tests/testthat/test-prep_combine_report_summaries.R

In dataquieR: Data Quality in Epidemiological Research

test_that("prep_combine_report_summaries works", {
  skip_if_offline(host = "dataquality.qihs.uni-greifswald.de")
  skip_on_cran()
  skip_if_not_installed("stringdist")
  study_data <- prep_get_data_frame("https://dataquality.qihs.uni-greifswald.de/extdata/fortests/study_data.RData", keep_types = TRUE)
  meta_data <- prep_get_data_frame("https://dataquality.qihs.uni-greifswald.de/extdata/fortests/meta_data.RData")
  sd0 <- study_data[, 1:6]
  sd0$v00012 <- study_data$v00012
  md0 <- subset(meta_data, VAR_NAMES %in% colnames(sd0))
  md0$PART_VAR <- NULL

  report <- dq_report2(sd0, md0,
                       resp_vars = c("v00000", "v00001", "v00002",
                                     "v00003", "v00004", "v00012"),
                       filter_indicator_functions =
                         c("^com_item_missingness$",
                           "^acc_varcomp$"),
                       filter_result_slots =
                         c("^SummaryTable$"),
                       cores = NULL,
                       dimensions = # for speed, omit Accuracy
                         c("Integrity",
                           "Completeness",
                           "Consistency",
                           "Accuracy"))

  report2 <- dq_report2(sd0, md0,
                       resp_vars = c("v00000", "v00001", "v00002",
                                     "v00003", "v00005", "v00012"),
                       filter_indicator_functions =
                         c("^com_item_missingness$",
                           "^acc_varcomp$"),
                       filter_result_slots =
                         c("^SummaryTable$"),
                       cores = NULL,
                       dimensions = # for speed, omit Accuracy
                         c("Integrity",
                           "Completeness",
                           "Consistency",
                           "Accuracy"))

  suppressWarnings({
    summary <- prep_extract_summary(report)
    summary2 <- prep_extract_summary(report2)
  })

  # ignore deprecation warning and known bug of a superfluous warning
  suppressWarnings(comb_sum <- prep_combine_report_summaries(summary, summary2))

  expect_snapshot(comb_sum)
})