tests/testthat/test-visit_structure.R

In secuTrialR: Handling of Data from the Clinical Data Management System 'secuTrial'

context("visit structure")

skip_on_cran()

test_that("secutrialdata object", expect_error(visit_structure(c(1:3))))



short_export_location <- system.file("extdata", "sT_exports", "BMD",
                                     "s_export_CSV-xls_BMD_short_en_utf8.zip",
                                     package = "secuTrialR")

long_export_location <- system.file("extdata", "sT_exports", "BMD",
                                    "s_export_CSV-xls_BMD_long_en_utf8.zip",
                                    package = "secuTrialR")

no_proj_setup_export_location <- system.file("extdata", "sT_exports", "exp_opt",
                                             "s_export_CSV-xls_CTU05_no_proj_setup.zip",
                                             package = "secuTrialR")

sT_export_short <- read_secuTrial_raw(data_dir = short_export_location)
sT_export_long <- read_secuTrial_raw(data_dir = long_export_location)
sT_no_proj_setup <- read_secuTrial_raw(data_dir = no_proj_setup_export_location)

test_that("failure", {
  expect_error(visit_structure(sT_export_short), regexp = NA)
  expect_error(visit_structure(sT_export_long), regexp = NA)
  expect_error(visit_structure(sT_no_proj_setup))
})


sdat <- read_secuTrial_raw(system.file("extdata", "sT_exports", "snames",
                                          "s_export_CSV-xls_CTU05_short_miss_en_utf8.zip",
                                          package = "secuTrialR"))
ldat <- read_secuTrial_raw(system.file("extdata", "sT_exports", "lnames",
                                          "s_export_CSV-xls_CTU05_long_miss_en_utf8.zip",
                                          package = "secuTrialR"))

test_that("failure on CTU05 data", {
  expect_error(visit_structure(sdat), regexp = NA)
  expect_error(visit_structure(ldat), regexp = NA)
})

# warning can be suppressed (it is expected)
suppressWarnings(
dat <- read_secuTrial(system.file("extdata", "sT_exports", "encodings",
                                  "s_export_CSV-xls_TES05_short_ref_en_iso8859-15.zip",
                                  package = "secuTrialR"))
)

test_that("no fail with TES05", {
          expect_error(visit_structure(dat), regexp = NA)
          expect_error(plot(visit_structure(dat)), regexp = NA)
})

vs <- visit_structure(dat)
test_that("correct dims", {
  expect_equal(dim(vs), c(3, 7))
  expect_true("formtablename" %in% names(vs))
})

test_that("all forms included", {
  expect_true(all(unique(as.character(dat$fs$formname)) %in% rownames(vs)))
  expect_true(all(rownames(vs) %in% unique(as.character(dat$fs$formname))))
})

test_that("all visits included", {
  expect_true(all(unique(as.character(dat$vp$mnpvislabel)) %in% names(vs)))
  expect_true(all(names(vs)[-(1:2)] %in% unique(as.character(dat$vp$mnpvislabel))))
})

test_that("colsums, rowsums correct", {
  cs <- colSums(vs[, -(1:2)], na.rm = TRUE)
  expect_equal(as.numeric(cs), c(1, 1, 1, 1, 2))
  rs <- rowSums(vs[, -(1:2)], na.rm = TRUE)
  expect_equal(as.numeric(rs), c(1, 4, 1))
})