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test-smk-ds.glmSummary.R
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test-smk-ds.glmSummary.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.glmSummary::smk::setup")
connect.studies.dataset.cnsim(list("LAB_TSC", "LAB_TRIG", "DIS_AMI", "DIS_DIAB", "GENDER"))
test_that("setup", {
ds_expect_variables(c("D"))
})
#
# Tests
#
context("ds.glmSummary::smk::gaussian")
test_that("simple glmSummary, gaussian, without newobj", {
glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="gaussian", newobj="gaussian.glmslma.obj")
expect_length(glmSLMA.res, 9)
expect_equal(glmSLMA.res$num.valid.studies, 3)
expect_length(glmSLMA.res$validity.check, 1)
expect_equal(glmSLMA.res$validity.check, "<gaussian.glmslma.obj> appears valid in all sources")
res <- ds.glmSummary("gaussian.glmslma.obj")
expect_length(res, 3)
expect_length(res$sim1, 2)
expect_length(res$sim1$glm.obj, 31)
expect_true('glm' %in% class(res$sim1$glm.obj))
expect_true('lm' %in% class(res$sim1$glm.obj))
expect_length(res$sim1$glm.summary.obj, 18)
expect_equal(class(res$sim1$glm.summary.obj), 'summary.glm')
expect_length(res$sim2, 2)
expect_length(res$sim2$glm.obj, 31)
expect_true('glm' %in% class(res$sim2$glm.obj))
expect_true('lm' %in% class(res$sim2$glm.obj))
expect_length(res$sim2$glm.summary.obj, 18)
expect_equal(class(res$sim2$glm.summary.obj), 'summary.glm')
expect_length(res$sim3, 2)
expect_length(res$sim3$glm.obj, 31)
expect_true('glm' %in% class(res$sim3$glm.obj))
expect_true('lm' %in% class(res$sim3$glm.obj))
expect_length(res$sim3$glm.summary.obj, 18)
expect_equal(class(res$sim3$glm.summary.obj), 'summary.glm')
})
test_that("simple glmSummary, gaussian", {
glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="gaussian", newobj="gaussian.glmslma.obj")
expect_length(glmSLMA.res, 9)
expect_equal(glmSLMA.res$num.valid.studies, 3)
expect_length(glmSLMA.res$validity.check, 1)
expect_equal(glmSLMA.res$validity.check, "<gaussian.glmslma.obj> appears valid in all sources")
res <- ds.glmSummary("gaussian.glmslma.obj", newobj="gaussian.glmsummary.obj")
expect_length(res, 3)
expect_length(res$sim1, 2)
expect_length(res$sim1$glm.obj, 31)
expect_true('glm' %in% class(res$sim1$glm.obj))
expect_true('lm' %in% class(res$sim1$glm.obj))
expect_length(res$sim1$glm.summary.obj, 18)
expect_equal(class(res$sim1$glm.summary.obj), 'summary.glm')
expect_length(res$sim2, 2)
expect_length(res$sim2$glm.obj, 31)
expect_true('glm' %in% class(res$sim2$glm.obj))
expect_true('lm' %in% class(res$sim2$glm.obj))
expect_length(res$sim2$glm.summary.obj, 18)
expect_equal(class(res$sim2$glm.summary.obj), 'summary.glm')
expect_length(res$sim3, 2)
expect_length(res$sim3$glm.obj, 31)
expect_true('glm' %in% class(res$sim3$glm.obj))
expect_true('lm' %in% class(res$sim3$glm.obj))
expect_length(res$sim3$glm.summary.obj, 18)
expect_equal(class(res$sim3$glm.summary.obj), 'summary.glm')
})
context("ds.glmSummary::smk::poisson")
test_that("simple glmSummary, poisson, without newobj", {
glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="poisson", newobj="poisson.glmslma.obj")
expect_length(glmSLMA.res, 9)
expect_equal(glmSLMA.res$num.valid.studies, 3)
expect_length(glmSLMA.res$validity.check, 1)
expect_equal(glmSLMA.res$validity.check, "<poisson.glmslma.obj> appears valid in all sources")
res <- ds.glmSummary("poisson.glmslma.obj")
expect_length(res, 3)
expect_length(res$sim1, 2)
expect_length(res$sim1$glm.obj, 31)
expect_true('glm' %in% class(res$sim1$glm.obj))
expect_true('lm' %in% class(res$sim1$glm.obj))
expect_length(res$sim1$glm.summary.obj, 18)
expect_equal(class(res$sim1$glm.summary.obj), 'summary.glm')
expect_length(res$sim2, 2)
expect_length(res$sim2$glm.obj, 31)
expect_true('glm' %in% class(res$sim2$glm.obj))
expect_true('lm' %in% class(res$sim2$glm.obj))
expect_length(res$sim2$glm.summary.obj, 18)
expect_equal(class(res$sim2$glm.summary.obj), 'summary.glm')
expect_length(res$sim3, 2)
expect_length(res$sim3$glm.obj, 31)
expect_true('glm' %in% class(res$sim3$glm.obj))
expect_true('lm' %in% class(res$sim3$glm.obj))
expect_length(res$sim3$glm.summary.obj, 18)
expect_equal(class(res$sim3$glm.summary.obj), 'summary.glm')
})
test_that("simple glmSummary, poisson", {
glmSLMA.res <- ds.glmSLMA('D$LAB_TSC~D$LAB_TRIG', family="poisson", newobj="poisson.glmslma.obj")
expect_length(glmSLMA.res, 9)
expect_equal(glmSLMA.res$num.valid.studies, 3)
expect_length(glmSLMA.res$validity.check, 1)
expect_equal(glmSLMA.res$validity.check, "<poisson.glmslma.obj> appears valid in all sources")
res <- ds.glmSummary("poisson.glmslma.obj", newobj="poisson.glmsummary.obj")
expect_length(res, 3)
expect_length(res$sim1, 2)
expect_length(res$sim1$glm.obj, 31)
expect_true('glm' %in% class(res$sim1$glm.obj))
expect_true('lm' %in% class(res$sim1$glm.obj))
expect_length(res$sim1$glm.summary.obj, 18)
expect_equal(class(res$sim1$glm.summary.obj), 'summary.glm')
expect_length(res$sim2, 2)
expect_length(res$sim2$glm.obj, 31)
expect_true('glm' %in% class(res$sim2$glm.obj))
expect_true('lm' %in% class(res$sim2$glm.obj))
expect_length(res$sim2$glm.summary.obj, 18)
expect_equal(class(res$sim2$glm.summary.obj), 'summary.glm')
expect_length(res$sim3, 2)
expect_length(res$sim3$glm.obj, 31)
expect_true('glm' %in% class(res$sim3$glm.obj))
expect_true('lm' %in% class(res$sim3$glm.obj))
expect_length(res$sim3$glm.summary.obj, 18)
expect_equal(class(res$sim3$glm.summary.obj), 'summary.glm')
})
#
# Shutdown
#
context("ds.glmSummary::smk::shutdown")
test_that("shutdown", {
ds_expect_variables(c("D", "gaussian.glmslma.obj", "gaussian.glmsummary.obj", "poisson.glmslma.obj", "poisson.glmsummary.obj", "summary_glm.newobj"))
})
disconnect.studies.dataset.cnsim()
#
# Done
#
context("ds.glmSummary::smk::done")