tests/testthat/test-diagnostic.R

In hxia/plp-git-demo: Package for patient level prediction using data in the OMOP Common Data Model

# Copyright 2020 Observational Health Data Sciences and Informatics
#
# This file is part of PatientLevelPrediction
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

context("Diagnostic")

test_that("test code works when using plpData", {
  test <- diagnostic(plpData = plpData, cdmDatabaseName = 'madeup', 
                     riskWindowStart = c(1,10), 
                     startAnchor = rep('cohort start',2), 
                     riskWindowEnd = c(365, 730),
                     endAnchor = rep('cohort start',2),
                     outputFolder = file.path(saveLoc, 'diagnostics'))
  #check results are a list
  testthat::expect_equal(class(test), 'list')
                         
  # check list names
  testthat::expect_equal(sum(names(test)%in%c('distribution','proportion','characterization')), 3)
  
  # check the results are saved into the databaseName directory
  testthat::expect_equal(T, dir.exists(file.path(saveLoc, 'diagnostics')))
  
  #check tar
  
  
  testthat::expect_equal(unique(test$proportion$TAR)[1], paste0('cohort start', ' + ', 1, ' days - ',
                                                        'cohort start', ' + ', 365, ' days'))
  testthat::expect_equal(unique(test$proportion$TAR)[2], paste0('cohort start', ' + ', 10, ' days - ',
                                                        'cohort start', ' + ', 730, ' days'))
})