#------------------------------------------------------------------------------- # Copyright (c) 2019-2022 University of Newcastle upon Tyne. All rights reserved. # Copyright (c) 2022 Arjuna Technologies, 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.kurtosis::smk::setup") connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL", "LAB_GLUC_ADJUSTED", "PM_BMI_CONTINUOUS")) test_that("setup", { ds_expect_variables(c("D")) }) # # Tests # # Method 1 context("ds.kurtosis::smk::method 1::split") test_that("simple kurtosis, method 1, split, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 1, type='split') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("0.171744367103707"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[2]), as.double("0.574419687874713"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[3]), as.double("0.674414218958169"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 3) expect_equal(kurtosis.res$Nvalid[1], "1807") expect_equal(kurtosis.res$Nvalid[2], "2539") expect_equal(kurtosis.res$Nvalid[3], "3479") expect_length(kurtosis.res$ValidityMessage, 3) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) test_that("simple kurtosis, method 1, split, on LAB_TRIG", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TRIG', method = 1, type='split') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("1.76749454806425"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[2]), as.double("1.04629523942343"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[3]), as.double("1.02128294035219"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 3) expect_equal(kurtosis.res$Nvalid[1], "1801") expect_equal(kurtosis.res$Nvalid[2], "2526") expect_equal(kurtosis.res$Nvalid[3], "3473") expect_length(kurtosis.res$ValidityMessage, 3) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) test_that("simple kurtosis, method 1, split, on LAB_HDL", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_HDL', method = 1, type='split') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("0.290702025953629"), tolerance = ds.test_env$low_tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[2]), as.double("0.494573359163136"), tolerance = ds.test_env$low_tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[3]), as.double("0.549162800210091"), tolerance = ds.test_env$low_tolerance) expect_length(kurtosis.res$Nvalid, 3) expect_equal(kurtosis.res$Nvalid[1], "1803") expect_equal(kurtosis.res$Nvalid[2], "2533") expect_equal(kurtosis.res$Nvalid[3], "3473") expect_length(kurtosis.res$ValidityMessage, 3) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) test_that("simple kurtosis, method 1, split, on LAB_GLUC_ADJUSTED", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_GLUC_ADJUSTED', method = 1, type='split') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("4.32162963839166"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[2]), as.double("4.38468288434594"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[3]), as.double("3.72493030465797"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 3) expect_equal(kurtosis.res$Nvalid[1], "1822") expect_equal(kurtosis.res$Nvalid[2], "2583") expect_equal(kurtosis.res$Nvalid[3], "3519") expect_length(kurtosis.res$ValidityMessage, 3) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) test_that("simple kurtosis, method 1, split, on PM_BMI_CONTINUOUS", { kurtosis.res <- ds.kurtosis(x = 'D$PM_BMI_CONTINUOUS', method = 1, type='split') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("0.671416534303503"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[2]), as.double("0.251325359087079"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[3]), as.double("0.187132199973004"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 3) expect_equal(kurtosis.res$Nvalid[1], "2066") expect_equal(kurtosis.res$Nvalid[2], "2938") expect_equal(kurtosis.res$Nvalid[3], "3923") expect_length(kurtosis.res$ValidityMessage, 3) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) context("ds.kurtosis::smk::method 1::combine") test_that("simple kurtosis, combine, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 1, type='combine') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("0.515598613390042"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 1) expect_equal(kurtosis.res$Nvalid[1], "7825") expect_length(kurtosis.res$ValidityMessage, 1) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 1, combine, on LAB_TRIG", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TRIG', method = 1, type='combine') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("1.21679529801477"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 1) expect_equal(kurtosis.res$Nvalid[1], "7800") expect_length(kurtosis.res$ValidityMessage, 1) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 1, combine, on LAB_HDL", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_HDL', method = 1, type='combine') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("0.472661436116919"), tolerance = ds.test_env$low_tolerance) expect_length(kurtosis.res$Nvalid, 1) expect_equal(kurtosis.res$Nvalid[1], "7809") expect_length(kurtosis.res$ValidityMessage, 1) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 1, combine, on LAB_GLUC_ADJUSTED", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_GLUC_ADJUSTED', method = 1, type='combine') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("4.08935226175995"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 1) expect_equal(kurtosis.res$Nvalid[1], "7924") expect_length(kurtosis.res$ValidityMessage, 1) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 1, combine, on PM_BMI_CONTINUOUS", { kurtosis.res <- ds.kurtosis(x = 'D$PM_BMI_CONTINUOUS', method = 1, type='combine') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("0.335021586102938"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 1) expect_equal(kurtosis.res$Nvalid[1], "8927") expect_length(kurtosis.res$ValidityMessage, 1) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) context("ds.kurtosis::smk::method 1::both") test_that("simple kurtosis, both, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 1, type='both') expect_equal(class(kurtosis.res), "list") expect_length(kurtosis.res, 2) expect_length(kurtosis.res$Kurtosis.by.Study, 3) expect_length(kurtosis.res$Kurtosis.by.Study$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[1]), as.double("0.171744367103707"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[2]), as.double("0.574419687874713"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[3]), as.double("0.674414218958169"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Kurtosis.by.Study$Nvalid, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[1], "1807") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[2], "2539") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[3], "3479") expect_length(kurtosis.res$Kurtosis.by.Study$ValidityMessage, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[3], "VALID ANALYSIS") expect_length(kurtosis.res$Global.Kurtosis, 3) expect_length(kurtosis.res$Global.Kurtosis$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Global.Kurtosis$Kurtosis[1]), as.double("0.515598613390042"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Global.Kurtosis$Nvalid, 1) expect_equal(kurtosis.res$Global.Kurtosis$Nvalid[1], "7825") expect_length(kurtosis.res$Global.Kurtosis$ValidityMessage, 1) expect_equal(kurtosis.res$Global.Kurtosis$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 1, both, on LAB_TRIG", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TRIG', method = 1, type='both') expect_equal(class(kurtosis.res), "list") expect_length(kurtosis.res, 2) expect_length(kurtosis.res$Kurtosis.by.Study, 3) expect_length(kurtosis.res$Kurtosis.by.Study$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[1]), as.double("1.76749454806425"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[2]), as.double("1.04629523942343"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[3]), as.double("1.02128294035219"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Kurtosis.by.Study$Nvalid, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[1], "1801") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[2], "2526") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[3], "3473") expect_length(kurtosis.res$Kurtosis.by.Study$ValidityMessage, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[3], "VALID ANALYSIS") expect_length(kurtosis.res$Global.Kurtosis, 3) expect_length(kurtosis.res$Global.Kurtosis$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Global.Kurtosis$Kurtosis[1]), as.double("1.21679529801477"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Global.Kurtosis$Nvalid, 1) expect_equal(kurtosis.res$Global.Kurtosis$Nvalid[1], "7800") expect_length(kurtosis.res$Global.Kurtosis$ValidityMessage, 1) expect_equal(kurtosis.res$Global.Kurtosis$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 1, both, on LAB_HDL", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_HDL', method = 1, type='both') expect_equal(class(kurtosis.res), "list") expect_length(kurtosis.res, 2) expect_length(kurtosis.res$Kurtosis.by.Study, 3) expect_length(kurtosis.res$Kurtosis.by.Study$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[1]), as.double("0.290702025953629"), tolerance = ds.test_env$low_tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[2]), as.double("0.494573359163136"), tolerance = ds.test_env$low_tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[3]), as.double("0.549162800210091"), tolerance = ds.test_env$low_tolerance) expect_length(kurtosis.res$Kurtosis.by.Study$Nvalid, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[1], "1803") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[2], "2533") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[3], "3473") expect_length(kurtosis.res$Kurtosis.by.Study$ValidityMessage, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[3], "VALID ANALYSIS") expect_length(kurtosis.res$Global.Kurtosis, 3) expect_length(kurtosis.res$Global.Kurtosis$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Global.Kurtosis$Kurtosis[1]), as.double("0.472661436116919"), tolerance = ds.test_env$low_tolerance) expect_length(kurtosis.res$Global.Kurtosis$Nvalid, 1) expect_equal(kurtosis.res$Global.Kurtosis$Nvalid[1], "7809") expect_length(kurtosis.res$Global.Kurtosis$ValidityMessage, 1) expect_equal(kurtosis.res$Global.Kurtosis$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 1, both, on LAB_GLUC_ADJUSTED", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_GLUC_ADJUSTED', method = 1, type='both') expect_equal(class(kurtosis.res), "list") expect_length(kurtosis.res, 2) expect_length(kurtosis.res$Kurtosis.by.Study, 3) expect_length(kurtosis.res$Kurtosis.by.Study$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[1]), as.double("4.32162963839166"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[2]), as.double("4.38468288434594"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[3]), as.double("3.72493030465797"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Kurtosis.by.Study$Nvalid, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[1], "1822") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[2], "2583") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[3], "3519") expect_length(kurtosis.res$Kurtosis.by.Study$ValidityMessage, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[3], "VALID ANALYSIS") expect_length(kurtosis.res$Global.Kurtosis, 3) expect_length(kurtosis.res$Global.Kurtosis$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Global.Kurtosis$Kurtosis[1]), as.double("4.08935226175995"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Global.Kurtosis$Nvalid, 1) expect_equal(kurtosis.res$Global.Kurtosis$Nvalid[1], "7924") expect_length(kurtosis.res$Global.Kurtosis$ValidityMessage, 1) expect_equal(kurtosis.res$Global.Kurtosis$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 1, both, on PM_BMI_CONTINUOUS", { kurtosis.res <- ds.kurtosis(x = 'D$PM_BMI_CONTINUOUS', method = 1, type='both') expect_equal(class(kurtosis.res), "list") expect_length(kurtosis.res, 2) expect_length(kurtosis.res$Kurtosis.by.Study, 3) expect_length(kurtosis.res$Kurtosis.by.Study$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[1]), as.double("0.671416534303503"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[2]), as.double("0.251325359087079"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[3]), as.double("0.187132199973004"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Kurtosis.by.Study$Nvalid, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[1], "2066") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[2], "2938") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[3], "3923") expect_length(kurtosis.res$Kurtosis.by.Study$ValidityMessage, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[3], "VALID ANALYSIS") expect_length(kurtosis.res$Global.Kurtosis, 3) expect_length(kurtosis.res$Global.Kurtosis$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Global.Kurtosis$Kurtosis[1]), as.double("0.335021586102938"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Global.Kurtosis$Nvalid, 1) expect_equal(kurtosis.res$Global.Kurtosis$Nvalid[1], "8927") expect_length(kurtosis.res$Global.Kurtosis$ValidityMessage, 1) expect_equal(kurtosis.res$Global.Kurtosis$ValidityMessage[1], "VALID ANALYSIS") }) # Method 2 context("ds.kurtosis::smk::method 2::split") test_that("simple kurtosis, method 2, split, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 2, type='split') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("0.175548320198465"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[2]), as.double("0.577919349817977"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[3]), as.double("0.677111105785997"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 3) expect_equal(kurtosis.res$Nvalid[1], "1807") expect_equal(kurtosis.res$Nvalid[2], "2539") expect_equal(kurtosis.res$Nvalid[3], "3479") expect_length(kurtosis.res$ValidityMessage, 3) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) test_that("simple kurtosis, method 2, split, on LAB_TRIG", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TRIG', method = 2, type='split') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("1.7757502518397"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[2]), as.double("1.0507483099711"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[3]), as.double("1.02448438876989"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 3) expect_equal(kurtosis.res$Nvalid[1], "1801") expect_equal(kurtosis.res$Nvalid[2], "2526") expect_equal(kurtosis.res$Nvalid[3], "3473") expect_length(kurtosis.res$ValidityMessage, 3) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) test_that("simple kurtosis, method 2, split, on LAB_HDL", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_HDL', method = 2, type='split') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("0.294844984757316"), tolerance = ds.test_env$low_tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[2]), as.double("0.497923487075878"), tolerance = ds.test_env$low_tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[3]), as.double("0.551683842646188"), tolerance = ds.test_env$low_tolerance) expect_length(kurtosis.res$Nvalid, 3) expect_equal(kurtosis.res$Nvalid[1], "1803") expect_equal(kurtosis.res$Nvalid[2], "2533") expect_equal(kurtosis.res$Nvalid[3], "3473") expect_length(kurtosis.res$ValidityMessage, 3) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) test_that("simple kurtosis, method 2, split, on LAB_GLUC_ADJUSTED", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_GLUC_ADJUSTED', method = 2, type='split') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("4.33681301852393"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[2]), as.double("4.39550878961539"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[3]), as.double("3.73193529182726"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 3) expect_equal(kurtosis.res$Nvalid[1], "1822") expect_equal(kurtosis.res$Nvalid[2], "2583") expect_equal(kurtosis.res$Nvalid[3], "3519") expect_length(kurtosis.res$ValidityMessage, 3) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) test_that("simple kurtosis, method 2, split, on PM_BMI_CONTINUOUS", { kurtosis.res <- ds.kurtosis(x = 'D$PM_BMI_CONTINUOUS', method = 2, type='split') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("0.675954084252309"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[2]), as.double("0.253798588114679"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[3]), as.double("0.188901928135923"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 3) expect_equal(kurtosis.res$Nvalid[1], "2066") expect_equal(kurtosis.res$Nvalid[2], "2938") expect_equal(kurtosis.res$Nvalid[3], "3923") expect_length(kurtosis.res$ValidityMessage, 3) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) context("ds.kurtosis::smk::method 2::combine") test_that("simple kurtosis, combine, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 2, type='combine') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("0.516695386307489"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 1) expect_equal(kurtosis.res$Nvalid[1], "7825") expect_length(kurtosis.res$ValidityMessage, 1) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 2, combine, on LAB_TRIG", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TRIG', method = 2, type='combine') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("1.21834528057683"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 1) expect_equal(kurtosis.res$Nvalid[1], "7800") expect_length(kurtosis.res$ValidityMessage, 1) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 2, combine, on LAB_HDL", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_HDL', method = 2, type='combine') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("0.473732952559591"), tolerance = ds.test_env$low_tolerance) expect_length(kurtosis.res$Nvalid, 1) expect_equal(kurtosis.res$Nvalid[1], "7809") expect_length(kurtosis.res$ValidityMessage, 1) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 2, combine, on LAB_GLUC_ADJUSTED", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_GLUC_ADJUSTED', method = 2, type='combine') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("4.09269136885493"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 1) expect_equal(kurtosis.res$Nvalid[1], "7924") expect_length(kurtosis.res$ValidityMessage, 1) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 2, combine, on PM_BMI_CONTINUOUS", { kurtosis.res <- ds.kurtosis(x = 'D$PM_BMI_CONTINUOUS', method = 2, type='combine') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("0.335881726489728"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 1) expect_equal(kurtosis.res$Nvalid[1], "8927") expect_length(kurtosis.res$ValidityMessage, 1) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) context("ds.kurtosis::smk::method 2::both") test_that("simple kurtosis, both, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 2, type='both') expect_equal(class(kurtosis.res), "list") expect_length(kurtosis.res, 2) expect_length(kurtosis.res$Kurtosis.by.Study, 3) expect_length(kurtosis.res$Kurtosis.by.Study$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[1]), as.double("0.175548320198465"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[2]), as.double("0.577919349817977"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[3]), as.double("0.677111105785997"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Kurtosis.by.Study$Nvalid, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[1], "1807") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[2], "2539") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[3], "3479") expect_length(kurtosis.res$Kurtosis.by.Study$ValidityMessage, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[3], "VALID ANALYSIS") expect_length(kurtosis.res$Global.Kurtosis, 3) expect_length(kurtosis.res$Global.Kurtosis$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Global.Kurtosis$Kurtosis[1]), as.double("0.516695386307489"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Global.Kurtosis$Nvalid, 1) expect_equal(kurtosis.res$Global.Kurtosis$Nvalid[1], "7825") expect_length(kurtosis.res$Global.Kurtosis$ValidityMessage, 1) expect_equal(kurtosis.res$Global.Kurtosis$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 2, both, on LAB_TRIG", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TRIG', method = 2, type='both') expect_equal(class(kurtosis.res), "list") expect_length(kurtosis.res, 2) expect_length(kurtosis.res$Kurtosis.by.Study, 3) expect_length(kurtosis.res$Kurtosis.by.Study$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[1]), as.double("1.7757502518397"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[2]), as.double("1.0507483099711"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[3]), as.double("1.02448438876989"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Kurtosis.by.Study$Nvalid, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[1], "1801") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[2], "2526") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[3], "3473") expect_length(kurtosis.res$Kurtosis.by.Study$ValidityMessage, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[3], "VALID ANALYSIS") expect_length(kurtosis.res$Global.Kurtosis, 3) expect_length(kurtosis.res$Global.Kurtosis$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Global.Kurtosis$Kurtosis[1]), as.double("1.21834528057683"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Global.Kurtosis$Nvalid, 1) expect_equal(kurtosis.res$Global.Kurtosis$Nvalid[1], "7800") expect_length(kurtosis.res$Global.Kurtosis$ValidityMessage, 1) expect_equal(kurtosis.res$Global.Kurtosis$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 2, both, on LAB_HDL", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_HDL', method = 2, type='both') expect_equal(class(kurtosis.res), "list") expect_length(kurtosis.res, 2) expect_length(kurtosis.res$Kurtosis.by.Study, 3) expect_length(kurtosis.res$Kurtosis.by.Study$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[1]), as.double("0.294844984757316"), tolerance = ds.test_env$low_tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[2]), as.double("0.497923487075878"), tolerance = ds.test_env$low_tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[3]), as.double("0.551683842646188"), tolerance = ds.test_env$low_tolerance) expect_length(kurtosis.res$Kurtosis.by.Study$Nvalid, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[1], "1803") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[2], "2533") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[3], "3473") expect_length(kurtosis.res$Kurtosis.by.Study$ValidityMessage, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[3], "VALID ANALYSIS") expect_length(kurtosis.res$Global.Kurtosis, 3) expect_length(kurtosis.res$Global.Kurtosis$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Global.Kurtosis$Kurtosis[1]), as.double("0.473732952559591"), tolerance = ds.test_env$low_tolerance) expect_length(kurtosis.res$Global.Kurtosis$Nvalid, 1) expect_equal(kurtosis.res$Global.Kurtosis$Nvalid[1], "7809") expect_length(kurtosis.res$Global.Kurtosis$ValidityMessage, 1) expect_equal(kurtosis.res$Global.Kurtosis$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 2, both, on LAB_GLUC_ADJUSTED", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_GLUC_ADJUSTED', method = 2, type='both') expect_equal(class(kurtosis.res), "list") expect_length(kurtosis.res, 2) expect_length(kurtosis.res$Kurtosis.by.Study, 3) expect_length(kurtosis.res$Kurtosis.by.Study$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[1]), as.double("4.33681301852393"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[2]), as.double("4.39550878961539"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[3]), as.double("3.73193529182726"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Kurtosis.by.Study$Nvalid, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[1], "1822") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[2], "2583") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[3], "3519") expect_length(kurtosis.res$Kurtosis.by.Study$ValidityMessage, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[3], "VALID ANALYSIS") expect_length(kurtosis.res$Global.Kurtosis, 3) expect_length(kurtosis.res$Global.Kurtosis$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Global.Kurtosis$Kurtosis[1]), as.double("4.09269136885493"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Global.Kurtosis$Nvalid, 1) expect_equal(kurtosis.res$Global.Kurtosis$Nvalid[1], "7924") expect_length(kurtosis.res$Global.Kurtosis$ValidityMessage, 1) expect_equal(kurtosis.res$Global.Kurtosis$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 2, both, on PM_BMI_CONTINUOUS", { kurtosis.res <- ds.kurtosis(x = 'D$PM_BMI_CONTINUOUS', method = 2, type='both') expect_equal(class(kurtosis.res), "list") expect_length(kurtosis.res, 2) expect_length(kurtosis.res$Kurtosis.by.Study, 3) expect_length(kurtosis.res$Kurtosis.by.Study$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[1]), as.double("0.675954084252309"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[2]), as.double("0.253798588114679"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[3]), as.double("0.188901928135923"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Kurtosis.by.Study$Nvalid, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[1], "2066") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[2], "2938") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[3], "3923") expect_length(kurtosis.res$Kurtosis.by.Study$ValidityMessage, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[3], "VALID ANALYSIS") expect_length(kurtosis.res$Global.Kurtosis, 3) expect_length(kurtosis.res$Global.Kurtosis$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Global.Kurtosis$Kurtosis[1]), as.double("0.335881726489728"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Global.Kurtosis$Nvalid, 1) expect_equal(kurtosis.res$Global.Kurtosis$Nvalid[1], "8927") expect_length(kurtosis.res$Global.Kurtosis$ValidityMessage, 1) expect_equal(kurtosis.res$Global.Kurtosis$ValidityMessage[1], "VALID ANALYSIS") }) # Method 3 context("ds.kurtosis::smk::method 3::split") test_that("simple kurtosis, method 3, split, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 3, type='split') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("0.16823483003675"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[2]), as.double("0.571604630147399"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[3]), as.double("0.672302183238634"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 3) expect_equal(kurtosis.res$Nvalid[1], "1807") expect_equal(kurtosis.res$Nvalid[2], "2539") expect_equal(kurtosis.res$Nvalid[3], "3479") expect_length(kurtosis.res$ValidityMessage, 3) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) test_that("simple kurtosis, method 3, split, on LAB_TRIG", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TRIG', method = 3, type='split') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("1.76220174297892"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[2]), as.double("1.04309215604256"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[3]), as.double("1.01896753349628"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 3) expect_equal(kurtosis.res$Nvalid[1], "1801") expect_equal(kurtosis.res$Nvalid[2], "2526") expect_equal(kurtosis.res$Nvalid[3], "3473") expect_length(kurtosis.res$ValidityMessage, 3) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) test_that("simple kurtosis, method 3, split, on LAB_HDL", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_HDL', method = 3, type='split') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("0.287052786394011"), tolerance = ds.test_env$low_tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[2]), as.double("0.491814667058934"), tolerance = ds.test_env$low_tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[3]), as.double("0.54711923451172"), tolerance = ds.test_env$low_tolerance) expect_length(kurtosis.res$Nvalid, 3) expect_equal(kurtosis.res$Nvalid[1], "1803") expect_equal(kurtosis.res$Nvalid[2], "2533") expect_equal(kurtosis.res$Nvalid[3], "3473") expect_length(kurtosis.res$ValidityMessage, 3) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) test_that("simple kurtosis, method 3, split, on LAB_GLUC_ADJUSTED", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_GLUC_ADJUSTED', method = 3, type='split') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("4.31359492883116"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[2]), as.double("4.37896607954034"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[3]), as.double("3.72110877877708"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 3) expect_equal(kurtosis.res$Nvalid[1], "1822") expect_equal(kurtosis.res$Nvalid[2], "2583") expect_equal(kurtosis.res$Nvalid[3], "3519") expect_length(kurtosis.res$ValidityMessage, 3) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) test_that("simple kurtosis, method 3, split, on PM_BMI_CONTINUOUS", { kurtosis.res <- ds.kurtosis(x = 'D$PM_BMI_CONTINUOUS', method = 3, type='split') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("0.667863264214689"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[2]), as.double("0.249112444154344"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis[3]), as.double("0.185507562711274"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 3) expect_equal(kurtosis.res$Nvalid[1], "2066") expect_equal(kurtosis.res$Nvalid[2], "2938") expect_equal(kurtosis.res$Nvalid[3], "3923") expect_length(kurtosis.res$ValidityMessage, 3) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$ValidityMessage[3], "VALID ANALYSIS") }) context("ds.kurtosis::smk::method 3::combine") test_that("simple kurtosis, combine, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 3, type='combine') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("0.514700115249594"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 1) expect_equal(kurtosis.res$Nvalid[1], "7825") expect_length(kurtosis.res$ValidityMessage, 1) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 3, combine, on LAB_TRIG", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TRIG', method = 3, type='combine') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("1.21571413776076"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 1) expect_equal(kurtosis.res$Nvalid[1], "7800") expect_length(kurtosis.res$ValidityMessage, 1) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 3, combine, on LAB_HDL", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_HDL', method = 3, type='combine') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("0.47177209328527"), tolerance = ds.test_env$low_tolerance) expect_length(kurtosis.res$Nvalid, 1) expect_equal(kurtosis.res$Nvalid[1], "7809") expect_length(kurtosis.res$ValidityMessage, 1) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 3, combine, on LAB_GLUC_ADJUSTED", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_GLUC_ADJUSTED', method = 3, type='combine') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("4.0875630379014"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 1) expect_equal(kurtosis.res$Nvalid[1], "7924") expect_length(kurtosis.res$ValidityMessage, 1) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 3, combine, on PM_BMI_CONTINUOUS", { kurtosis.res <- ds.kurtosis(x = 'D$PM_BMI_CONTINUOUS', method = 3, type='combine') expect_equal(class(kurtosis.res), "data.frame") expect_length(kurtosis.res, 3) expect_length(kurtosis.res$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Kurtosis[1]), as.double("0.334274451613855"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Nvalid, 1) expect_equal(kurtosis.res$Nvalid[1], "8927") expect_length(kurtosis.res$ValidityMessage, 1) expect_equal(kurtosis.res$ValidityMessage[1], "VALID ANALYSIS") }) context("ds.kurtosis::smk::method 3::both") test_that("simple kurtosis, both, on LAB_TSC", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TSC', method = 3, type='both') expect_equal(class(kurtosis.res), "list") expect_length(kurtosis.res, 2) expect_length(kurtosis.res$Kurtosis.by.Study, 3) expect_length(kurtosis.res$Kurtosis.by.Study$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[1]), as.double("0.16823483003675"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[2]), as.double("0.571604630147399"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[3]), as.double("0.672302183238634"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Kurtosis.by.Study$Nvalid, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[1], "1807") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[2], "2539") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[3], "3479") expect_length(kurtosis.res$Kurtosis.by.Study$ValidityMessage, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[3], "VALID ANALYSIS") expect_length(kurtosis.res$Global.Kurtosis, 3) expect_length(kurtosis.res$Global.Kurtosis$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Global.Kurtosis$Kurtosis[1]), as.double("0.514700115249594"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Global.Kurtosis$Nvalid, 1) expect_equal(kurtosis.res$Global.Kurtosis$Nvalid[1], "7825") expect_length(kurtosis.res$Global.Kurtosis$ValidityMessage, 1) expect_equal(kurtosis.res$Global.Kurtosis$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 3, both, on LAB_TRIG", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_TRIG', method = 3, type='both') expect_equal(class(kurtosis.res), "list") expect_length(kurtosis.res, 2) expect_length(kurtosis.res$Kurtosis.by.Study, 3) expect_length(kurtosis.res$Kurtosis.by.Study$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[1]), as.double("1.76220174297892"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[2]), as.double("1.04309215604256"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[3]), as.double("1.01896753349628"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Kurtosis.by.Study$Nvalid, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[1], "1801") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[2], "2526") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[3], "3473") expect_length(kurtosis.res$Kurtosis.by.Study$ValidityMessage, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[3], "VALID ANALYSIS") expect_length(kurtosis.res$Global.Kurtosis, 3) expect_length(kurtosis.res$Global.Kurtosis$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Global.Kurtosis$Kurtosis[1]), as.double("1.21571413776076"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Global.Kurtosis$Nvalid, 1) expect_equal(kurtosis.res$Global.Kurtosis$Nvalid[1], "7800") expect_length(kurtosis.res$Global.Kurtosis$ValidityMessage, 1) expect_equal(kurtosis.res$Global.Kurtosis$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 3, both, on LAB_HDL", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_HDL', method = 3, type='both') expect_equal(class(kurtosis.res), "list") expect_length(kurtosis.res, 2) expect_length(kurtosis.res$Kurtosis.by.Study, 3) expect_length(kurtosis.res$Kurtosis.by.Study$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[1]), as.double("0.287052786394011"), tolerance = ds.test_env$low_tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[2]), as.double("0.491814667058934"), tolerance = ds.test_env$low_tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[3]), as.double("0.54711923451172"), tolerance = ds.test_env$low_tolerance) expect_length(kurtosis.res$Kurtosis.by.Study$Nvalid, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[1], "1803") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[2], "2533") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[3], "3473") expect_length(kurtosis.res$Kurtosis.by.Study$ValidityMessage, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[3], "VALID ANALYSIS") expect_length(kurtosis.res$Global.Kurtosis, 3) expect_length(kurtosis.res$Global.Kurtosis$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Global.Kurtosis$Kurtosis[1]), as.double("0.47177209328527"), tolerance = ds.test_env$low_tolerance) expect_length(kurtosis.res$Global.Kurtosis$Nvalid, 1) expect_equal(kurtosis.res$Global.Kurtosis$Nvalid[1], "7809") expect_length(kurtosis.res$Global.Kurtosis$ValidityMessage, 1) expect_equal(kurtosis.res$Global.Kurtosis$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 3, both, on LAB_GLUC_ADJUSTED", { kurtosis.res <- ds.kurtosis(x = 'D$LAB_GLUC_ADJUSTED', method = 3, type='both') expect_equal(class(kurtosis.res), "list") expect_length(kurtosis.res, 2) expect_length(kurtosis.res$Kurtosis.by.Study, 3) expect_length(kurtosis.res$Kurtosis.by.Study$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[1]), as.double("4.31359492883116"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[2]), as.double("4.37896607954034"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[3]), as.double("3.72110877877708"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Kurtosis.by.Study$Nvalid, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[1], "1822") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[2], "2583") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[3], "3519") expect_length(kurtosis.res$Kurtosis.by.Study$ValidityMessage, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[3], "VALID ANALYSIS") expect_length(kurtosis.res$Global.Kurtosis, 3) expect_length(kurtosis.res$Global.Kurtosis$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Global.Kurtosis$Kurtosis[1]), as.double("4.0875630379014"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Global.Kurtosis$Nvalid, 1) expect_equal(kurtosis.res$Global.Kurtosis$Nvalid[1], "7924") expect_length(kurtosis.res$Global.Kurtosis$ValidityMessage, 1) expect_equal(kurtosis.res$Global.Kurtosis$ValidityMessage[1], "VALID ANALYSIS") }) test_that("simple kurtosis, method 3, both, on PM_BMI_CONTINUOUS", { kurtosis.res <- ds.kurtosis(x = 'D$PM_BMI_CONTINUOUS', method = 3, type='both') expect_equal(class(kurtosis.res), "list") expect_length(kurtosis.res, 2) expect_length(kurtosis.res$Kurtosis.by.Study, 3) expect_length(kurtosis.res$Kurtosis.by.Study$Kurtosis, 3) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[1]), as.double("0.667863264214689"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[2]), as.double("0.249112444154344"), tolerance = ds.test_env$tolerance) expect_equal(as.double(kurtosis.res$Kurtosis.by.Study$Kurtosis[3]), as.double("0.185507562711274"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Kurtosis.by.Study$Nvalid, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[1], "2066") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[2], "2938") expect_equal(kurtosis.res$Kurtosis.by.Study$Nvalid[3], "3923") expect_length(kurtosis.res$Kurtosis.by.Study$ValidityMessage, 3) expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[1], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[2], "VALID ANALYSIS") expect_equal(kurtosis.res$Kurtosis.by.Study$ValidityMessage[3], "VALID ANALYSIS") expect_length(kurtosis.res$Global.Kurtosis, 3) expect_length(kurtosis.res$Global.Kurtosis$Kurtosis, 1) expect_equal(as.double(kurtosis.res$Global.Kurtosis$Kurtosis[1]), as.double("0.334274451613855"), tolerance = ds.test_env$tolerance) expect_length(kurtosis.res$Global.Kurtosis$Nvalid, 1) expect_equal(kurtosis.res$Global.Kurtosis$Nvalid[1], "8927") expect_length(kurtosis.res$Global.Kurtosis$ValidityMessage, 1) expect_equal(kurtosis.res$Global.Kurtosis$ValidityMessage[1], "VALID ANALYSIS") }) # # Done # context("ds.kurtosis::smk::shutdown") test_that("shutdown", { ds_expect_variables(c("D")) }) disconnect.studies.dataset.cnsim() context("ds.kurtosis::smk::done")