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test-smk-ds.cor.R
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test-smk-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::smk::setup")
connect.studies.dataset.survival(list("survtime", "time.id", "female"))
test_that("setup", {
ds_expect_variables(c("D"))
})
#
# Tests
#
context("ds.cor::smk")
test_that("simple test, combine, pairwise.complete", {
res <- ds.cor(x="D$survtime", y="D$time.id", type="combine", naAction="pairwise.complete")
expect_length(res, 5)
expect_true("matrix" %in% class(res$`Number of missing values in each variable`))
expect_true("matrix" %in% class(res$`Number of missing values pairwise`))
expect_true("matrix" %in% class(res$`Correlation Matrix`))
expect_true("matrix" %in% class(res$`Number of complete cases used`))
expect_length(res$`Error message`, 3)
expect_equal(res$`Error message`[[1]], NA)
expect_equal(res$`Error message`[[2]], NA)
expect_equal(res$`Error message`[[3]], NA)
})
test_that("simple test, combine, casewise.complete", {
res <- ds.cor(x="D$survtime", y="D$time.id", type="combine", naAction="casewise.complete")
expect_length(res, 5)
expect_true("matrix" %in% class(res$`Number of missing values in each variable`))
expect_true("matrix" %in% class(res$`Number of missing values casewise`))
expect_true("matrix" %in% class(res$`Correlation Matrix`))
expect_true("matrix" %in% class(res$`Number of complete cases used`))
expect_length(res$`Error message`, 3)
expect_equal(res$`Error message`[[1]], NA)
expect_equal(res$`Error message`[[2]], NA)
expect_equal(res$`Error message`[[3]], NA)
})
test_that("simple test, split, pairwise.complete", {
res <- ds.cor(x="D$survtime", y="D$time.id", type="split", naAction="pairwise.complete")
expect_length(res, 3)
expect_length(res[[1]], 5)
expect_true("matrix" %in% class(res[[1]]$`Number of missing values in each variable`))
expect_true("matrix" %in% class(res[[1]]$`Number of missing values pairwise`))
expect_true("matrix" %in% class(res[[1]]$`Correlation Matrix`))
expect_true("matrix" %in% class(res[[1]]$`Number of complete cases used`))
expect_equal(res[[1]]$`Error message`, NA)
expect_length(res[[2]], 5)
expect_true("matrix" %in% class(res[[2]]$`Number of missing values in each variable`))
expect_true("matrix" %in% class(res[[2]]$`Number of missing values pairwise`))
expect_true("matrix" %in% class(res[[2]]$`Correlation Matrix`))
expect_true("matrix" %in% class(res[[2]]$`Number of complete cases used`))
expect_equal(res[[2]]$`Error message`, NA)
expect_length(res[[3]], 5)
expect_true("matrix" %in% class(res[[3]]$`Number of missing values in each variable`))
expect_true("matrix" %in% class(res[[3]]$`Number of missing values pairwise`))
expect_true("matrix" %in% class(res[[3]]$`Correlation Matrix`))
expect_true("matrix" %in% class(res[[3]]$`Number of complete cases used`))
expect_equal(res[[3]]$`Error message`, NA)
})
test_that("simple test, split, casewise.complete", {
res <- ds.cor(x="D$survtime", y="D$time.id", type="split", naAction="casewise.complete")
expect_length(res, 3)
expect_length(res[[1]], 5)
expect_true("matrix" %in% class(res[[1]]$`Number of missing values in each variable`))
expect_true("matrix" %in% class(res[[1]]$`Number of missing values casewise`))
expect_true("matrix" %in% class(res[[1]]$`Correlation Matrix`))
expect_true("matrix" %in% class(res[[1]]$`Number of complete cases used`))
expect_equal(res[[1]]$`Error message`, NA)
expect_length(res[[2]], 5)
expect_true("matrix" %in% class(res[[2]]$`Number of missing values in each variable`))
expect_true("matrix" %in% class(res[[2]]$`Number of missing values casewise`))
expect_true("matrix" %in% class(res[[2]]$`Correlation Matrix`))
expect_true("matrix" %in% class(res[[2]]$`Number of complete cases used`))
expect_equal(res[[2]]$`Error message`, NA)
expect_length(res[[3]], 5)
expect_true("matrix" %in% class(res[[3]]$`Number of missing values in each variable`))
expect_true("matrix" %in% class(res[[3]]$`Number of missing values casewise`))
expect_true("matrix" %in% class(res[[3]]$`Correlation Matrix`))
expect_true("matrix" %in% class(res[[3]]$`Number of complete cases used`))
expect_equal(res[[3]]$`Error message`, NA)
})
#
# Done
#
context("ds.cor::smk::setup::shutdown")
test_that("shutdown", {
ds_expect_variables(c("D"))
})
disconnect.studies.dataset.survival()
context("ds.cor::smk::setup::done")