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test-disc-ds.cor.R
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test-disc-ds.cor.R
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#-------------------------------------------------------------------------------
# Copyright (c) 2018-2020 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 <http://www.gnu.org/licenses/>.
#-------------------------------------------------------------------------------
#
# Set up
#
context("ds.cor::disc::setup")
connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "LAB_HDL", "LAB_GLUC_ADJUSTED", "GENDER"))
test_that("setup", {
ds_expect_variables(c("D"))
})
#
# Tests
#
context("ds.cor::disc")
test_that("simple D3 setup", {
ds.dataFrameSubset('D',V1.name = 'D$GENDER', V2.name = '0', Boolean.operator = '==', newobj='D1')
ds.dataFrameSubset('D1',V1.name = 'D1$LAB_TSC', V2.name = '3.5', Boolean.operator = '<', newobj='D2')
ds.dataFrame(c('D2$LAB_TSC', 'D2$LAB_TRIG', 'D2$LAB_HDL', 'D2$LAB_GLUC_ADJUSTED'), newobj='D3')
res <- ds.dim('D3')
expect_length(res, 4)
expect_length(res$`dimensions of D3 in sim1`, 2)
expect_equal(res$`dimensions of D3 in sim1`[1], 15)
expect_equal(res$`dimensions of D3 in sim1`[2], 4)
expect_length(res$`dimensions of D3 in sim2`, 2)
expect_equal(res$`dimensions of D3 in sim2`[1], 11)
expect_equal(res$`dimensions of D3 in sim2`[2], 4)
expect_length(res$`dimensions of D3 in sim3`, 2)
expect_equal(res$`dimensions of D3 in sim3`[1], 16)
expect_equal(res$`dimensions of D3 in sim3`[2], 4)
expect_length(res$`dimensions of D3 in combined studies`, 2)
expect_equal(res$`dimensions of D3 in combined studies`[1], 42)
expect_equal(res$`dimensions of D3 in combined studies`[2], 4)
})
test_that("simple disc test, naAction='casewise.complete', type='split'", {
res <- ds.cor('D3', naAction='casewise.complete', type='split')
expect_length(res, 3)
expect_length(res[[1]], 5)
expect_length(res[[1]]$`Error message`, 1)
expect_true(is.na(res[[1]]$`Error message`))
expect_length(res[[2]], 5)
expect_length(res[[2]]$`Error message`, 1)
expect_equal(res[[2]]$`Error message`, "ERROR: The ratio of the number of variables over the number of individual-level records exceeds the allowed threshold, there is a possible risk of disclosure", fixed=TRUE)
expect_length(res[[3]], 5)
expect_length(res[[3]]$`Error message`, 1)
expect_true(is.na(res[[3]]$`Error message`))
})
test_that("simple disc test, naAction='pairwise.complete', type='split'", {
# res <- ds.cor('D3', naAction='pairwise.complete', type='split')
#
# expect_length(res, 3)
# expect_length(res[[1]], 5)
# expect_length(res[[1]]$`Error message`, 1)
# expect_true(is.na(res[[1]]$`Error message`))
# expect_length(res[[2]], 5)
# expect_length(res[[2]]$`Error message`, 1)
# expect_equal(res[[2]]$`Error message`, "ERROR: The ratio of the number of variables over the number of individual-level records exceeds the allowed threshold, there is a possible risk of disclosure", fixed=TRUE)
# expect_length(res[[3]], 5)
# expect_length(res[[3]]$`Error message`, 1)
# expect_true(is.na(res[[3]]$`Error message`))
})
test_that("simple disc test, naAction='casewise.complete', type='combine'", {
res <- ds.cor('D3', naAction='casewise.complete', type='combine')
expect_length(res, 5)
expect_length(res$`Error message`, 3)
expect_length(res$`Error message`[[1]], 1)
expect_true(is.na(res$`Error message`[[1]]))
expect_length(res$`Error message`[[2]], 1)
expect_equal(res$`Error message`[[2]], "ERROR: The ratio of the number of variables over the number of individual-level records exceeds the allowed threshold, there is a possible risk of disclosure", fixed=TRUE)
expect_length(res$`Error message`[[3]], 1)
expect_true(is.na(res$`Error message`[[3]]))
})
test_that("simple disc test, naAction='pairwise.complete', type='combine'", {
# res <- ds.cor('D3', naAction='pairwise.complete', type='combine')
#
# expect_length(res, 5)
# expect_length(res$`Error message`, 3)
# expect_length(res$`Error message`[[1]], 1)
# expect_true(is.na(res$`Error message`[[1]]))
# expect_length(res$`Error message`[[2]], 1)
# expect_equal(res$`Error message`[[2]], "ERROR: The ratio of the number of variables over the number of individual-level records exceeds the allowed threshold, there is a possible risk of disclosure", fixed=TRUE)
# expect_length(res$`Error message`[[3]], 1)
# expect_true(is.na(res$`Error message`[[3]]))
})
#
# Done
#
context("ds.cor::disc::shutdown")
test_that("shutdown", {
ds_expect_variables(c("D", "D1", "D2", "D3"))
})
disconnect.studies.dataset.cnsim()
context("ds.cor::disc::done")