#------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. # # You should have received a copy of the GNU General Public License # along with this program. If not, see . #------------------------------------------------------------------------------- # # Set up # context("ds.qlspline::smk::setup") connect.studies.dataset.cnsim(list("LAB_TRIG", "PM_BMI_CONTINUOUS")) test_that("setup", { ds_expect_variables(c("D")) }) # # Tests # context("ds.qlspline::smk::test1") test_that("qlspline", { ds.qlspline(x="D$PM_BMI_CONTINUOUS", q=4, na.rm=TRUE, newobj="qlsplineDS", datasources=ds.test_env$connections) res.class <- ds.class("qlsplineDS", datasources=ds.test_env$connections) expect_length(res.class, 3) expect_equal(res.class$sim1[1], "lspline") expect_equal(res.class$sim1[2], "matrix") expect_equal(res.class$sim2[1], "lspline") expect_equal(res.class$sim2[2], "matrix") expect_equal(res.class$sim3[1], "lspline") expect_equal(res.class$sim3[2], "matrix") res.mod <- ds.glm(formula = "D$LAB_TRIG~qlsplineDS", family='gaussian', datasources=ds.test_env$connections) expect_length(res.mod, 13) expect_equal(res.mod$Nvalid, 7477) expect_equal(res.mod$Nmissing, 1902) expect_equal(res.mod$Ntotal, 9379) expect_length(res.mod$disclosure.risk, 3) expect_equal(res.mod$disclosure[1], 0) expect_equal(res.mod$disclosure[3], 0) expect_equal(res.mod$disclosure[2], 0) expect_length(res.mod$errorMessage, 3) expect_equal(res.mod$errorMessage[1], "No errors") expect_equal(res.mod$errorMessage[2], "No errors") expect_equal(res.mod$errorMessage[3], "No errors") expect_equal(res.mod$nsubs, 7477) expect_equal(res.mod$iter, 3) expect_true("family" %in% class(res.mod$family)) expect_equal(res.mod$formula, "D$LAB_TRIG ~ qlsplineDS") expect_true("matrix" %in% class(res.mod$coefficients)) expect_true("array" %in% class(res.mod$coefficients)) expect_equal(res.mod$coefficients['(Intercept)','Estimate'], -1.019282794, tolerance = ds.test_env$tolerance) expect_equal(res.mod$coefficients['qlsplineDS1','Estimate'], 0.120196255, tolerance = ds.test_env$tolerance) expect_equal(res.mod$coefficients['qlsplineDS2','Estimate'], 0.067803329, tolerance = ds.test_env$tolerance) expect_equal(res.mod$coefficients['qlsplineDS3','Estimate'], 0.006651009, tolerance = ds.test_env$tolerance) expect_equal(res.mod$coefficients['qlsplineDS4','Estimate'], 0.133116769, tolerance = ds.test_env$tolerance) expect_equal(res.mod$coefficients['(Intercept)','Std. Error'], 0.27768921, tolerance = ds.test_env$tolerance) expect_equal(res.mod$coefficients['qlsplineDS1','Std. Error'], 0.01259812, tolerance = ds.test_env$tolerance) expect_equal(res.mod$coefficients['qlsplineDS2','Std. Error'], 0.02097099, tolerance = ds.test_env$tolerance) expect_equal(res.mod$coefficients['qlsplineDS3','Std. Error'], 0.02072403, tolerance = ds.test_env$tolerance) expect_equal(res.mod$coefficients['qlsplineDS4','Std. Error'], 0.01201930, tolerance = ds.test_env$tolerance) expect_equal(res.mod$dev, 17000.26, tolerance = ds.test_env$tolerance) expect_equal(res.mod$df, 7472) expect_equal(res.mod$output.information, "SEE TOP OF OUTPUT FOR INFORMATION ON MISSING DATA AND ERROR MESSAGES") }) context("ds.qlspline::smk::test2") test_that("qlspline", { ds.qlspline(x="D$PM_BMI_CONTINUOUS", q=c(0.3,0.6), na.rm=TRUE, newobj="qlsplineDS2", datasources=ds.test_env$connections) res.class <- ds.class("qlsplineDS2", datasources=ds.test_env$connections) expect_length(res.class, 3) expect_equal(res.class$sim1[1], "lspline") expect_equal(res.class$sim1[2], "matrix") expect_equal(res.class$sim2[1], "lspline") expect_equal(res.class$sim2[2], "matrix") expect_equal(res.class$sim3[1], "lspline") expect_equal(res.class$sim3[2], "matrix") res.mod <- ds.glm(formula = "D$LAB_TRIG~qlsplineDS2", family='gaussian', datasources=ds.test_env$connections) expect_length(res.mod, 13) expect_equal(res.mod$Nvalid, 7477) expect_equal(res.mod$Nmissing, 1902) expect_equal(res.mod$Ntotal, 9379) expect_length(res.mod$disclosure.risk, 3) expect_equal(res.mod$disclosure[1], 0) expect_equal(res.mod$disclosure[3], 0) expect_equal(res.mod$disclosure[2], 0) expect_length(res.mod$errorMessage, 3) expect_equal(res.mod$errorMessage[1], "No errors") expect_equal(res.mod$errorMessage[2], "No errors") expect_equal(res.mod$errorMessage[3], "No errors") expect_equal(res.mod$nsubs, 7477) expect_equal(res.mod$iter, 3) expect_true("family" %in% class(res.mod$family)) expect_equal(res.mod$formula, "D$LAB_TRIG ~ qlsplineDS2") expect_true("matrix" %in% class(res.mod$coefficients)) expect_true("array" %in% class(res.mod$coefficients)) expect_equal(res.mod$coefficients['(Intercept)','Estimate'], -1.04058508, tolerance = ds.test_env$tolerance) expect_equal(res.mod$coefficients['qlsplineDS21','Estimate'], 0.12128692, tolerance = ds.test_env$tolerance) expect_equal(res.mod$coefficients['qlsplineDS22','Estimate'], 0.01708104, tolerance = ds.test_env$tolerance) expect_equal(res.mod$coefficients['qlsplineDS23','Estimate'], 0.10189071, tolerance = ds.test_env$tolerance) expect_equal(res.mod$coefficients['(Intercept)','Std. Error'], 0.248311459, tolerance = ds.test_env$tolerance) expect_equal(res.mod$coefficients['qlsplineDS21','Std. Error'], 0.010959394, tolerance = ds.test_env$tolerance) expect_equal(res.mod$coefficients['qlsplineDS22','Std. Error'], 0.015233708, tolerance = ds.test_env$tolerance) expect_equal(res.mod$coefficients['qlsplineDS23','Std. Error'], 0.008551969, tolerance = ds.test_env$tolerance) expect_equal(res.mod$dev, 17031.72, tolerance = ds.test_env$tolerance) expect_equal(res.mod$df, 7473) expect_equal(res.mod$output.information, "SEE TOP OF OUTPUT FOR INFORMATION ON MISSING DATA AND ERROR MESSAGES") }) # # Done # context("ds.qlspline::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D", "LAB_TRIG", "qlsplineDS", "qlsplineDS2")) }) disconnect.studies.dataset.cnsim() context("ds.qlspline::smk::done")