The benchmark values have been obtained by creating an # equivalent design in SAS 9.4- Proc Seqdesign : SAS_nsurv_01.html test_that( desc = "check expected # of events and expected sample size", code = { x <- nSurv( lambdaC = log(2) / 20, hr = .5, gamma = 6, R = 25 ) # check expected # of events expect_lte(abs(x$d - 89.07848), 2) # check expected sample size expect_lte(abs(x$n - 149.861), 2) } ) # vary follow-up duration to obtain power # the benchmark values have been obtained by creating an # equivalent design in East 6.5. The sample size used to # create the design in East is taken from the output of # nSurv() : TestnSurv_EastData_Des1.html test_that( desc = "check computed events and power", code = { x <- nSurv( lambdaC = log(2) / 10, hr = .5, gamma = 4, T = 50, minfup = 30, beta = NULL ) ## compare the expected # of events expect_lte(abs(x$d - 39.02121789), 2) ## compare the power x$power ## tolerance is high as the power computation depends ## upon # of events which have differences between different gsDesign and East 6.5. expect_lte(abs(x$power - 0.58120457), 0.02) } )