tests/testthat/test-reader.R
In atorus-research/metacore: A Centralized Metadata Object Focus on Clinical Trial Data Programming Workflows
# Read in doc to be used for testing
define <- read_xml("define-2021.xml")
xml_ns_strip(define)
spec <- read_all_sheets(metacore_example("p21_mock.xlsx"))
#### Fist checking some reading in
test_that("Check spec_type", {
expect_equal(spec_type(metacore_example("p21_mock.xlsx")), "by_type")
expect_equal(spec_type(metacore_example("mock_spec.xlsx")), "by_type")
# Check it errors when format is not acceptable
expect_error(spec_type("example_spec.xlsx"))
})
#### Check reads are consistent between formats
test_that("Test ds_spec readers", {
# Create a reference spec to match to
ref_ds_spec <-
tribble(~dataset, ~structure, ~label,
"DM" ,"One record per subject", "Demographics",
"EX" ,"One record per constant dosing interval per subject", "Exposure",
"AE" ,"One record per adverse event per subject", "Adverse Events",
"SUPPAE" ,"One record per IDVAR, IDVARVAL, and QNAM value per subject", "Supplemental Qualifiers for AE",
"SUPPDM" ,"One record per IDVAR, IDVARVAL, and QNAM value per subject", "Supplemental Qualifiers for DM")
# Read from define
def_ds_spec <- xml_to_ds_spec(define)
# Read from spec
spec_ds_spec <- spec_type_to_ds_spec(spec)
spec_ds_spec2 <- spec_type_to_ds_spec(spec, sheet = "D")
# Test against reference
expect_equal(def_ds_spec, ref_ds_spec)
expect_equal(spec_ds_spec, arrange(ref_ds_spec, dataset))
expect_equal(spec_ds_spec2, arrange(ref_ds_spec, dataset))
})
test_that("Test ds_vars readers", {
# Create a reference ds_vars
ref_ds_vars <- tibble::tribble(
~dataset, ~variable, ~key_seq, ~order, ~keep, ~core, ~supp_flag,
"AE", "AEACN", NA, 21L, FALSE, NA_character_, NA,
"AE", "AEBDSYCD", NA, 16L, FALSE, NA_character_, NA,
"AE", "AEBODSYS", NA, 15L, FALSE, NA_character_, NA,
"AE", "AEDECOD", NA, 9L, FALSE, NA_character_, NA,
"AE", "AEDTC", NA, 32L, FALSE, NA_character_, NA,
"AE", "AEDY", NA, 35L, FALSE, NA_character_, NA,
"AE", "AEENDTC", NA, 34L, FALSE, NA_character_, NA,
"AE", "AEENDY", NA, 37L, FALSE, NA_character_, NA,
"AE", "AEHLGT", NA, 13L, FALSE, NA_character_, NA,
"AE", "AEHLGTCD", NA, 14L, FALSE, NA_character_, NA,
"AE", "AEHLT", NA, 11L, FALSE, NA_character_, NA,
"AE", "AEHLTCD", NA, 12L, FALSE, NA_character_, NA,
"AE", "AELLT", NA, 7L, FALSE, NA_character_, NA,
"AE", "AELLTCD", NA, 8L, FALSE, NA_character_, NA,
"AE", "AEOUT", NA, 23L, FALSE, NA_character_, NA,
"AE", "AEPTCD", NA, 10L, FALSE, NA_character_, NA,
"AE", "AEREL", NA, 22L, FALSE, NA_character_, NA,
"AE", "AESCAN", NA, 24L, FALSE, NA_character_, NA,
"AE", "AESCONG", NA, 25L, FALSE, NA_character_, NA,
"AE", "AESDISAB", NA, 26L, FALSE, NA_character_, NA,
"AE", "AESDTH", NA, 27L, FALSE, NA_character_, NA,
"AE", "AESEQ", 5L, 4L, TRUE, NA_character_, NA,
"AE", "AESER", NA, 20L, FALSE, NA_character_, NA,
"AE", "AESEV", NA, 19L, FALSE, NA_character_, NA,
"AE", "AESHOSP", NA, 28L, FALSE, NA_character_, NA,
"AE", "AESLIFE", NA, 29L, FALSE, NA_character_, NA,
"AE", "AESOC", NA, 17L, FALSE, NA_character_, NA,
"AE", "AESOCCD", NA, 18L, FALSE, NA_character_, NA,
"AE", "AESOD", NA, 30L, FALSE, NA_character_, NA,
"AE", "AESPID", NA, 5L, FALSE, NA_character_, NA,
"AE", "AESTDTC", 4L, 33L, FALSE, NA_character_, NA,
"AE", "AESTDY", NA, 36L, FALSE, NA_character_, NA,
"AE", "AETERM", 3L, 6L, TRUE, NA_character_, NA,
"AE", "DOMAIN", NA, 2L, TRUE, NA_character_, NA,
"AE", "EPOCH", NA, 31L, FALSE, NA_character_, NA,
"AE", "STUDYID", 1L, 1L, TRUE, NA_character_, NA,
"AE", "USUBJID", 2L, 3L, TRUE, NA_character_, NA,
"DM", "ACTARM", NA, 22L, TRUE, NA_character_, NA,
"DM", "ACTARMCD", NA, 21L, TRUE, NA_character_, NA,
"DM", "AGE", NA, 14L, FALSE, NA_character_, NA,
"DM", "AGEU", NA, 15L, FALSE, NA_character_, NA,
"DM", "ARM", NA, 20L, TRUE, NA_character_, NA,
"DM", "ARMCD", NA, 19L, TRUE, NA_character_, NA,
"DM", "COUNTRY", NA, 23L, TRUE, NA_character_, NA,
"DM", "DMDTC", NA, 24L, FALSE, NA_character_, NA,
"DM", "DMDY", NA, 25L, FALSE, NA_character_, NA,
"DM", "DOMAIN", NA, 2L, TRUE, NA_character_, NA,
"DM", "DTHDTC", NA, 11L, FALSE, NA_character_, NA,
"DM", "DTHFL", NA, 12L, FALSE, NA_character_, NA,
"DM", "ETHNIC", NA, 18L, FALSE, NA_character_, NA,
"DM", "RACE", NA, 17L, FALSE, NA_character_, NA,
"DM", "RFENDTC", NA, 6L, FALSE, NA_character_, NA,
"DM", "RFICDTC", NA, 9L, FALSE, NA_character_, NA,
"DM", "RFPENDTC", NA, 10L, FALSE, NA_character_, NA,
"DM", "RFSTDTC", NA, 5L, FALSE, NA_character_, NA,
"DM", "RFXENDTC", NA, 8L, FALSE, NA_character_, NA,
"DM", "RFXSTDTC", NA, 7L, FALSE, NA_character_, NA,
"DM", "SEX", NA, 16L, TRUE, NA_character_, NA,
"DM", "SITEID", NA, 13L, TRUE, NA_character_, NA,
"DM", "STUDYID", 1L, 1L, TRUE, NA_character_, NA,
"DM", "SUBJID", NA, 4L, TRUE, NA_character_, NA,
"DM", "USUBJID", 2L, 3L, TRUE, NA_character_, NA,
"EX", "DOMAIN", NA, 2L, TRUE, NA_character_, NA,
"EX", "EPOCH", NA, 14L, FALSE, NA_character_, NA,
"EX", "EXDOSE", NA, 6L, FALSE, NA_character_, NA,
"EX", "EXDOSFRM", NA, 8L, FALSE, NA_character_, NA,
"EX", "EXDOSFRQ", NA, 9L, FALSE, NA_character_, NA,
"EX", "EXDOSU", NA, 7L, FALSE, NA_character_, NA,
"EX", "EXENDTC", NA, 16L, FALSE, NA_character_, NA,
"EX", "EXENDY", NA, 18L, FALSE, NA_character_, NA,
"EX", "EXROUTE", NA, 10L, FALSE, NA_character_, NA,
"EX", "EXSEQ", NA, 4L, TRUE, NA_character_, NA,
"EX", "EXSTDTC", 4L, 15L, FALSE, NA_character_, NA,
"EX", "EXSTDY", NA, 17L, FALSE, NA_character_, NA,
"EX", "EXTRT", 3L, 5L, TRUE, NA_character_, NA,
"EX", "STUDYID", 1L, 1L, TRUE, NA_character_, NA,
"EX", "USUBJID", 2L, 3L, TRUE, NA_character_, NA,
"EX", "VISIT", NA, 12L, FALSE, NA_character_, NA,
"EX", "VISITDY", NA, 13L, FALSE, NA_character_, NA,
"EX", "VISITNUM", NA, 11L, FALSE, NA_character_, NA,
"SUPPAE", "IDVAR", 4L, 4L, FALSE, NA_character_, NA,
"SUPPAE", "IDVARVAL", 5L, 5L, FALSE, NA_character_, NA,
"SUPPAE", "QEVAL", NA, 10L, FALSE, NA_character_, NA,
"SUPPAE", "QLABEL", NA, 7L, TRUE, NA_character_, NA,
"SUPPAE", "QNAM", 6L, 6L, TRUE, NA_character_, NA,
"SUPPAE", "QORIG", NA, 9L, TRUE, NA_character_, NA,
"SUPPAE", "QVAL", NA, 8L, TRUE, NA_character_, NA,
"SUPPAE", "RDOMAIN", 2L, 2L, TRUE, NA_character_, NA,
"SUPPAE", "STUDYID", 1L, 1L, TRUE, NA_character_, NA,
"SUPPAE", "USUBJID", 3L, 3L, TRUE, NA_character_, NA,
"SUPPDM", "IDVAR", 4L, 4L, FALSE, NA_character_, NA,
"SUPPDM", "IDVARVAL", 5L, 5L, FALSE, NA_character_, NA,
"SUPPDM", "QEVAL", NA, 10L, FALSE, NA_character_, NA,
"SUPPDM", "QLABEL", NA, 7L, TRUE, NA_character_, NA,
"SUPPDM", "QNAM", 6L, 6L, TRUE, NA_character_, NA,
"SUPPDM", "QORIG", NA, 9L, TRUE, NA_character_, NA,
"SUPPDM", "QVAL", NA, 8L, TRUE, NA_character_, NA,
"SUPPDM", "RDOMAIN", 2L, 2L, TRUE, NA_character_, NA,
"SUPPDM", "STUDYID", 1L, 1L, TRUE, NA_character_, NA,
"SUPPDM", "USUBJID", 3L, 3L, TRUE, NA_character_, NA,
)
# Read from define
def_ds_vars <- xml_to_ds_vars(define) %>%
arrange(dataset, variable)
# Read from spec
spec_ds_vars <- spec_type_to_ds_vars(spec) %>%
arrange(dataset, variable) %>%
select(dataset, variable, key_seq, order, keep, core, supp_flag)
# Tests
expect_equal(def_ds_vars, ref_ds_vars)
expect_equal(spec_ds_vars, ref_ds_vars)
})
test_that("Test var_spec readers", {
ref_var_spec <-
tibble::tribble(
~variable, ~type, ~length, ~label, ~format, ~common,
"ACTARM", "text", 20L, "Description of Actual Arm", NA, NA,
"ACTARMCD", "text", 8L, "Actual Arm Code", NA, NA,
"AEACN", "text", 30L, "Action Taken with Study Treatment", NA, NA,
"AEBDSYCD", "integer", 8L, "Body System or Organ Class Code", NA, NA,
"AEBODSYS", "text", 67L, "Body System or Organ Class", NA, NA,
"AEDECOD", "text", 200L, "Dictionary-Derived Term", NA, NA,
"AEDTC", "date", 10L, "Date/Time of Collection", NA, NA,
"AEDY", "integer", 8L, "Study Day of Visit/Collection/Exam", NA, NA,
"AEENDTC", "date", 10L, "End Date/Time of Adverse Event", NA, NA,
"AEENDY", "integer", 8L, "Study Day of End of Adverse Event", NA, NA,
"AEHLGT", "text", 100L, "High Level Group Term", NA, NA,
"AEHLGTCD", "integer", 8L, "High Level Group Term Code", NA, NA,
"AEHLT", "text", 100L, "High Level Term", NA, NA,
"AEHLTCD", "integer", 8L, "High Level Term Code", NA, NA,
"AELLT", "text", 100L, "Lowest Level Term", NA, NA,
"AELLTCD", "integer", 8L, "Lowest Level Term Code", NA, NA,
"AEOUT", "text", 200L, "Outcome of Adverse Event", NA, NA,
"AEPTCD", "integer", 8L, "Preferred Term Code", NA, NA,
"AEREL", "text", 8L, "Causality", NA, NA,
"AESCAN", "text", 1L, "Involves Cancer", NA, NA,
"AESCONG", "text", 1L, "Congenital Anomaly or Birth Defect", NA, NA,
"AESDISAB", "text", 1L, "Persist or Signif Disability/Incapacity", NA, NA,
"AESDTH", "text", 1L, "Results in Death", NA, NA,
"AESEQ", "integer", 8L, "Sequence Number", NA, NA,
"AESER", "text", 1L, "Serious Event", NA, NA,
"AESEV", "text", 8L, "Severity/Intensity", NA, NA,
"AESHOSP", "text", 1L, "Requires or Prolongs Hospitalization", NA, NA,
"AESLIFE", "text", 1L, "Is Life Threatening", NA, NA,
"AESOC", "text", 100L, "Primary System Organ Class", NA, NA,
"AESOCCD", "integer", 8L, "Primary System Organ Class Code", NA, NA,
"AESOD", "text", 1L, "Occurred with Overdose", NA, NA,
"AESPID", "text", 3L, "Sponsor-Defined Identifier", NA, NA,
"AESTDTC", "date", 10L, "Start Date/Time of Adverse Event", NA, NA,
"AESTDY", "integer", 8L, "Study Day of Start of Adverse Event", NA, NA,
"AETERM", "text", 200L, "Reported Term for the Adverse Event", NA, NA,
"AGE", "integer", 8L, "Age", NA, NA,
"AGEU", "text", 6L, "Age Units", NA, NA,
"ARM", "text", 20L, "Description of Planned Arm", NA, NA,
"ARMCD", "text", 8L, "Planned Arm Code", NA, NA,
"COUNTRY", "text", 3L, "Country", NA, NA,
"DMDTC", "date", 10L, "Date/Time of Collection", NA, NA,
"DMDY", "integer", 8L, "Study Day of Collection", NA, NA,
"DOMAIN", "text", 2L, "Domain Abbreviation", NA, NA,
"DTHDTC", "datetime", 20L, "Date/Time of Death", NA, NA,
"DTHFL", "text", 1L, "Subject Death Flag", NA, NA,
"EPOCH", "text", 9L, "Epoch", NA, NA,
"ETHNIC", "text", 25L, "Ethnicity", NA, NA,
"EXDOSE", "integer", 8L, "Dose", NA, NA,
"EXDOSFRM", "text", 5L, "Dose Form", NA, NA,
"EXDOSFRQ", "text", 2L, "Dosing Frequency per Interval", NA, NA,
"EXDOSU", "text", 2L, "Dose Units", NA, NA,
"EXENDTC", "date", 10L, "End Date/Time of Treatment", NA, NA,
"EXENDY", "integer", 8L, "Study Day of End of Treatment", NA, NA,
"EXROUTE", "text", 11L, "Route of Administration", NA, NA,
"EXSEQ", "integer", 8L, "Sequence Number", NA, NA,
"EXSTDTC", "date", 10L, "Start Date/Time of Treatment", NA, NA,
"EXSTDY", "integer", 8L, "Study Day of Start of Treatment", NA, NA,
"EXTRT", "text", 10L, "Name of Treatment", NA, NA,
"IDVAR", "text", 8L, "Identifying Variable", NA, NA,
"IDVARVAL", "text", 200L, "Identifying Variable Value", NA, NA,
"QEVAL", "text", 200L, "Evaluator", NA, NA,
"QLABEL", "text", 40L, "Qualifier Variable Label", NA, NA,
"QNAM", "text", 8L, "Qualifier Variable Name", NA, NA,
"QORIG", "text", 200L, "Origin", NA, NA,
"QVAL", "text", 200L, "Data Value", NA, NA,
"RACE", "text", 78L, "Race", NA, NA,
"RDOMAIN", "text", 2L, "Related Domain Abbreviation", NA, NA,
"RFENDTC", "date", 10L, "Subject Reference End Date/Time", NA, NA,
"RFICDTC", "datetime", 20L, "Date/Time of Informed Consent", NA, NA,
"RFPENDTC", "datetime", 20L, "Date/Time of End of Participation", NA, NA,
"RFSTDTC", "date", 10L, "Subject Reference Start Date/Time", NA, NA,
"RFXENDTC", "datetime", 20L, "Date/Time of Last Study Treatment", NA, NA,
"RFXSTDTC", "datetime", 20L, "Date/Time of First Study Treatment", NA, NA,
"SEX", "text", 1L, "Sex", NA, NA,
"SITEID", "text", 3L, "Study Site Identifier", NA, NA,
"STUDYID", "text", 12L, "Study Identifier", NA, NA,
"SUBJID", "text", 4L, "Subject Identifier for the Study", NA, NA,
"USUBJID", "text", 11L, "Unique Subject Identifier", NA, NA,
"VISIT", "text", 19L, "Visit Name", NA, NA,
"VISITDY", "integer", 8L, "Planned Study Day of Visit", NA, NA,
"VISITNUM", "float", 8L, "Visit Number", "8.1", NA
)
# Read from define
def_var_spec <- xml_to_var_spec(define) %>%
arrange(variable)
# Read from spec
spec_var_spec <- spec_type_to_var_spec(spec) %>%
arrange(variable) %>%
select(variable, type, length, label, format)
spec2 <- spec
spec2$Variables |>
select(-Dataset)
no_ds <- spec_type_to_var_spec(spec2) |>
arrange(variable) %>%
select(variable, type, length, label, format)
expect_equal(no_ds, spec_var_spec)
# Tests
expect_equal(def_var_spec, ref_var_spec)
# remove common as it is derived when reading in specs but left alone from defines
expect_equal(spec_var_spec,
ref_var_spec %>%
select(-common))
})
test_that("values_spec reader tests", {
ref_value_spec <- tibble::tribble(
~dataset, ~variable, ~type, ~origin, ~code_id, ~sig_dig, ~where, ~derivation_id,
"AE", "AEACN", "text", "Derived", NA, NA, NA, "MT.AE.AEACN",
"AE", "AEBDSYCD", "integer", "Assigned", NA, NA, NA, NA,
"AE", "AEBODSYS", "text", "Assigned", "CL.AEDICT", NA, NA, NA,
"AE", "AEDECOD", "text", "Assigned", "CL.AEDICT", NA, NA, NA,
"AE", "AEDTC", "date", "Derived", NA, NA, NA, "MT.AE.AEDTC",
"AE", "AEDY", "integer", "Derived", NA, NA, NA, "MT.COMPMETHOD.STUDY_DAY",
"AE", "AEENDTC", "date", "CRF", NA, NA, NA, NA,
"AE", "AEENDY", "integer", "Derived", NA, NA, NA, "MT.COMPMETHOD.STUDY_DAY",
"AE", "AEHLGT", "text", "Assigned", "CL.AEDICT", NA, NA, NA,
"AE", "AEHLGTCD", "integer", "Assigned", NA, NA, NA, NA,
"AE", "AEHLT", "text", "Assigned", "CL.AEDICT", NA, NA, NA,
"AE", "AEHLTCD", "integer", "Assigned", NA, NA, NA, NA,
"AE", "AELLT", "text", "Assigned", "CL.AEDICT", NA, NA, NA,
"AE", "AELLTCD", "integer", "Assigned", NA, NA, NA, NA,
"AE", "AEOUT", "text", "CRF", "CL.OUT", NA, NA, NA,
"AE", "AEPTCD", "integer", "Assigned", NA, NA, NA, NA,
"AE", "AEREL", "text", "CRF", "CL.AECAUS", NA, NA, NA,
"AE", "AESCAN", "text", "CRF", "CL.YN", NA, NA, NA,
"AE", "AESCONG", "text", "CRF", "CL.YN", NA, NA, NA,
"AE", "AESDISAB", "text", "CRF", "CL.YN", NA, NA, NA,
"AE", "AESDTH", "text", "CRF", "CL.YN", NA, NA, NA,
"AE", "AESEQ", "integer", "Derived", NA, NA, NA, "MT.AE.AESEQ",
"AE", "AESER", "text", "CRF", "CL.YN", NA, NA, NA,
"AE", "AESEV", "text", "CRF", "CL.SEV", NA, NA, NA,
"AE", "AESHOSP", "text", "CRF", "CL.YN", NA, NA, NA,
"AE", "AESLIFE", "text", "CRF", "CL.YN", NA, NA, NA,
"AE", "AESOC", "text", "Assigned", "CL.AEDICT", NA, NA, NA,
"AE", "AESOCCD", "integer", "Assigned", NA, NA, NA, NA,
"AE", "AESOD", "text", "CRF", "CL.YN", NA, NA, NA,
"AE", "AESPID", "text", "CRF", NA, NA, NA, NA,
"AE", "AESTDTC", "date", "CRF", NA, NA, NA, NA,
"AE", "AESTDY", "integer", "Derived", NA, NA, NA, "MT.COMPMETHOD.STUDY_DAY",
"AE", "AETERM", "text", "CRF", NA, NA, NA, NA,
"AE", "DOMAIN", "text", "Assigned", NA, NA, NA, NA,
"AE", "EPOCH", "text", "Derived", "CL.EPOCH", NA, NA, "MT.AE.EPOCH",
"AE", "STUDYID", "text", "CRF", NA, NA, NA, NA,
"AE", "USUBJID", "text", "Derived", NA, NA, NA, "MT.AE.USUBJID",
"DM", "ACTARM", "text", "Derived", "CL.ARM", NA, NA, "MT.DM.ACTARM",
"DM", "ACTARMCD", "text", "Derived", "CL.ARMCD", NA, NA, "MT.DM.ACTARMCD",
"DM", "AGE", "integer", "Derived", NA, NA, NA, "MT.DM.AGE",
"DM", "AGEU", "text", "Assigned", "CL.AGEU", NA, NA, "COM.DM.AGEU",
"DM", "ARM", "text", "Assigned", "CL.ARM", NA, NA, "COM.DM.ARM",
"DM", "ARMCD", "text", "Assigned", "CL.ARMCD", NA, NA, "COM.DM.ARMCD",
"DM", "COUNTRY", "text", "Derived", "CL.COUNTRY", NA, NA, "MT.DM.COUNTRY",
"DM", "DMDTC", "date", "CRF", NA, NA, NA, NA,
"DM", "DMDY", "integer", "Derived", NA, NA, NA, "MT.COMPMETHOD.STUDY_DAY",
"DM", "DOMAIN", "text", "Assigned", NA, NA, NA, NA,
"DM", "DTHDTC", "datetime", "Derived", NA, NA, NA, "MT.DM.DTHDTC",
"DM", "DTHFL", "text", "Derived", "CL.Y_BLANK", NA, NA, "MT.DM.DTHFL",
"DM", "ETHNIC", "text", "Derived", "CL.ETHNIC", NA, NA, "MT.DM.ETHNIC",
"DM", "RACE", "text", "CRF", "CL.RACE", NA, NA, NA,
"DM", "RFENDTC", "date", "Derived", NA, NA, NA, "MT.DM.RFENDTC",
"DM", "RFICDTC", "datetime", "Derived", NA, NA, NA, "MT.DM.RFICDTC",
"DM", "RFPENDTC", "datetime", "Derived", NA, NA, NA, "MT.DM.RFPENDTC",
"DM", "RFSTDTC", "date", "Derived", NA, NA, NA, "MT.DM.RFSTDTC",
"DM", "RFXENDTC", "datetime", "Derived", NA, NA, NA, "MT.DM.RFXENDTC",
"DM", "RFXSTDTC", "datetime", "Derived", NA, NA, NA, "MT.DM.RFXSTDTC",
"DM", "SEX", "text", "CRF", "CL.SEX", NA, NA, NA,
"DM", "SITEID", "text", "Assigned", NA, NA, NA, NA,
"DM", "STUDYID", "text", "CRF", NA, NA, NA, NA,
"DM", "SUBJID", "text", "CRF", NA, NA, NA, NA,
"DM", "USUBJID", "text", "Derived", NA, NA, NA, "MT.DM.USUBJID",
"EX", "DOMAIN", "text", "Assigned", NA, NA, NA, NA,
"EX", "EPOCH", "text", "Derived", "CL.EPOCH", NA, NA, "MT.EX.EPOCH",
"EX", "EXDOSE", "integer", "eDT", NA, NA, NA, NA,
"EX", "EXDOSFRM", "text", "eDT", "CL.EXDOSFRM", NA, NA, NA,
"EX", "EXDOSFRQ", "text", "eDT", "CL.EXFREQ", NA, NA, NA,
"EX", "EXDOSU", "text", "eDT", "CL.EXDOSEU", NA, NA, NA,
"EX", "EXENDTC", "date", "CRF", NA, NA, NA, NA,
"EX", "EXENDY", "integer", "Derived", NA, NA, NA, "MT.COMPMETHOD.STUDY_DAY",
"EX", "EXROUTE", "text", "eDT", "CL.EXROUTE", NA, NA, NA,
"EX", "EXSEQ", "integer", "Derived", NA, NA, NA, "MT.EX.EXSEQ",
"EX", "EXSTDTC", "date", "CRF", NA, NA, NA, NA,
"EX", "EXSTDY", "integer", "Derived", NA, NA, NA, "MT.COMPMETHOD.STUDY_DAY",
"EX", "EXTRT", "text", "eDT", "CL.EXTRT", NA, NA, NA,
"EX", "STUDYID", "text", "CRF", NA, NA, NA, NA,
"EX", "USUBJID", "text", "Derived", NA, NA, NA, "MT.EX.USUBJID",
"EX", "VISIT", "text", "CRF", "CL.VISIT", NA, NA, NA,
"EX", "VISITDY", "integer", "Derived", NA, NA, NA, "MT.EX.VISITDY",
"EX", "VISITNUM", "float", "CRF", "CL.VISITNUM", 1L, NA, NA,
"SUPPAE", "IDVAR", "text", "Assigned", NA, NA, NA, "COM.SUPPAE.IDVAR",
"SUPPAE", "IDVARVAL", "text", "Derived", NA, NA, NA, "MT.SUPPAE.IDVARVAL",
"SUPPAE", "QEVAL", "text", "Assigned", "CL.QEVAL", NA, NA, NA,
"SUPPAE", "QLABEL", "text", "Assigned", NA, NA, NA, NA,
"SUPPAE", "QNAM", "text", "Assigned", "CL.SUPPAE.QNAM", NA, NA, NA,
"SUPPAE", "QORIG", "text", "Assigned", NA, NA, NA, NA,
"SUPPAE", "QVAL", "text", "Derived", "CL.YN", NA, "QNAM == 'TRTEMFL'", "MT.SUPPAE.QNAM.TRTEMFL",
"SUPPAE", "RDOMAIN", "text", "Assigned", NA, NA, NA, "COM.SUPPAE.RDOMAIN",
"SUPPAE", "STUDYID", "text", "CRF", NA, NA, NA, NA,
"SUPPAE", "USUBJID", "text", "Derived", NA, NA, NA, "MT.SUPPAE.USUBJID",
"SUPPDM", "IDVAR", "text", "Assigned", NA, NA, NA, "COM.SUPPDM.IDVAR",
"SUPPDM", "IDVARVAL", "text", "Assigned", NA, NA, NA, "COM.SUPPDM.IDVARVAL",
"SUPPDM", "QEVAL", "text", "Assigned", "CL.QEVAL", NA, NA, NA,
"SUPPDM", "QLABEL", "text", "Assigned", NA, NA, NA, NA,
"SUPPDM", "QNAM", "text", "Assigned", "CL.SUPPDM.QNAM", NA, NA, NA,
"SUPPDM", "QORIG", "text", "Assigned", NA, NA, NA, NA,
"SUPPDM", "QVAL", "text", "Derived", "CL.Y_BLANK", NA, "QNAM == 'COMPLT16'", "MT.SUPPDM.QNAM.COMPLT16",
"SUPPDM", "QVAL", "text", "Derived", "CL.Y_BLANK", NA, "QNAM == 'COMPLT24'", "MT.SUPPDM.QNAM.COMPLT24",
"SUPPDM", "QVAL", "text", "Derived", "CL.Y_BLANK", NA, "QNAM == 'COMPLT8'", "MT.SUPPDM.QNAM.COMPLT8",
"SUPPDM", "QVAL", "text", "Derived", "CL.Y_BLANK", NA, "QNAM == 'EFFICACY'", "MT.SUPPDM.QNAM.EFFICACY",
"SUPPDM", "QVAL", "text", "Derived", "CL.Y_BLANK", NA, "QNAM == 'SAFETY'", "MT.SUPPDM.QNAM.SAFETY",
"SUPPDM", "QVAL", "text", "Derived", "CL.Y_BLANK", NA, "QNAM == 'ITT'", "MT.SUPPDM.QNAM.ITT",
"SUPPDM", "RDOMAIN", "text", "Assigned", NA, NA, NA, "COM.SUPPDM.RDOMAIN",
"SUPPDM", "STUDYID", "text", "CRF", NA, NA, NA, NA,
"SUPPDM", "USUBJID", "text", "Derived", NA, NA, NA, "MT.SUPPDM.USUBJID"
)
# Read from define
def_value_spec <- xml_to_value_spec(define) %>%
arrange(dataset, variable) %>%
select(dataset, variable, type, origin, code_id, sig_dig, where, derivation_id )
# Read from spec
comments <- spec$Comments$ID
spec_value_spec <- spec_type_to_value_spec(spec) %>%
arrange(dataset, variable) %>%
select(dataset, variable, type, origin, code_id, sig_dig, where, derivation_id) %>%
#Fix naming as it is slightly different, but matches within metacore
mutate(code_id = if_else(!is.na(code_id), paste0("CL.", code_id), code_id, NA_character_),
derivation_id = case_when(
origin == "Derived" ~ paste0("MT.", derivation_id),
origin == "Assigned" & derivation_id %in% comments ~ paste0("COM.", derivation_id),
TRUE ~ NA_character_),
where = str_replace(where, "EQ", "=="),
where = str_split(where, "\\s(?=(\\w*$))") %>%
map(~paste0(.[1], " '", .[2])),
where = if_else(where == "NA 'NA", NA_character_, paste0(where, "'")))
# Tests
expect_equal(def_value_spec, ref_value_spec)
expect_equal(spec_value_spec, ref_value_spec)
})
test_that("derivation reader tests", {
# Create reference derivation tibble
ref_derivation <- tibble::tribble(
~derivation_id, ~derivation,
"COM.DM.AGEU", "AGEU='YEARS'",
"COM.DM.ARM", "According to randomization list",
"COM.DM.ARMCD", "According to randomization list",
"COM.SUPPAE.IDVAR", "IDVAR='AESEQ'",
"COM.SUPPAE.RDOMAIN", "RDOMAIN='AE'",
"COM.SUPPDM.IDVAR", "IDVAR=' '",
"COM.SUPPDM.IDVARVAL", "IDVARVAL= ' '",
"COM.SUPPDM.RDOMAIN", "RDOMAIN='AE'",
"MT.AE.AEACN" , "AEACN=Null (data on action taken concerning study treatment was not collected)" ,
"MT.AE.AEDTC" , "Date of final visit (SV)" ,
"MT.AE.AESEQ" , "Sequential number identifying records within each USUBJID" ,
"MT.AE.EPOCH" , "Use AESTDTC to determine from the SDTM SE what EPOCH this record falls under.\nIf SE.SESTDTC <= AESTDTC < SE.SEENDTC, then use that EPOCH.",
"MT.AE.USUBJID" ,"Concatenation of STUDYID, DM.SITEID and DM.SUBJID" ,
"MT.COMPMETHOD.STUDY_DAY" ,"(date portion of --DTC) minus (date portion of RFSTDTC) , add 1 if -- DTC >= RFSTDC" ,
"MT.DM.ACTARM" ,"Derived from EX" ,
"MT.DM.ACTARMCD" ,"Derived from EX" ,
"MT.DM.AGE" ,"Subject's Age at start of study drug (RFSTDTC)." ,
"MT.DM.COUNTRY" ,"Derived from site information" ,
"MT.DM.DTHDTC" ,"If DS record exists with DSDECOD='DEATH' then DTHDTC=AEENDTC." ,
"MT.DM.DTHFL" ,"If DS record exists with DSDECOD='DEATH' then DEATHFL=Y." ,
"MT.DM.ETHNIC" ,"Derived from Origin entered on CRF: ETHINC='HISPANIC OR LATINO' if Origin='Hispanic'. Otherwise ETHNIC='NOT HISPANIC OR LATINO'" ,
"MT.DM.RFENDTC" ,"Date/time of last study drug treatment derived from EX" ,
"MT.DM.RFICDTC" ,"Date of informed consent was not entered in database (see annotated CRF)" ,
"MT.DM.RFPENDTC" ,"DSSTDTC of last disposition event" ,
"MT.DM.RFSTDTC" ,"Date/time of first study drug treatment derived from EX" ,
"MT.DM.RFXENDTC" ,"RFXENDTC=RFENDTC" ,
"MT.DM.RFXSTDTC" ,"RFXSTDTC=RFSTDTC" ,
"MT.DM.USUBJID" ,"Concatenation of STUDYID, DM.SITEID and DM.SUBJID" ,
"MT.EX.EPOCH" ,"Use EXDTC to determine from the SDTM SE what EPOCH this record falls under.\nIf SE.SESTDTC <= EXDTC < SE.SEENDTC, then use that EPOCH.",
"MT.EX.EXSEQ" ,"Sequential number identifying records within each USUBJID" ,
"MT.EX.USUBJID" ,"Concatenation of STUDYID, DM.SITEID and DM.SUBJID" ,
"MT.EX.VISITDY" ,"TV.VISITDY" ,
"MT.SUPPAE.IDVARVAL" ,"Value of AESEQ of corresponding parent record" ,
"MT.SUPPAE.QNAM.TRTEMFL" ,"see SAP" ,
"MT.SUPPAE.QVAL" ,"see value level metadata" ,
"MT.SUPPAE.USUBJID" ,"Concatenation of STUDYID, DM.SITEID and DM.SUBJID" ,
"MT.SUPPDM.QNAM.COMPLT16" ,"see SAP" ,
"MT.SUPPDM.QNAM.COMPLT24" ,"see SAP" ,
"MT.SUPPDM.QNAM.COMPLT8" ,"see SAP" ,
"MT.SUPPDM.QNAM.EFFICACY" ,"see SAP" ,
"MT.SUPPDM.QNAM.ITT" ,"see SAP" ,
"MT.SUPPDM.QNAM.SAFETY" ,"see SAP" ,
"MT.SUPPDM.QVAL" ,"see value level metadata" ,
"MT.SUPPDM.USUBJID" ,"Concatenation of STUDYID, DM.SITEID and DM.SUBJID" ,
)
# Read from define
def_derivation <- xml_to_derivations(define) %>%
arrange(derivation_id) %>%
mutate(derivation = str_replace_all(derivation, '\\"', "\\'"))
# Read from spec
ref_deriv <- spec$Methods %>%
select(derivation_id = ID,
derivation = Description) %>%
mutate(derivation_id = paste0("MT.", derivation_id))
ref_deriv <- spec$Variables %>%
filter(Origin %in% c("Assigned")) %>%
left_join(select(spec$Comments, ID, Description), by = c("Comment" = "ID")) %>%
mutate(derivation_id = paste0("MT.", Dataset, ".", Variable),
derivation = Description) %>%
select(starts_with("derivation")) %>%
bind_rows(ref_deriv, .) %>%
arrange(derivation_id) %>%
distinct()
spec_derivation <- spec_type_to_derivations(spec) %>%
arrange(derivation_id) %>%
mutate(derivation_id = paste0("MT.", derivation_id))
# Tests
expect_equal(def_derivation, ref_derivation)
expect_equal(spec_derivation, ref_deriv)
})
test_that("codelist reader tests", {
# Create reference derivation tibble
ref_codelist <- tibble::tribble(
~code_id, ~name, ~codes, ~type,
"CL.AECAUS", "AECAUS", tibble(code = c("NONE", "POSSIBLE", "PROBABLE", "REMOTE"), decode = c("NONE", "POSSIBLE", "PROBABLE", "REMOTE")), "code_decode",
"CL.AEDICT", "ADVERSE EVENT DICTIONARY", tibble(dictionary = "MEDDRA", version = "8.0"), "external_library",
"CL.AGEU", "AGEU", tibble(code = "YEARS", decode = "YEARS"), "code_decode",
"CL.ARM", "ARM", tibble(code = c("Screen Failure", "Placebo", "Xanomeline Low Dose", "Xanomeline High Dose"), decode = c("Screen Failure", "Placebo", "Xanomeline Low Dose", "Xanomeline High Dose")), "code_decode",
"CL.ARMCD", "ARMCD", tibble(code = c("Scrnfail", "Pbo", "Xan_Lo", "Xan_Hi"), decode = c("Screen Failure", "Placebo", "Xanomeline Low Dose", "Xanomeline High Dose")), "code_decode",
"CL.COUNTRY", "COUNTRY", tibble(code = "USA", decode = "USA"), "code_decode",
"CL.DRUGDICT", "DRUG DICTIONARY", tibble(dictionary = "WHODRUG", version = "200604"), "external_library",
"CL.EPOCH", "EPOCH", tibble(code = c("SCREENING", "TREATMENT", "FOLLOW-UP"), decode = c("Screening", "Treatment", "Follow-Up")), "code_decode",
"CL.ETHNIC", "ETHNIC", tibble(code = c("NOT HISPANIC OR LATINO", "HISPANIC OR LATINO"), decode = c("NOT HISPANIC OR LATINO", "HISPANIC OR LATINO")), "code_decode",
"CL.EXDOSEU", "EXDOSEU", tibble(code = "mg", decode = "mg"), "code_decode",
"CL.EXDOSFRM", "EXDOSFRM", tibble(code = "PATCH", decode = "PATCH"), "code_decode",
"CL.EXFREQ", "EXFREQ", tibble(code = "QD", decode = "QD"), "code_decode",
"CL.EXROUTE", "EXROUTE", tibble(code = "TRANSDERMAL", decode = "TRANSDERMAL"), "code_decode",
"CL.EXTRT", "EXTRT", tibble(code = c("PLACEBO", "XANOMELINE"), decode = c("PLACEBO", "XANOMELINE")), "code_decode",
"CL.MHDICT", "MEDICAL HISTORY DICTIONARY", tibble(dictionary = "MEDDRA", version = "8.0"), "external_library",
"CL.OUT", "OUT", tibble(code = c("RECOVERED/RESOLVED", "NOT RECOVERED/NOT RESOLVED", "FATAL"), decode = c("RECOVERED/RESOLVED", "NOT RECOVERED/NOT RESOLVED", "FATAL")), "code_decode",
"CL.QEVAL", "QEVAL", tibble(code = "CLINICAL STUDY SPONSOR", decode = "CLINICAL STUDY SPONSOR"), "code_decode",
"CL.RACE", "RACE", tibble(code = c("WHITE", "BLACK OR AFRICAN AMERICAN", "AMERICAN INDIAN OR ALASKA NATIVE", "ASIAN"), decode = c("WHITE", "BLACK OR AFRICAN AMERICAN", "AMERICAN INDIAN OR ALASKA NATIVE", "ASIAN")), "code_decode",
"CL.SEV", "SEV", tibble(code = c("MILD", "MODERATE", "SEVERE"), decode = c("MILD", "MODERATE", "SEVERE")), "code_decode",
"CL.SEX", "SEX", tibble(code = c("F", "M", "U"), decode = c("Female", "Male", "Unknown")), "code_decode",
"CL.SUPPAE.QNAM", "SUPPAE.QNAM", tibble(code = "AETRTEM", decode = "TREAMENT EMERGENT FLAG"), "code_decode",
"CL.SUPPDM.QNAM", "SUPPDM.QNAM", tibble(code = c("COMPLT16", "COMPLT24", "COMPLT8", "EFFICACY", "ITT", "SAFETY"), decode = c("Completers of Week 16 Population Flag", "Completers of Week 24 Population Flag", "Completers of Week 8 Population Flag", "Efficacy Population Flag", "Intent to Treat Population Flag", "Safety Population Flag")), "code_decode",
"CL.VISIT", "VISIT", tibble(code = c("SCREENING 1", "UNSCHEDULED 1.1", "UNSCHEDULED 1.2", "UNSCHEDULED 1.3", "SCREENING 2", "BASELINE", "UNSCHEDULED 3.1", "AMBUL ECG PLACEMENT", "WEEK 2", "UNSCHEDULED 4.1", "UNSCHEDULED 4.2", "WEEK 4", "UNSCHEDULED 5.1", "AMBUL ECG REMOVAL", "UNSCHEDULED 6.1", "WEEK 6", "UNSCHEDULED 7.1", "WEEK 8", "WEEK 10 (T)", "UNSCHEDULED 8.2", "WEEK 12", "WEEK 14 (T)", "UNSCHEDULED 9.2", "UNSCHEDULED 9.3", "WEEK 16", "WEEK 18 (T)", "UNSCHEDULED 10.2", "WEEK 20", "WEEK 22 (T)", "UNSCHEDULED 11.2",
"WEEK 24", "UNSCHEDULED 12.1", "WEEK 26", "UNSCHEDULED 13.1", "AE FOLLOW-UP", "RETRIEVAL", "Rash followup"), decode = c("SCREENING 1", "UNSCHEDULED 1.1", "UNSCHEDULED 1.2", "UNSCHEDULED 1.3", "SCREENING 2", "BASELINE", "UNSCHEDULED 3.1", "AMBUL ECG PLACEMENT", "WEEK 2", "UNSCHEDULED 4.1", "UNSCHEDULED 4.2", "WEEK 4", "UNSCHEDULED 5.1", "AMBUL ECG REMOVAL", "UNSCHEDULED 6.1", "WEEK 6", "UNSCHEDULED 7.1", "WEEK 8", "WEEK 10 (T)", "UNSCHEDULED 8.2", "WEEK 12", "WEEK 14 (T)", "UNSCHEDULED 9.2", "UNSCHEDULED 9.3",
"WEEK 16", "WEEK 18 (T)", "UNSCHEDULED 10.2", "WEEK 20", "WEEK 22 (T)", "UNSCHEDULED 11.2", "WEEK 24", "UNSCHEDULED 12.1", "WEEK 26", "UNSCHEDULED 13.1", "AE FOLLOW-UP", "RETRIEVAL", "Rash followup")), "code_decode",
"CL.VISITNUM", "VISITNUM", tibble(code = c("1", "1.1", "1.2", "1.3", "2", "3", "3.1", "3.5", "4", "4.1", "4.2", "5", "5.1", "6", "6.1", "7", "7.1", "8", "8.1", "8.2", "9", "9.1", "9.2", "9.3", "10", "10.1", "10.2", "11", "11.1", "11.2", "12", "12.1", "13", "13.1", "101", "201", "501"), decode = c("SCREENING 1", "UNSCHEDULED 1.1", "UNSCHEDULED 1.2", "UNSCHEDULED 1.3", "SCREENING 2", "BASELINE", "UNSCHEDULED 3.1", "AMBUL ECG PLACEMENT", "WEEK 2", "UNSCHEDULED 4.1", "UNSCHEDULED 4.2", "WEEK 4", "UNSCHEDULED 5.1", "AMBUL ECG REMOVAL",
"UNSCHEDULED 6.1", "WEEK 6", "UNSCHEDULED 7.1", "WEEK 8", "WEEK 10 (T)", "UNSCHEDULED 8.2", "WEEK 12", "WEEK 14 (T)", "UNSCHEDULED 9.2", "UNSCHEDULED 9.3", "WEEK 16", "WEEK 18 (T)", "UNSCHEDULED 10.2", "WEEK 20", "WEEK 22 (T)", "UNSCHEDULED 11.2", "WEEK 24", "UNSCHEDULED 12.1", "WEEK 26", "UNSCHEDULED 13.1", "AE FOLLOW-UP", "RETRIEVAL", "Rash followup")), "code_decode",
#"CL.Y_BLANK", "Y_BLANK", tibble(code = "Y", decode = "Yes"), "code_decode",
"CL.YN", "YN", tibble(code = c("N", "Y"), decode = c("No", "Yes")), "code_decode"
)
# Read from define
def_codelist <- xml_to_codelist(define) %>%
filter(code_id != "CL.Y_BLANK") %>%
arrange(code_id) %>%
select(code_id, name, codes, type)
# Read from spec
spec_codelist <- spec_type_to_codelist(spec, simplify = FALSE) %>%
mutate(code_id = paste0("CL.", code_id)) %>%
filter(code_id != "CL.Y_BLANK") %>%
arrange(code_id) %>%
select(code_id, name, codes, type)
# Tests
expect_equal(def_codelist, ref_codelist)
expect_equal(spec_codelist, ref_codelist)
})
test_that("Specification Reader's errors and warnings", {
# Check the name-checks work for each
expect_error(spec_type_to_ds_spec(spec, cols = c("foo")))
expect_error(spec_type_to_ds_spec(spec, cols = c("foo" = "foo")))
expect_error(spec_type_to_ds_vars(spec, cols = c("foo")))
expect_error(spec_type_to_ds_vars(spec, cols = c("foo" = "foo")))
expect_error(spec_type_to_var_spec(spec, cols = c("foo")))
expect_error(spec_type_to_var_spec(spec, cols = c("foo" = "foo")))
expect_error(spec_type_to_value_spec(spec, cols = c("foo")))
expect_error(spec_type_to_value_spec(spec, cols = c("foo" = "foo")))
expect_error(spec_type_to_derivations(spec, cols = c("foo")))
expect_error(spec_type_to_derivations(spec, cols = c("foo" = "foo")))
expect_error(spec_type_to_codelist(spec, cols = c("foo")))
expect_error(spec_type_to_codelist(spec, cols = c("foo" = "foo")))
})
test_that("Check no value reader",{
empty_val_check <- spec_to_metacore("spec_no_val.xlsx", quiet = TRUE,
where_sep_sheet = FALSE)
auto_val <- empty_val_check$value_spec %>%
filter(where != "TRUE")
expect_equal(nrow(auto_val), 0L)
})
atorus-research/metacore documentation built on May 7, 2024, 6:38 a.m.
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# Read in doc to be used for testing
define <- read_xml("define-2021.xml")
xml_ns_strip(define)
spec <- read_all_sheets(metacore_example("p21_mock.xlsx"))
#### Fist checking some reading in
test_that("Check spec_type", {
expect_equal(spec_type(metacore_example("p21_mock.xlsx")), "by_type")
expect_equal(spec_type(metacore_example("mock_spec.xlsx")), "by_type")
# Check it errors when format is not acceptable
expect_error(spec_type("example_spec.xlsx"))
})
#### Check reads are consistent between formats
test_that("Test ds_spec readers", {
# Create a reference spec to match to
ref_ds_spec <-
tribble(~dataset, ~structure, ~label,
"DM" ,"One record per subject", "Demographics",
"EX" ,"One record per constant dosing interval per subject", "Exposure",
"AE" ,"One record per adverse event per subject", "Adverse Events",
"SUPPAE" ,"One record per IDVAR, IDVARVAL, and QNAM value per subject", "Supplemental Qualifiers for AE",
"SUPPDM" ,"One record per IDVAR, IDVARVAL, and QNAM value per subject", "Supplemental Qualifiers for DM")
# Read from define
def_ds_spec <- xml_to_ds_spec(define)
# Read from spec
spec_ds_spec <- spec_type_to_ds_spec(spec)
spec_ds_spec2 <- spec_type_to_ds_spec(spec, sheet = "D")
# Test against reference
expect_equal(def_ds_spec, ref_ds_spec)
expect_equal(spec_ds_spec, arrange(ref_ds_spec, dataset))
expect_equal(spec_ds_spec2, arrange(ref_ds_spec, dataset))
})
test_that("Test ds_vars readers", {
# Create a reference ds_vars
ref_ds_vars <- tibble::tribble(
~dataset, ~variable, ~key_seq, ~order, ~keep, ~core, ~supp_flag,
"AE", "AEACN", NA, 21L, FALSE, NA_character_, NA,
"AE", "AEBDSYCD", NA, 16L, FALSE, NA_character_, NA,
"AE", "AEBODSYS", NA, 15L, FALSE, NA_character_, NA,
"AE", "AEDECOD", NA, 9L, FALSE, NA_character_, NA,
"AE", "AEDTC", NA, 32L, FALSE, NA_character_, NA,
"AE", "AEDY", NA, 35L, FALSE, NA_character_, NA,
"AE", "AEENDTC", NA, 34L, FALSE, NA_character_, NA,
"AE", "AEENDY", NA, 37L, FALSE, NA_character_, NA,
"AE", "AEHLGT", NA, 13L, FALSE, NA_character_, NA,
"AE", "AEHLGTCD", NA, 14L, FALSE, NA_character_, NA,
"AE", "AEHLT", NA, 11L, FALSE, NA_character_, NA,
"AE", "AEHLTCD", NA, 12L, FALSE, NA_character_, NA,
"AE", "AELLT", NA, 7L, FALSE, NA_character_, NA,
"AE", "AELLTCD", NA, 8L, FALSE, NA_character_, NA,
"AE", "AEOUT", NA, 23L, FALSE, NA_character_, NA,
"AE", "AEPTCD", NA, 10L, FALSE, NA_character_, NA,
"AE", "AEREL", NA, 22L, FALSE, NA_character_, NA,
"AE", "AESCAN", NA, 24L, FALSE, NA_character_, NA,
"AE", "AESCONG", NA, 25L, FALSE, NA_character_, NA,
"AE", "AESDISAB", NA, 26L, FALSE, NA_character_, NA,
"AE", "AESDTH", NA, 27L, FALSE, NA_character_, NA,
"AE", "AESEQ", 5L, 4L, TRUE, NA_character_, NA,
"AE", "AESER", NA, 20L, FALSE, NA_character_, NA,
"AE", "AESEV", NA, 19L, FALSE, NA_character_, NA,
"AE", "AESHOSP", NA, 28L, FALSE, NA_character_, NA,
"AE", "AESLIFE", NA, 29L, FALSE, NA_character_, NA,
"AE", "AESOC", NA, 17L, FALSE, NA_character_, NA,
"AE", "AESOCCD", NA, 18L, FALSE, NA_character_, NA,
"AE", "AESOD", NA, 30L, FALSE, NA_character_, NA,
"AE", "AESPID", NA, 5L, FALSE, NA_character_, NA,
"AE", "AESTDTC", 4L, 33L, FALSE, NA_character_, NA,
"AE", "AESTDY", NA, 36L, FALSE, NA_character_, NA,
"AE", "AETERM", 3L, 6L, TRUE, NA_character_, NA,
"AE", "DOMAIN", NA, 2L, TRUE, NA_character_, NA,
"AE", "EPOCH", NA, 31L, FALSE, NA_character_, NA,
"AE", "STUDYID", 1L, 1L, TRUE, NA_character_, NA,
"AE", "USUBJID", 2L, 3L, TRUE, NA_character_, NA,
"DM", "ACTARM", NA, 22L, TRUE, NA_character_, NA,
"DM", "ACTARMCD", NA, 21L, TRUE, NA_character_, NA,
"DM", "AGE", NA, 14L, FALSE, NA_character_, NA,
"DM", "AGEU", NA, 15L, FALSE, NA_character_, NA,
"DM", "ARM", NA, 20L, TRUE, NA_character_, NA,
"DM", "ARMCD", NA, 19L, TRUE, NA_character_, NA,
"DM", "COUNTRY", NA, 23L, TRUE, NA_character_, NA,
"DM", "DMDTC", NA, 24L, FALSE, NA_character_, NA,
"DM", "DMDY", NA, 25L, FALSE, NA_character_, NA,
"DM", "DOMAIN", NA, 2L, TRUE, NA_character_, NA,
"DM", "DTHDTC", NA, 11L, FALSE, NA_character_, NA,
"DM", "DTHFL", NA, 12L, FALSE, NA_character_, NA,
"DM", "ETHNIC", NA, 18L, FALSE, NA_character_, NA,
"DM", "RACE", NA, 17L, FALSE, NA_character_, NA,
"DM", "RFENDTC", NA, 6L, FALSE, NA_character_, NA,
"DM", "RFICDTC", NA, 9L, FALSE, NA_character_, NA,
"DM", "RFPENDTC", NA, 10L, FALSE, NA_character_, NA,
"DM", "RFSTDTC", NA, 5L, FALSE, NA_character_, NA,
"DM", "RFXENDTC", NA, 8L, FALSE, NA_character_, NA,
"DM", "RFXSTDTC", NA, 7L, FALSE, NA_character_, NA,
"DM", "SEX", NA, 16L, TRUE, NA_character_, NA,
"DM", "SITEID", NA, 13L, TRUE, NA_character_, NA,
"DM", "STUDYID", 1L, 1L, TRUE, NA_character_, NA,
"DM", "SUBJID", NA, 4L, TRUE, NA_character_, NA,
"DM", "USUBJID", 2L, 3L, TRUE, NA_character_, NA,
"EX", "DOMAIN", NA, 2L, TRUE, NA_character_, NA,
"EX", "EPOCH", NA, 14L, FALSE, NA_character_, NA,
"EX", "EXDOSE", NA, 6L, FALSE, NA_character_, NA,
"EX", "EXDOSFRM", NA, 8L, FALSE, NA_character_, NA,
"EX", "EXDOSFRQ", NA, 9L, FALSE, NA_character_, NA,
"EX", "EXDOSU", NA, 7L, FALSE, NA_character_, NA,
"EX", "EXENDTC", NA, 16L, FALSE, NA_character_, NA,
"EX", "EXENDY", NA, 18L, FALSE, NA_character_, NA,
"EX", "EXROUTE", NA, 10L, FALSE, NA_character_, NA,
"EX", "EXSEQ", NA, 4L, TRUE, NA_character_, NA,
"EX", "EXSTDTC", 4L, 15L, FALSE, NA_character_, NA,
"EX", "EXSTDY", NA, 17L, FALSE, NA_character_, NA,
"EX", "EXTRT", 3L, 5L, TRUE, NA_character_, NA,
"EX", "STUDYID", 1L, 1L, TRUE, NA_character_, NA,
"EX", "USUBJID", 2L, 3L, TRUE, NA_character_, NA,
"EX", "VISIT", NA, 12L, FALSE, NA_character_, NA,
"EX", "VISITDY", NA, 13L, FALSE, NA_character_, NA,
"EX", "VISITNUM", NA, 11L, FALSE, NA_character_, NA,
"SUPPAE", "IDVAR", 4L, 4L, FALSE, NA_character_, NA,
"SUPPAE", "IDVARVAL", 5L, 5L, FALSE, NA_character_, NA,
"SUPPAE", "QEVAL", NA, 10L, FALSE, NA_character_, NA,
"SUPPAE", "QLABEL", NA, 7L, TRUE, NA_character_, NA,
"SUPPAE", "QNAM", 6L, 6L, TRUE, NA_character_, NA,
"SUPPAE", "QORIG", NA, 9L, TRUE, NA_character_, NA,
"SUPPAE", "QVAL", NA, 8L, TRUE, NA_character_, NA,
"SUPPAE", "RDOMAIN", 2L, 2L, TRUE, NA_character_, NA,
"SUPPAE", "STUDYID", 1L, 1L, TRUE, NA_character_, NA,
"SUPPAE", "USUBJID", 3L, 3L, TRUE, NA_character_, NA,
"SUPPDM", "IDVAR", 4L, 4L, FALSE, NA_character_, NA,
"SUPPDM", "IDVARVAL", 5L, 5L, FALSE, NA_character_, NA,
"SUPPDM", "QEVAL", NA, 10L, FALSE, NA_character_, NA,
"SUPPDM", "QLABEL", NA, 7L, TRUE, NA_character_, NA,
"SUPPDM", "QNAM", 6L, 6L, TRUE, NA_character_, NA,
"SUPPDM", "QORIG", NA, 9L, TRUE, NA_character_, NA,
"SUPPDM", "QVAL", NA, 8L, TRUE, NA_character_, NA,
"SUPPDM", "RDOMAIN", 2L, 2L, TRUE, NA_character_, NA,
"SUPPDM", "STUDYID", 1L, 1L, TRUE, NA_character_, NA,
"SUPPDM", "USUBJID", 3L, 3L, TRUE, NA_character_, NA,
)
# Read from define
def_ds_vars <- xml_to_ds_vars(define) %>%
arrange(dataset, variable)
# Read from spec
spec_ds_vars <- spec_type_to_ds_vars(spec) %>%
arrange(dataset, variable) %>%
select(dataset, variable, key_seq, order, keep, core, supp_flag)
# Tests
expect_equal(def_ds_vars, ref_ds_vars)
expect_equal(spec_ds_vars, ref_ds_vars)
})
test_that("Test var_spec readers", {
ref_var_spec <-
tibble::tribble(
~variable, ~type, ~length, ~label, ~format, ~common,
"ACTARM", "text", 20L, "Description of Actual Arm", NA, NA,
"ACTARMCD", "text", 8L, "Actual Arm Code", NA, NA,
"AEACN", "text", 30L, "Action Taken with Study Treatment", NA, NA,
"AEBDSYCD", "integer", 8L, "Body System or Organ Class Code", NA, NA,
"AEBODSYS", "text", 67L, "Body System or Organ Class", NA, NA,
"AEDECOD", "text", 200L, "Dictionary-Derived Term", NA, NA,
"AEDTC", "date", 10L, "Date/Time of Collection", NA, NA,
"AEDY", "integer", 8L, "Study Day of Visit/Collection/Exam", NA, NA,
"AEENDTC", "date", 10L, "End Date/Time of Adverse Event", NA, NA,
"AEENDY", "integer", 8L, "Study Day of End of Adverse Event", NA, NA,
"AEHLGT", "text", 100L, "High Level Group Term", NA, NA,
"AEHLGTCD", "integer", 8L, "High Level Group Term Code", NA, NA,
"AEHLT", "text", 100L, "High Level Term", NA, NA,
"AEHLTCD", "integer", 8L, "High Level Term Code", NA, NA,
"AELLT", "text", 100L, "Lowest Level Term", NA, NA,
"AELLTCD", "integer", 8L, "Lowest Level Term Code", NA, NA,
"AEOUT", "text", 200L, "Outcome of Adverse Event", NA, NA,
"AEPTCD", "integer", 8L, "Preferred Term Code", NA, NA,
"AEREL", "text", 8L, "Causality", NA, NA,
"AESCAN", "text", 1L, "Involves Cancer", NA, NA,
"AESCONG", "text", 1L, "Congenital Anomaly or Birth Defect", NA, NA,
"AESDISAB", "text", 1L, "Persist or Signif Disability/Incapacity", NA, NA,
"AESDTH", "text", 1L, "Results in Death", NA, NA,
"AESEQ", "integer", 8L, "Sequence Number", NA, NA,
"AESER", "text", 1L, "Serious Event", NA, NA,
"AESEV", "text", 8L, "Severity/Intensity", NA, NA,
"AESHOSP", "text", 1L, "Requires or Prolongs Hospitalization", NA, NA,
"AESLIFE", "text", 1L, "Is Life Threatening", NA, NA,
"AESOC", "text", 100L, "Primary System Organ Class", NA, NA,
"AESOCCD", "integer", 8L, "Primary System Organ Class Code", NA, NA,
"AESOD", "text", 1L, "Occurred with Overdose", NA, NA,
"AESPID", "text", 3L, "Sponsor-Defined Identifier", NA, NA,
"AESTDTC", "date", 10L, "Start Date/Time of Adverse Event", NA, NA,
"AESTDY", "integer", 8L, "Study Day of Start of Adverse Event", NA, NA,
"AETERM", "text", 200L, "Reported Term for the Adverse Event", NA, NA,
"AGE", "integer", 8L, "Age", NA, NA,
"AGEU", "text", 6L, "Age Units", NA, NA,
"ARM", "text", 20L, "Description of Planned Arm", NA, NA,
"ARMCD", "text", 8L, "Planned Arm Code", NA, NA,
"COUNTRY", "text", 3L, "Country", NA, NA,
"DMDTC", "date", 10L, "Date/Time of Collection", NA, NA,
"DMDY", "integer", 8L, "Study Day of Collection", NA, NA,
"DOMAIN", "text", 2L, "Domain Abbreviation", NA, NA,
"DTHDTC", "datetime", 20L, "Date/Time of Death", NA, NA,
"DTHFL", "text", 1L, "Subject Death Flag", NA, NA,
"EPOCH", "text", 9L, "Epoch", NA, NA,
"ETHNIC", "text", 25L, "Ethnicity", NA, NA,
"EXDOSE", "integer", 8L, "Dose", NA, NA,
"EXDOSFRM", "text", 5L, "Dose Form", NA, NA,
"EXDOSFRQ", "text", 2L, "Dosing Frequency per Interval", NA, NA,
"EXDOSU", "text", 2L, "Dose Units", NA, NA,
"EXENDTC", "date", 10L, "End Date/Time of Treatment", NA, NA,
"EXENDY", "integer", 8L, "Study Day of End of Treatment", NA, NA,
"EXROUTE", "text", 11L, "Route of Administration", NA, NA,
"EXSEQ", "integer", 8L, "Sequence Number", NA, NA,
"EXSTDTC", "date", 10L, "Start Date/Time of Treatment", NA, NA,
"EXSTDY", "integer", 8L, "Study Day of Start of Treatment", NA, NA,
"EXTRT", "text", 10L, "Name of Treatment", NA, NA,
"IDVAR", "text", 8L, "Identifying Variable", NA, NA,
"IDVARVAL", "text", 200L, "Identifying Variable Value", NA, NA,
"QEVAL", "text", 200L, "Evaluator", NA, NA,
"QLABEL", "text", 40L, "Qualifier Variable Label", NA, NA,
"QNAM", "text", 8L, "Qualifier Variable Name", NA, NA,
"QORIG", "text", 200L, "Origin", NA, NA,
"QVAL", "text", 200L, "Data Value", NA, NA,
"RACE", "text", 78L, "Race", NA, NA,
"RDOMAIN", "text", 2L, "Related Domain Abbreviation", NA, NA,
"RFENDTC", "date", 10L, "Subject Reference End Date/Time", NA, NA,
"RFICDTC", "datetime", 20L, "Date/Time of Informed Consent", NA, NA,
"RFPENDTC", "datetime", 20L, "Date/Time of End of Participation", NA, NA,
"RFSTDTC", "date", 10L, "Subject Reference Start Date/Time", NA, NA,
"RFXENDTC", "datetime", 20L, "Date/Time of Last Study Treatment", NA, NA,
"RFXSTDTC", "datetime", 20L, "Date/Time of First Study Treatment", NA, NA,
"SEX", "text", 1L, "Sex", NA, NA,
"SITEID", "text", 3L, "Study Site Identifier", NA, NA,
"STUDYID", "text", 12L, "Study Identifier", NA, NA,
"SUBJID", "text", 4L, "Subject Identifier for the Study", NA, NA,
"USUBJID", "text", 11L, "Unique Subject Identifier", NA, NA,
"VISIT", "text", 19L, "Visit Name", NA, NA,
"VISITDY", "integer", 8L, "Planned Study Day of Visit", NA, NA,
"VISITNUM", "float", 8L, "Visit Number", "8.1", NA
)
# Read from define
def_var_spec <- xml_to_var_spec(define) %>%
arrange(variable)
# Read from spec
spec_var_spec <- spec_type_to_var_spec(spec) %>%
arrange(variable) %>%
select(variable, type, length, label, format)
spec2 <- spec
spec2$Variables |>
select(-Dataset)
no_ds <- spec_type_to_var_spec(spec2) |>
arrange(variable) %>%
select(variable, type, length, label, format)
expect_equal(no_ds, spec_var_spec)
# Tests
expect_equal(def_var_spec, ref_var_spec)
# remove common as it is derived when reading in specs but left alone from defines
expect_equal(spec_var_spec,
ref_var_spec %>%
select(-common))
})
test_that("values_spec reader tests", {
ref_value_spec <- tibble::tribble(
~dataset, ~variable, ~type, ~origin, ~code_id, ~sig_dig, ~where, ~derivation_id,
"AE", "AEACN", "text", "Derived", NA, NA, NA, "MT.AE.AEACN",
"AE", "AEBDSYCD", "integer", "Assigned", NA, NA, NA, NA,
"AE", "AEBODSYS", "text", "Assigned", "CL.AEDICT", NA, NA, NA,
"AE", "AEDECOD", "text", "Assigned", "CL.AEDICT", NA, NA, NA,
"AE", "AEDTC", "date", "Derived", NA, NA, NA, "MT.AE.AEDTC",
"AE", "AEDY", "integer", "Derived", NA, NA, NA, "MT.COMPMETHOD.STUDY_DAY",
"AE", "AEENDTC", "date", "CRF", NA, NA, NA, NA,
"AE", "AEENDY", "integer", "Derived", NA, NA, NA, "MT.COMPMETHOD.STUDY_DAY",
"AE", "AEHLGT", "text", "Assigned", "CL.AEDICT", NA, NA, NA,
"AE", "AEHLGTCD", "integer", "Assigned", NA, NA, NA, NA,
"AE", "AEHLT", "text", "Assigned", "CL.AEDICT", NA, NA, NA,
"AE", "AEHLTCD", "integer", "Assigned", NA, NA, NA, NA,
"AE", "AELLT", "text", "Assigned", "CL.AEDICT", NA, NA, NA,
"AE", "AELLTCD", "integer", "Assigned", NA, NA, NA, NA,
"AE", "AEOUT", "text", "CRF", "CL.OUT", NA, NA, NA,
"AE", "AEPTCD", "integer", "Assigned", NA, NA, NA, NA,
"AE", "AEREL", "text", "CRF", "CL.AECAUS", NA, NA, NA,
"AE", "AESCAN", "text", "CRF", "CL.YN", NA, NA, NA,
"AE", "AESCONG", "text", "CRF", "CL.YN", NA, NA, NA,
"AE", "AESDISAB", "text", "CRF", "CL.YN", NA, NA, NA,
"AE", "AESDTH", "text", "CRF", "CL.YN", NA, NA, NA,
"AE", "AESEQ", "integer", "Derived", NA, NA, NA, "MT.AE.AESEQ",
"AE", "AESER", "text", "CRF", "CL.YN", NA, NA, NA,
"AE", "AESEV", "text", "CRF", "CL.SEV", NA, NA, NA,
"AE", "AESHOSP", "text", "CRF", "CL.YN", NA, NA, NA,
"AE", "AESLIFE", "text", "CRF", "CL.YN", NA, NA, NA,
"AE", "AESOC", "text", "Assigned", "CL.AEDICT", NA, NA, NA,
"AE", "AESOCCD", "integer", "Assigned", NA, NA, NA, NA,
"AE", "AESOD", "text", "CRF", "CL.YN", NA, NA, NA,
"AE", "AESPID", "text", "CRF", NA, NA, NA, NA,
"AE", "AESTDTC", "date", "CRF", NA, NA, NA, NA,
"AE", "AESTDY", "integer", "Derived", NA, NA, NA, "MT.COMPMETHOD.STUDY_DAY",
"AE", "AETERM", "text", "CRF", NA, NA, NA, NA,
"AE", "DOMAIN", "text", "Assigned", NA, NA, NA, NA,
"AE", "EPOCH", "text", "Derived", "CL.EPOCH", NA, NA, "MT.AE.EPOCH",
"AE", "STUDYID", "text", "CRF", NA, NA, NA, NA,
"AE", "USUBJID", "text", "Derived", NA, NA, NA, "MT.AE.USUBJID",
"DM", "ACTARM", "text", "Derived", "CL.ARM", NA, NA, "MT.DM.ACTARM",
"DM", "ACTARMCD", "text", "Derived", "CL.ARMCD", NA, NA, "MT.DM.ACTARMCD",
"DM", "AGE", "integer", "Derived", NA, NA, NA, "MT.DM.AGE",
"DM", "AGEU", "text", "Assigned", "CL.AGEU", NA, NA, "COM.DM.AGEU",
"DM", "ARM", "text", "Assigned", "CL.ARM", NA, NA, "COM.DM.ARM",
"DM", "ARMCD", "text", "Assigned", "CL.ARMCD", NA, NA, "COM.DM.ARMCD",
"DM", "COUNTRY", "text", "Derived", "CL.COUNTRY", NA, NA, "MT.DM.COUNTRY",
"DM", "DMDTC", "date", "CRF", NA, NA, NA, NA,
"DM", "DMDY", "integer", "Derived", NA, NA, NA, "MT.COMPMETHOD.STUDY_DAY",
"DM", "DOMAIN", "text", "Assigned", NA, NA, NA, NA,
"DM", "DTHDTC", "datetime", "Derived", NA, NA, NA, "MT.DM.DTHDTC",
"DM", "DTHFL", "text", "Derived", "CL.Y_BLANK", NA, NA, "MT.DM.DTHFL",
"DM", "ETHNIC", "text", "Derived", "CL.ETHNIC", NA, NA, "MT.DM.ETHNIC",
"DM", "RACE", "text", "CRF", "CL.RACE", NA, NA, NA,
"DM", "RFENDTC", "date", "Derived", NA, NA, NA, "MT.DM.RFENDTC",
"DM", "RFICDTC", "datetime", "Derived", NA, NA, NA, "MT.DM.RFICDTC",
"DM", "RFPENDTC", "datetime", "Derived", NA, NA, NA, "MT.DM.RFPENDTC",
"DM", "RFSTDTC", "date", "Derived", NA, NA, NA, "MT.DM.RFSTDTC",
"DM", "RFXENDTC", "datetime", "Derived", NA, NA, NA, "MT.DM.RFXENDTC",
"DM", "RFXSTDTC", "datetime", "Derived", NA, NA, NA, "MT.DM.RFXSTDTC",
"DM", "SEX", "text", "CRF", "CL.SEX", NA, NA, NA,
"DM", "SITEID", "text", "Assigned", NA, NA, NA, NA,
"DM", "STUDYID", "text", "CRF", NA, NA, NA, NA,
"DM", "SUBJID", "text", "CRF", NA, NA, NA, NA,
"DM", "USUBJID", "text", "Derived", NA, NA, NA, "MT.DM.USUBJID",
"EX", "DOMAIN", "text", "Assigned", NA, NA, NA, NA,
"EX", "EPOCH", "text", "Derived", "CL.EPOCH", NA, NA, "MT.EX.EPOCH",
"EX", "EXDOSE", "integer", "eDT", NA, NA, NA, NA,
"EX", "EXDOSFRM", "text", "eDT", "CL.EXDOSFRM", NA, NA, NA,
"EX", "EXDOSFRQ", "text", "eDT", "CL.EXFREQ", NA, NA, NA,
"EX", "EXDOSU", "text", "eDT", "CL.EXDOSEU", NA, NA, NA,
"EX", "EXENDTC", "date", "CRF", NA, NA, NA, NA,
"EX", "EXENDY", "integer", "Derived", NA, NA, NA, "MT.COMPMETHOD.STUDY_DAY",
"EX", "EXROUTE", "text", "eDT", "CL.EXROUTE", NA, NA, NA,
"EX", "EXSEQ", "integer", "Derived", NA, NA, NA, "MT.EX.EXSEQ",
"EX", "EXSTDTC", "date", "CRF", NA, NA, NA, NA,
"EX", "EXSTDY", "integer", "Derived", NA, NA, NA, "MT.COMPMETHOD.STUDY_DAY",
"EX", "EXTRT", "text", "eDT", "CL.EXTRT", NA, NA, NA,
"EX", "STUDYID", "text", "CRF", NA, NA, NA, NA,
"EX", "USUBJID", "text", "Derived", NA, NA, NA, "MT.EX.USUBJID",
"EX", "VISIT", "text", "CRF", "CL.VISIT", NA, NA, NA,
"EX", "VISITDY", "integer", "Derived", NA, NA, NA, "MT.EX.VISITDY",
"EX", "VISITNUM", "float", "CRF", "CL.VISITNUM", 1L, NA, NA,
"SUPPAE", "IDVAR", "text", "Assigned", NA, NA, NA, "COM.SUPPAE.IDVAR",
"SUPPAE", "IDVARVAL", "text", "Derived", NA, NA, NA, "MT.SUPPAE.IDVARVAL",
"SUPPAE", "QEVAL", "text", "Assigned", "CL.QEVAL", NA, NA, NA,
"SUPPAE", "QLABEL", "text", "Assigned", NA, NA, NA, NA,
"SUPPAE", "QNAM", "text", "Assigned", "CL.SUPPAE.QNAM", NA, NA, NA,
"SUPPAE", "QORIG", "text", "Assigned", NA, NA, NA, NA,
"SUPPAE", "QVAL", "text", "Derived", "CL.YN", NA, "QNAM == 'TRTEMFL'", "MT.SUPPAE.QNAM.TRTEMFL",
"SUPPAE", "RDOMAIN", "text", "Assigned", NA, NA, NA, "COM.SUPPAE.RDOMAIN",
"SUPPAE", "STUDYID", "text", "CRF", NA, NA, NA, NA,
"SUPPAE", "USUBJID", "text", "Derived", NA, NA, NA, "MT.SUPPAE.USUBJID",
"SUPPDM", "IDVAR", "text", "Assigned", NA, NA, NA, "COM.SUPPDM.IDVAR",
"SUPPDM", "IDVARVAL", "text", "Assigned", NA, NA, NA, "COM.SUPPDM.IDVARVAL",
"SUPPDM", "QEVAL", "text", "Assigned", "CL.QEVAL", NA, NA, NA,
"SUPPDM", "QLABEL", "text", "Assigned", NA, NA, NA, NA,
"SUPPDM", "QNAM", "text", "Assigned", "CL.SUPPDM.QNAM", NA, NA, NA,
"SUPPDM", "QORIG", "text", "Assigned", NA, NA, NA, NA,
"SUPPDM", "QVAL", "text", "Derived", "CL.Y_BLANK", NA, "QNAM == 'COMPLT16'", "MT.SUPPDM.QNAM.COMPLT16",
"SUPPDM", "QVAL", "text", "Derived", "CL.Y_BLANK", NA, "QNAM == 'COMPLT24'", "MT.SUPPDM.QNAM.COMPLT24",
"SUPPDM", "QVAL", "text", "Derived", "CL.Y_BLANK", NA, "QNAM == 'COMPLT8'", "MT.SUPPDM.QNAM.COMPLT8",
"SUPPDM", "QVAL", "text", "Derived", "CL.Y_BLANK", NA, "QNAM == 'EFFICACY'", "MT.SUPPDM.QNAM.EFFICACY",
"SUPPDM", "QVAL", "text", "Derived", "CL.Y_BLANK", NA, "QNAM == 'SAFETY'", "MT.SUPPDM.QNAM.SAFETY",
"SUPPDM", "QVAL", "text", "Derived", "CL.Y_BLANK", NA, "QNAM == 'ITT'", "MT.SUPPDM.QNAM.ITT",
"SUPPDM", "RDOMAIN", "text", "Assigned", NA, NA, NA, "COM.SUPPDM.RDOMAIN",
"SUPPDM", "STUDYID", "text", "CRF", NA, NA, NA, NA,
"SUPPDM", "USUBJID", "text", "Derived", NA, NA, NA, "MT.SUPPDM.USUBJID"
)
# Read from define
def_value_spec <- xml_to_value_spec(define) %>%
arrange(dataset, variable) %>%
select(dataset, variable, type, origin, code_id, sig_dig, where, derivation_id )
# Read from spec
comments <- spec$Comments$ID
spec_value_spec <- spec_type_to_value_spec(spec) %>%
arrange(dataset, variable) %>%
select(dataset, variable, type, origin, code_id, sig_dig, where, derivation_id) %>%
#Fix naming as it is slightly different, but matches within metacore
mutate(code_id = if_else(!is.na(code_id), paste0("CL.", code_id), code_id, NA_character_),
derivation_id = case_when(
origin == "Derived" ~ paste0("MT.", derivation_id),
origin == "Assigned" & derivation_id %in% comments ~ paste0("COM.", derivation_id),
TRUE ~ NA_character_),
where = str_replace(where, "EQ", "=="),
where = str_split(where, "\\s(?=(\\w*$))") %>%
map(~paste0(.[1], " '", .[2])),
where = if_else(where == "NA 'NA", NA_character_, paste0(where, "'")))
# Tests
expect_equal(def_value_spec, ref_value_spec)
expect_equal(spec_value_spec, ref_value_spec)
})
test_that("derivation reader tests", {
# Create reference derivation tibble
ref_derivation <- tibble::tribble(
~derivation_id, ~derivation,
"COM.DM.AGEU", "AGEU='YEARS'",
"COM.DM.ARM", "According to randomization list",
"COM.DM.ARMCD", "According to randomization list",
"COM.SUPPAE.IDVAR", "IDVAR='AESEQ'",
"COM.SUPPAE.RDOMAIN", "RDOMAIN='AE'",
"COM.SUPPDM.IDVAR", "IDVAR=' '",
"COM.SUPPDM.IDVARVAL", "IDVARVAL= ' '",
"COM.SUPPDM.RDOMAIN", "RDOMAIN='AE'",
"MT.AE.AEACN" , "AEACN=Null (data on action taken concerning study treatment was not collected)" ,
"MT.AE.AEDTC" , "Date of final visit (SV)" ,
"MT.AE.AESEQ" , "Sequential number identifying records within each USUBJID" ,
"MT.AE.EPOCH" , "Use AESTDTC to determine from the SDTM SE what EPOCH this record falls under.\nIf SE.SESTDTC <= AESTDTC < SE.SEENDTC, then use that EPOCH.",
"MT.AE.USUBJID" ,"Concatenation of STUDYID, DM.SITEID and DM.SUBJID" ,
"MT.COMPMETHOD.STUDY_DAY" ,"(date portion of --DTC) minus (date portion of RFSTDTC) , add 1 if -- DTC >= RFSTDC" ,
"MT.DM.ACTARM" ,"Derived from EX" ,
"MT.DM.ACTARMCD" ,"Derived from EX" ,
"MT.DM.AGE" ,"Subject's Age at start of study drug (RFSTDTC)." ,
"MT.DM.COUNTRY" ,"Derived from site information" ,
"MT.DM.DTHDTC" ,"If DS record exists with DSDECOD='DEATH' then DTHDTC=AEENDTC." ,
"MT.DM.DTHFL" ,"If DS record exists with DSDECOD='DEATH' then DEATHFL=Y." ,
"MT.DM.ETHNIC" ,"Derived from Origin entered on CRF: ETHINC='HISPANIC OR LATINO' if Origin='Hispanic'. Otherwise ETHNIC='NOT HISPANIC OR LATINO'" ,
"MT.DM.RFENDTC" ,"Date/time of last study drug treatment derived from EX" ,
"MT.DM.RFICDTC" ,"Date of informed consent was not entered in database (see annotated CRF)" ,
"MT.DM.RFPENDTC" ,"DSSTDTC of last disposition event" ,
"MT.DM.RFSTDTC" ,"Date/time of first study drug treatment derived from EX" ,
"MT.DM.RFXENDTC" ,"RFXENDTC=RFENDTC" ,
"MT.DM.RFXSTDTC" ,"RFXSTDTC=RFSTDTC" ,
"MT.DM.USUBJID" ,"Concatenation of STUDYID, DM.SITEID and DM.SUBJID" ,
"MT.EX.EPOCH" ,"Use EXDTC to determine from the SDTM SE what EPOCH this record falls under.\nIf SE.SESTDTC <= EXDTC < SE.SEENDTC, then use that EPOCH.",
"MT.EX.EXSEQ" ,"Sequential number identifying records within each USUBJID" ,
"MT.EX.USUBJID" ,"Concatenation of STUDYID, DM.SITEID and DM.SUBJID" ,
"MT.EX.VISITDY" ,"TV.VISITDY" ,
"MT.SUPPAE.IDVARVAL" ,"Value of AESEQ of corresponding parent record" ,
"MT.SUPPAE.QNAM.TRTEMFL" ,"see SAP" ,
"MT.SUPPAE.QVAL" ,"see value level metadata" ,
"MT.SUPPAE.USUBJID" ,"Concatenation of STUDYID, DM.SITEID and DM.SUBJID" ,
"MT.SUPPDM.QNAM.COMPLT16" ,"see SAP" ,
"MT.SUPPDM.QNAM.COMPLT24" ,"see SAP" ,
"MT.SUPPDM.QNAM.COMPLT8" ,"see SAP" ,
"MT.SUPPDM.QNAM.EFFICACY" ,"see SAP" ,
"MT.SUPPDM.QNAM.ITT" ,"see SAP" ,
"MT.SUPPDM.QNAM.SAFETY" ,"see SAP" ,
"MT.SUPPDM.QVAL" ,"see value level metadata" ,
"MT.SUPPDM.USUBJID" ,"Concatenation of STUDYID, DM.SITEID and DM.SUBJID" ,
)
# Read from define
def_derivation <- xml_to_derivations(define) %>%
arrange(derivation_id) %>%
mutate(derivation = str_replace_all(derivation, '\\"', "\\'"))
# Read from spec
ref_deriv <- spec$Methods %>%
select(derivation_id = ID,
derivation = Description) %>%
mutate(derivation_id = paste0("MT.", derivation_id))
ref_deriv <- spec$Variables %>%
filter(Origin %in% c("Assigned")) %>%
left_join(select(spec$Comments, ID, Description), by = c("Comment" = "ID")) %>%
mutate(derivation_id = paste0("MT.", Dataset, ".", Variable),
derivation = Description) %>%
select(starts_with("derivation")) %>%
bind_rows(ref_deriv, .) %>%
arrange(derivation_id) %>%
distinct()
spec_derivation <- spec_type_to_derivations(spec) %>%
arrange(derivation_id) %>%
mutate(derivation_id = paste0("MT.", derivation_id))
# Tests
expect_equal(def_derivation, ref_derivation)
expect_equal(spec_derivation, ref_deriv)
})
test_that("codelist reader tests", {
# Create reference derivation tibble
ref_codelist <- tibble::tribble(
~code_id, ~name, ~codes, ~type,
"CL.AECAUS", "AECAUS", tibble(code = c("NONE", "POSSIBLE", "PROBABLE", "REMOTE"), decode = c("NONE", "POSSIBLE", "PROBABLE", "REMOTE")), "code_decode",
"CL.AEDICT", "ADVERSE EVENT DICTIONARY", tibble(dictionary = "MEDDRA", version = "8.0"), "external_library",
"CL.AGEU", "AGEU", tibble(code = "YEARS", decode = "YEARS"), "code_decode",
"CL.ARM", "ARM", tibble(code = c("Screen Failure", "Placebo", "Xanomeline Low Dose", "Xanomeline High Dose"), decode = c("Screen Failure", "Placebo", "Xanomeline Low Dose", "Xanomeline High Dose")), "code_decode",
"CL.ARMCD", "ARMCD", tibble(code = c("Scrnfail", "Pbo", "Xan_Lo", "Xan_Hi"), decode = c("Screen Failure", "Placebo", "Xanomeline Low Dose", "Xanomeline High Dose")), "code_decode",
"CL.COUNTRY", "COUNTRY", tibble(code = "USA", decode = "USA"), "code_decode",
"CL.DRUGDICT", "DRUG DICTIONARY", tibble(dictionary = "WHODRUG", version = "200604"), "external_library",
"CL.EPOCH", "EPOCH", tibble(code = c("SCREENING", "TREATMENT", "FOLLOW-UP"), decode = c("Screening", "Treatment", "Follow-Up")), "code_decode",
"CL.ETHNIC", "ETHNIC", tibble(code = c("NOT HISPANIC OR LATINO", "HISPANIC OR LATINO"), decode = c("NOT HISPANIC OR LATINO", "HISPANIC OR LATINO")), "code_decode",
"CL.EXDOSEU", "EXDOSEU", tibble(code = "mg", decode = "mg"), "code_decode",
"CL.EXDOSFRM", "EXDOSFRM", tibble(code = "PATCH", decode = "PATCH"), "code_decode",
"CL.EXFREQ", "EXFREQ", tibble(code = "QD", decode = "QD"), "code_decode",
"CL.EXROUTE", "EXROUTE", tibble(code = "TRANSDERMAL", decode = "TRANSDERMAL"), "code_decode",
"CL.EXTRT", "EXTRT", tibble(code = c("PLACEBO", "XANOMELINE"), decode = c("PLACEBO", "XANOMELINE")), "code_decode",
"CL.MHDICT", "MEDICAL HISTORY DICTIONARY", tibble(dictionary = "MEDDRA", version = "8.0"), "external_library",
"CL.OUT", "OUT", tibble(code = c("RECOVERED/RESOLVED", "NOT RECOVERED/NOT RESOLVED", "FATAL"), decode = c("RECOVERED/RESOLVED", "NOT RECOVERED/NOT RESOLVED", "FATAL")), "code_decode",
"CL.QEVAL", "QEVAL", tibble(code = "CLINICAL STUDY SPONSOR", decode = "CLINICAL STUDY SPONSOR"), "code_decode",
"CL.RACE", "RACE", tibble(code = c("WHITE", "BLACK OR AFRICAN AMERICAN", "AMERICAN INDIAN OR ALASKA NATIVE", "ASIAN"), decode = c("WHITE", "BLACK OR AFRICAN AMERICAN", "AMERICAN INDIAN OR ALASKA NATIVE", "ASIAN")), "code_decode",
"CL.SEV", "SEV", tibble(code = c("MILD", "MODERATE", "SEVERE"), decode = c("MILD", "MODERATE", "SEVERE")), "code_decode",
"CL.SEX", "SEX", tibble(code = c("F", "M", "U"), decode = c("Female", "Male", "Unknown")), "code_decode",
"CL.SUPPAE.QNAM", "SUPPAE.QNAM", tibble(code = "AETRTEM", decode = "TREAMENT EMERGENT FLAG"), "code_decode",
"CL.SUPPDM.QNAM", "SUPPDM.QNAM", tibble(code = c("COMPLT16", "COMPLT24", "COMPLT8", "EFFICACY", "ITT", "SAFETY"), decode = c("Completers of Week 16 Population Flag", "Completers of Week 24 Population Flag", "Completers of Week 8 Population Flag", "Efficacy Population Flag", "Intent to Treat Population Flag", "Safety Population Flag")), "code_decode",
"CL.VISIT", "VISIT", tibble(code = c("SCREENING 1", "UNSCHEDULED 1.1", "UNSCHEDULED 1.2", "UNSCHEDULED 1.3", "SCREENING 2", "BASELINE", "UNSCHEDULED 3.1", "AMBUL ECG PLACEMENT", "WEEK 2", "UNSCHEDULED 4.1", "UNSCHEDULED 4.2", "WEEK 4", "UNSCHEDULED 5.1", "AMBUL ECG REMOVAL", "UNSCHEDULED 6.1", "WEEK 6", "UNSCHEDULED 7.1", "WEEK 8", "WEEK 10 (T)", "UNSCHEDULED 8.2", "WEEK 12", "WEEK 14 (T)", "UNSCHEDULED 9.2", "UNSCHEDULED 9.3", "WEEK 16", "WEEK 18 (T)", "UNSCHEDULED 10.2", "WEEK 20", "WEEK 22 (T)", "UNSCHEDULED 11.2",
"WEEK 24", "UNSCHEDULED 12.1", "WEEK 26", "UNSCHEDULED 13.1", "AE FOLLOW-UP", "RETRIEVAL", "Rash followup"), decode = c("SCREENING 1", "UNSCHEDULED 1.1", "UNSCHEDULED 1.2", "UNSCHEDULED 1.3", "SCREENING 2", "BASELINE", "UNSCHEDULED 3.1", "AMBUL ECG PLACEMENT", "WEEK 2", "UNSCHEDULED 4.1", "UNSCHEDULED 4.2", "WEEK 4", "UNSCHEDULED 5.1", "AMBUL ECG REMOVAL", "UNSCHEDULED 6.1", "WEEK 6", "UNSCHEDULED 7.1", "WEEK 8", "WEEK 10 (T)", "UNSCHEDULED 8.2", "WEEK 12", "WEEK 14 (T)", "UNSCHEDULED 9.2", "UNSCHEDULED 9.3",
"WEEK 16", "WEEK 18 (T)", "UNSCHEDULED 10.2", "WEEK 20", "WEEK 22 (T)", "UNSCHEDULED 11.2", "WEEK 24", "UNSCHEDULED 12.1", "WEEK 26", "UNSCHEDULED 13.1", "AE FOLLOW-UP", "RETRIEVAL", "Rash followup")), "code_decode",
"CL.VISITNUM", "VISITNUM", tibble(code = c("1", "1.1", "1.2", "1.3", "2", "3", "3.1", "3.5", "4", "4.1", "4.2", "5", "5.1", "6", "6.1", "7", "7.1", "8", "8.1", "8.2", "9", "9.1", "9.2", "9.3", "10", "10.1", "10.2", "11", "11.1", "11.2", "12", "12.1", "13", "13.1", "101", "201", "501"), decode = c("SCREENING 1", "UNSCHEDULED 1.1", "UNSCHEDULED 1.2", "UNSCHEDULED 1.3", "SCREENING 2", "BASELINE", "UNSCHEDULED 3.1", "AMBUL ECG PLACEMENT", "WEEK 2", "UNSCHEDULED 4.1", "UNSCHEDULED 4.2", "WEEK 4", "UNSCHEDULED 5.1", "AMBUL ECG REMOVAL",
"UNSCHEDULED 6.1", "WEEK 6", "UNSCHEDULED 7.1", "WEEK 8", "WEEK 10 (T)", "UNSCHEDULED 8.2", "WEEK 12", "WEEK 14 (T)", "UNSCHEDULED 9.2", "UNSCHEDULED 9.3", "WEEK 16", "WEEK 18 (T)", "UNSCHEDULED 10.2", "WEEK 20", "WEEK 22 (T)", "UNSCHEDULED 11.2", "WEEK 24", "UNSCHEDULED 12.1", "WEEK 26", "UNSCHEDULED 13.1", "AE FOLLOW-UP", "RETRIEVAL", "Rash followup")), "code_decode",
#"CL.Y_BLANK", "Y_BLANK", tibble(code = "Y", decode = "Yes"), "code_decode",
"CL.YN", "YN", tibble(code = c("N", "Y"), decode = c("No", "Yes")), "code_decode"
)
# Read from define
def_codelist <- xml_to_codelist(define) %>%
filter(code_id != "CL.Y_BLANK") %>%
arrange(code_id) %>%
select(code_id, name, codes, type)
# Read from spec
spec_codelist <- spec_type_to_codelist(spec, simplify = FALSE) %>%
mutate(code_id = paste0("CL.", code_id)) %>%
filter(code_id != "CL.Y_BLANK") %>%
arrange(code_id) %>%
select(code_id, name, codes, type)
# Tests
expect_equal(def_codelist, ref_codelist)
expect_equal(spec_codelist, ref_codelist)
})
test_that("Specification Reader's errors and warnings", {
# Check the name-checks work for each
expect_error(spec_type_to_ds_spec(spec, cols = c("foo")))
expect_error(spec_type_to_ds_spec(spec, cols = c("foo" = "foo")))
expect_error(spec_type_to_ds_vars(spec, cols = c("foo")))
expect_error(spec_type_to_ds_vars(spec, cols = c("foo" = "foo")))
expect_error(spec_type_to_var_spec(spec, cols = c("foo")))
expect_error(spec_type_to_var_spec(spec, cols = c("foo" = "foo")))
expect_error(spec_type_to_value_spec(spec, cols = c("foo")))
expect_error(spec_type_to_value_spec(spec, cols = c("foo" = "foo")))
expect_error(spec_type_to_derivations(spec, cols = c("foo")))
expect_error(spec_type_to_derivations(spec, cols = c("foo" = "foo")))
expect_error(spec_type_to_codelist(spec, cols = c("foo")))
expect_error(spec_type_to_codelist(spec, cols = c("foo" = "foo")))
})
test_that("Check no value reader",{
empty_val_check <- spec_to_metacore("spec_no_val.xlsx", quiet = TRUE,
where_sep_sheet = FALSE)
auto_val <- empty_val_check$value_spec %>%
filter(where != "TRUE")
expect_equal(nrow(auto_val), 0L)
})
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