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test-smk-ds.lexis.R
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test-smk-ds.lexis.R
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#-------------------------------------------------------------------------------
# Copyright (c) 2019-2020 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.lexis::smk::setup")
connect.studies.dataset.survival(list("id", "starttime", "endtime", "cens", "age.60"))
test_that("setup", {
ds_expect_variables(c("D"))
})
#
# Tests
#
context("ds.lexis::smk")
test_that("simple lexis", {
res <- ds.lexis(data='D', intervalWidth = c(1.0, 1.5, 2.5), idCol = 'D$id', entryCol = 'D$starttime', exitCol = 'D$endtime', statusCol = 'D$cens', variables = c('D$age.60'), expandDF = 'EM.new')
expect_length(res, 5)
expect_equal(res$maxmaxtime, 10.25, tolerance=0.5)
expect_equal(res$Note1, "END OF LAST FOLLOW-UP PERIOD SET (RANDOMLY) AT maxmaxtime:")
expect_equal(res$Note2, "ASSIGN FUNCTION COMPLETED - USE ds.ls() TO CONFIRM")
expect_equal(res$Note3, "IF FUNCTION FAILED ON ONE OR MORE STUDIES WITHOUT EXPLANATION, TYPE [PRECISELY] THE COMMAND:")
expect_equal(res$Note4, "ds.message('messageobj') FOR MORE ERROR MESSAGES")
res.exists <- ds.exists('EM.new')
expect_length(res.exists, 3)
expect_true(res.exists$survival1)
expect_true(res.exists$survival2)
expect_true(res.exists$survival3)
res.message <- ds.message('messageobj')
expect_length(res.message, 3)
expect_equal(res.message$survival1, "ALL OK: there are no studysideMessage(s) on this datasource")
expect_equal(res.message$survival2, "ALL OK: there are no studysideMessage(s) on this datasource")
expect_equal(res.message$survival3, "ALL OK: there are no studysideMessage(s) on this datasource")
})
#
# Done
#
context("ds.lexis::smk::shutdown")
test_that("shutdown", {
ds_expect_variables(c("D", "EM.new", "messageobj"))
})
disconnect.studies.dataset.survival()
context("ds.lexis::smk::done")