tests/testthat/test-summariseCodeUse.R
In oxford-pharmacoepi/CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use
test_that("summarise code use - eunomia", {
skip_on_cran()
if (Sys.getenv("EUNOMIA_DATA_FOLDER") == "") {
Sys.setenv("EUNOMIA_DATA_FOLDER" = tempdir())
}
if (!dir.exists(Sys.getenv("EUNOMIA_DATA_FOLDER"))) {
dir.create(Sys.getenv("EUNOMIA_DATA_FOLDER"))
}
if (!CDMConnector::eunomia_is_available()) {
invisible(utils::capture.output(CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER"))))
}
con <- DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir())
cdm <- CDMConnector::cdm_from_con(con, cdm_schem = "main", write_schema = "main")
acetiminophen <- c(1125315, 1127433, 40229134,
40231925, 40162522, 19133768, 1127078)
poliovirus_vaccine <- c(40213160)
cs <- list(acetiminophen = acetiminophen,
poliovirus_vaccine = poliovirus_vaccine)
results <- summariseCodeUse(cs,
cdm = cdm,
byYear = TRUE,
bySex = TRUE,
ageGroup = list(c(0,17),
c(18,65),
c(66, 100)))
# column names
expect_true(tibble::is_tibble(results))
expect_equal(colnames(results),
c("group_name", "group_level",
"strata_name", "strata_level",
"variable_name", "variable_level",
"variable_type",
"estimate_type", "estimate",
"estimate_suppressed",
"standard_concept_name",
"standard_concept_id",
"source_concept_name",
"source_concept_id",
"domain_id",
"codelist_name",
"cohort_name"))
# overall record count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Overall" &
strata_level == "Overall" &
codelist_name == "acetiminophen" &
variable_name == "Record count") %>%
dplyr::pull("estimate") ==
cdm$drug_exposure %>%
dplyr::filter(drug_concept_id %in% acetiminophen) %>%
dplyr::tally() %>%
dplyr::pull("n"))
# overall person count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Overall" &
strata_level == "Overall" &
codelist_name == "acetiminophen" &
variable_name == "Person count") %>%
dplyr::pull("estimate") ==
cdm$drug_exposure %>%
dplyr::filter(drug_concept_id %in% acetiminophen) %>%
dplyr::select("person_id") %>%
dplyr::distinct() %>%
dplyr::tally() %>%
dplyr::pull("n"))
# by year
# overall record count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Year" &
strata_level == "2008" &
codelist_name == "acetiminophen" &
variable_name == "Record count") %>%
dplyr::pull("estimate") ==
cdm$drug_exposure %>%
dplyr::filter(drug_concept_id %in% acetiminophen) %>%
dplyr::filter(year(drug_exposure_start_date) == 2008) %>%
dplyr::tally() %>%
dplyr::pull("n"))
# overall person count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Year" &
strata_level == "2008" &
codelist_name == "acetiminophen" &
variable_name == "Person count") %>%
dplyr::pull("estimate") ==
cdm$drug_exposure %>%
dplyr::filter(drug_concept_id %in% acetiminophen) %>%
dplyr::filter(year(drug_exposure_start_date) == 2008) %>%
dplyr::select("person_id") %>%
dplyr::distinct() %>%
dplyr::tally() %>%
dplyr::pull("n"))
# by age group and sex
# overall record count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Sex" &
strata_level == "Male" &
codelist_name == "acetiminophen" &
variable_name == "Record count") %>%
dplyr::pull("estimate") ==
cdm$drug_exposure %>%
dplyr::filter(drug_concept_id %in% acetiminophen) %>%
PatientProfiles::addSex(cdm) %>%
dplyr::filter(sex == "Male") %>%
dplyr::tally() %>%
dplyr::pull("n"))
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Age group and sex" &
strata_level == "18 to 65 and Male" &
codelist_name == "acetiminophen" &
variable_name == "Record count") %>%
dplyr::pull("estimate") ==
cdm$drug_exposure %>%
dplyr::filter(drug_concept_id %in% acetiminophen) %>%
PatientProfiles::addAge(cdm,
indexDate = "drug_exposure_start_date") %>%
PatientProfiles::addSex(cdm) %>%
dplyr::filter(sex == "Male" &
age >= "18" &
age <= "65") %>%
dplyr::tally() %>%
dplyr::pull("n"))
# overall person count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Age group and sex" &
strata_level == "18 to 65 and Male" &
codelist_name == "acetiminophen" &
variable_name == "Person count") %>%
dplyr::pull("estimate") ==
cdm$drug_exposure %>%
dplyr::filter(drug_concept_id %in% acetiminophen) %>%
PatientProfiles::addAge(cdm,
indexDate = "drug_exposure_start_date") %>%
PatientProfiles::addSex(cdm) %>%
dplyr::filter(sex == "Male" &
age >= "18" &
age <= "65") %>%
dplyr::select("person_id") %>%
dplyr::distinct() %>%
dplyr::tally() %>%
dplyr::pull("n"))
results <- summariseCodeUse(list("acetiminophen" = acetiminophen),
cdm = cdm, countBy = "person",
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL)
expect_true(nrow(results %>%
dplyr::filter(variable_name == "Person count")) > 0)
expect_true(nrow(results %>%
dplyr::filter(variable_name == "Record count")) == 0)
results <- summariseCodeUse(list("acetiminophen" = acetiminophen),
cdm = cdm, countBy = "record",
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL)
expect_true(nrow(results %>%
dplyr::filter(variable_name == "Person count")) == 0)
expect_true(nrow(results %>%
dplyr::filter(variable_name == "Record count")) > 0)
# check min cell count
results <- summariseCodeUse(list("acetiminophen" = acetiminophen),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL,
minCellCount = 75)
expect_true(max(results$estimate, na.rm = TRUE) >=75)
# domains covered
# condition
expect_true(nrow(summariseCodeUse(list(cs= c(4112343)),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# visit
expect_true(nrow(summariseCodeUse(list(cs= c(9201)),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# drug
expect_true(nrow(summariseCodeUse(list(cs= c(40213160)),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# measurement
expect_true(nrow(summariseCodeUse(list(cs= c(3006322)),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# procedure and condition
expect_true(nrow(summariseCodeUse(list(cs= c(4107731,4112343)),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# no records
expect_message(results <- summariseCodeUse(list(cs= c(999999)),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))
expect_true(nrow(results) == 0)
# expected errors
expect_error(summariseCodeUse("not a concept",
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))
expect_error(summariseCodeUse("123",
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))
expect_error(summariseCodeUse(list("123"), # not named
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))
expect_error(summariseCodeUse(list(a = 123),
cdm = "not a cdm",
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))
expect_error(summariseCodeUse(list(a = 123),
cdm = cdm,
byYear = "Maybe",
bySex = FALSE,
ageGroup = NULL))
expect_error(summariseCodeUse(list(a = 123),
cdm = cdm,
byYear = FALSE,
bySex = "Maybe",
ageGroup = NULL))
expect_error(summariseCodeUse(list(a = 123),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = 25))
expect_error(summariseCodeUse(list(a = 123),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = list(c(18,17))))
expect_error(summariseCodeUse(list(a = 123),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = list(c(0,17),
c(15,20))))
CDMConnector::cdmDisconnect(cdm)
})
test_that("summarise cohort code use - eunomia", {
skip_on_cran()
if (Sys.getenv("EUNOMIA_DATA_FOLDER") == "") {
Sys.setenv("EUNOMIA_DATA_FOLDER" = tempdir())
}
if (!dir.exists(Sys.getenv("EUNOMIA_DATA_FOLDER"))) {
dir.create(Sys.getenv("EUNOMIA_DATA_FOLDER"))
}
if (!CDMConnector::eunomia_is_available()) {
invisible(utils::capture.output(CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER"))))
}
con <- DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir())
cdm <- CDMConnector::cdm_from_con(con, cdm_schem = "main", write_schema = "main")
pharyngitis <- c(4112343)
cdm <- CDMConnector::generateConceptCohortSet(cdm = cdm,
conceptSet = list(pharyngitis = pharyngitis),
name = "pharyngitis",
end = "observation_period_end_date",
overwrite = TRUE)
# any
results_all <- summariseCodeUse(list(cs = 4134304),
cdm = cdm, minCellCount = 0)
results_cohort <- summariseCohortCodeUse(list(cs = 4134304),
cdm = cdm,
cohortTable = "pharyngitis",
timing = "any", minCellCount = 0)
expect_true(tibble::is_tibble(results_cohort))
expect_true(all(colnames(results_cohort) %in%
c("group_name", "group_level",
"strata_name", "strata_level",
"variable_name", "variable_level",
"variable_type",
"estimate_type", "estimate",
"estimate_suppressed",
"standard_concept_name",
"standard_concept_id",
"source_concept_name",
"source_concept_id",
"domain_id",
"codelist_name",
"cohort_name")
))
expect_true(results_cohort %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Overall" &
strata_level == "Overall" &
variable_name == "Person count") %>%
dplyr::pull("estimate") <
results_all %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Overall" &
strata_level == "Overall" &
variable_name == "Person count") %>%
dplyr::pull("estimate"))
# at entry - everyone in the cohort should have the code
results_cohort <- summariseCohortCodeUse(list(pharyngitis = pharyngitis),
cdm = cdm,
cohortTable = "pharyngitis",
timing = "entry",
minCellCount = 0)
results_cohort %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Overall" &
strata_level == "Overall" &
variable_name == "Person count") %>%
dplyr::pull("estimate") ==
CDMConnector::cohortCount(cdm$pharyngitis) %>%
dplyr::pull("number_subjects")
# 260139
# on index
index_260139 <- cdm$pharyngitis %>%
dplyr::left_join(cdm$condition_occurrence,
by=c("subject_id"="person_id")) %>%
dplyr::filter(condition_start_date == cohort_start_date) %>%
dplyr::filter(condition_concept_id == 260139) %>%
dplyr::select("subject_id") %>%
dplyr::distinct() %>%
dplyr::count() %>%
dplyr::pull()
results_cohort_260139 <- summariseCohortCodeUse(list(cs = 260139),
cdm = cdm,
cohortTable = "pharyngitis",
timing = "entry",
minCellCount = 0)
expect_equal(results_cohort_260139 %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Overall" &
strata_level == "Overall" &
variable_name == "Person count") %>%
dplyr::pull("estimate"), index_260139)
# 260139 or 19133873 or 1127433
# on index
index_260139_19133873_1127433 <- dplyr::union_all(
cdm$pharyngitis %>%
dplyr::left_join(cdm$condition_occurrence,
by=c("subject_id"="person_id")) %>%
dplyr::filter(condition_start_date == cohort_start_date) %>%
dplyr::filter(condition_concept_id == 260139) %>%
dplyr::select("subject_id"),
cdm$pharyngitis %>%
dplyr::left_join(cdm$drug_exposure,
by=c("subject_id"="person_id")) %>%
dplyr::filter(drug_exposure_start_date == cohort_start_date) %>%
dplyr::filter(drug_concept_id %in% c(19133873,1127433)) %>%
dplyr::select("subject_id")) %>%
dplyr::count() %>%
dplyr::pull()
results_cohort_260139_19133873_1127433<- summariseCohortCodeUse(list(cs = c(260139,19133873,1127433)),
cdm = cdm,
cohortTable = "pharyngitis",
timing = "entry",
minCellCount = 0)
expect_equal(results_cohort_260139_19133873_1127433 %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Overall" &
strata_level == "Overall" &
variable_name == "Record count") %>%
dplyr::pull("estimate"),
index_260139_19133873_1127433)
expect_equal(results_cohort_260139_19133873_1127433 %>%
dplyr::filter(stringr::str_detect(group_level, "Acute bronchitis")) %>%
dplyr::filter(strata_name == "Overall" &
strata_level == "Overall" &
variable_name == "Person count") %>%
dplyr::pull("estimate"),
index_260139)
# multiple cohorts
cdm <- CDMConnector::generateConceptCohortSet(cdm = cdm,
conceptSet = list(a = 260139,
b = 1127433 ),
name = "cohorts",
end = "observation_period_end_date",
overwrite = TRUE)
results_cohort_mult <- summariseCohortCodeUse(list(cs = c(260139,19133873,1127433)),
cdm = cdm,
cohortTable = "cohorts",
timing = "entry",
minCellCount = 0)
expect_true(nrow(results_cohort_mult %>%
dplyr::filter(stringr::str_detect(group_level, "Acute bronchitis")) %>%
dplyr::filter(strata_name == "Overall" &
strata_level == "Overall" &
variable_name == "Person count")) == 2)
expect_equal(c("a", "b"), results_cohort_mult %>%
dplyr::filter(stringr::str_detect(group_level, "Acute bronchitis")) %>%
dplyr::filter(strata_name == "Overall" &
strata_level == "Overall" &
variable_name == "Person count") %>%
dplyr::pull("cohort_name"))
# empty cohort - no results
cdm$pharyngitis <- cdm$pharyngitis %>%
dplyr::filter(cohort_definition_id == 99)
expect_true(nrow(summariseCohortCodeUse(list(cs = 4134304),
cdm = cdm,
cohortTable = "pharyngitis",
timing = "any", minCellCount = 0)) == 0)
# expected errors
expect_error(summariseCohortCodeUse(4134304,
cdm = cdm,
cohortTable = "not_a_cohort",
timing = "any"))
expect_error(summariseCohortCodeUse(list(4134304),
cdm = cdm,
cohortTable = "not_a_cohort",
timing = "any"))
expect_error(summariseCohortCodeUse(list(cs = 4134304),
cdm = cdm,
cohortTable = "not_a_cohort",
timing = "any"))
expect_error(summariseCohortCodeUse(list(cs = 4134304),
cdm = cdm,
cohortTable = "pharyngitis",
timing = "not_a_option"))
expect_error(summariseCohortCodeUse(list(cs = 4134304),
cdm = cdm,
cohortTable = "pharyngitis",
timing = c("any", "entry")))
CDMConnector::cdmDisconnect(cdm)
})
test_that("summarise code use - redshift", {
testthat::skip_if(Sys.getenv("CDM5_REDSHIFT_DBNAME") == "")
db <- DBI::dbConnect(RPostgres::Redshift(),
dbname = Sys.getenv("CDM5_REDSHIFT_DBNAME"),
host = Sys.getenv("CDM5_REDSHIFT_HOST"),
port = Sys.getenv("CDM5_REDSHIFT_PORT"),
user = Sys.getenv("CDM5_REDSHIFT_USER"),
password = Sys.getenv("CDM5_REDSHIFT_PASSWORD"))
cdm <- CDMConnector::cdm_from_con(con = db,
cdm_schema = Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA"),
write_schema = Sys.getenv("CDM5_REDSHIFT_SCRATCH_SCHEMA"))
asthma <- list(asthma = c(317009, 257581))
results <- summariseCodeUse(asthma,
cdm = cdm,
byYear = TRUE,
bySex = TRUE,
ageGroup = list(c(0,17),
c(18,65),
c(66, 100)))
# column names
expect_true(tibble::is_tibble(results))
expect_true(all(colnames(results) %in%
c("group_name", "group_level",
"strata_name", "strata_level",
"variable_name", "variable_level",
"variable_type",
"estimate_type", "estimate",
"estimate_suppressed",
"standard_concept_name",
"standard_concept_id",
"source_concept_name",
"source_concept_id",
"domain_id",
"codelist_name",
"cohort_name")
))
# overall record count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Overall" &
strata_level == "Overall",
variable_name == "Record count") %>%
dplyr::pull("estimate") ==
cdm$condition_occurrence %>%
dplyr::filter(condition_concept_id %in% !!asthma[[1]]) %>%
dplyr::tally() %>%
dplyr::pull("n"))
# overall person count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Overall" &
strata_level == "Overall" &
variable_name == "Person count") %>%
dplyr::pull("estimate") ==
cdm$condition_occurrence %>%
dplyr::filter(condition_concept_id %in% !!asthma[[1]]) %>%
dplyr::select("person_id") %>%
dplyr::distinct() %>%
dplyr::tally() %>%
dplyr::pull("n"))
# by year
# overall record count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Year" &
strata_level == "2008",
variable_name == "Record count") %>%
dplyr::pull("estimate") ==
cdm$condition_occurrence %>%
dplyr::filter(condition_concept_id %in% !!asthma[[1]]) %>%
dplyr::filter(year(condition_start_date) == 2008) %>%
dplyr::tally() %>%
dplyr::pull("n"))
# overall person count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Year" &
strata_level == "2008",
variable_name == "Person count") %>%
dplyr::pull("estimate") ==
cdm$condition_occurrence %>%
dplyr::filter(condition_concept_id %in% !!asthma[[1]]) %>%
dplyr::filter(year(condition_start_date) == 2008) %>%
dplyr::select("person_id") %>%
dplyr::distinct() %>%
dplyr::tally() %>%
dplyr::pull("n"))
# by age group and sex
# overall record count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Sex" &
strata_level == "Male",
variable_name == "Record count") %>%
dplyr::pull("estimate") ==
cdm$condition_occurrence %>%
dplyr::filter(condition_concept_id %in% !!asthma[[1]]) %>%
PatientProfiles::addSex(cdm) %>%
dplyr::filter(sex == "Male") %>%
dplyr::tally() %>%
dplyr::pull("n"))
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Age group and sex" &
strata_level == "18 to 65 and Male",
variable_name == "Record count") %>%
dplyr::pull("estimate") ==
cdm$condition_occurrence %>%
dplyr::filter(condition_concept_id %in% !!asthma[[1]]) %>%
PatientProfiles::addAge(cdm,
indexDate = "condition_start_date") %>%
PatientProfiles::addSex(cdm) %>%
dplyr::filter(sex == "Male" &
age >= "18" &
age <= "65") %>%
dplyr::tally() %>%
dplyr::pull("n"))
# overall person count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Age group and sex" &
strata_level == "18 to 65 and Male",
variable_name == "Person count") %>%
dplyr::pull("estimate") ==
cdm$condition_occurrence %>%
dplyr::filter(condition_concept_id %in% !!asthma[[1]]) %>%
PatientProfiles::addAge(cdm,
indexDate = "condition_start_date") %>%
PatientProfiles::addSex(cdm) %>%
dplyr::filter(sex == "Male" &
age >= "18" &
age <= "65") %>%
dplyr::select("person_id") %>%
dplyr::distinct() %>%
dplyr::tally() %>%
dplyr::pull("n"))
results <- summariseCodeUse(asthma,
cdm = cdm, countBy = "person",
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL)
expect_true(nrow(results %>%
dplyr::filter(variable_name == "Person count")) > 0)
expect_true(nrow(results %>%
dplyr::filter(variable_name == "Record count")) == 0)
results <- summariseCodeUse(asthma,
cdm = cdm, countBy = "record",
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL)
expect_true(nrow(results %>%
dplyr::filter(variable_name == "Person count")) == 0)
expect_true(nrow(results %>%
dplyr::filter(variable_name == "Record count")) > 0)
# check min cell count
results <- summariseCodeUse(asthma,
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL,
minCellCount = 75)
expect_true(max(results$estimate, na.rm = TRUE) >=75)
# domains covered
# condition
expect_true(nrow(summariseCodeUse(list(cs = c(317009)),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# visit
expect_true(nrow(summariseCodeUse(list(cs = 9201),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# drug
expect_true(nrow(summariseCodeUse(list(cs = 19071493),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# measurement
expect_true(nrow(summariseCodeUse(list(cs = 2212542),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# procedure and condition
expect_true(nrow(summariseCodeUse(list(cs = c(4261206,317009)),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# no records
expect_message(results <- summariseCodeUse(list(cs = c(999999)),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))
expect_true(nrow(results) == 0)
# expected errors
expect_error(summariseCodeUse(list(cs = "not a concept"),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))
expect_error(summariseCodeUse(list(cs = 123),
cdm = "not a cdm",
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))
expect_error(summariseCodeUse(list(cs = 123),
cdm = cdm,
byYear = "Maybe",
bySex = FALSE,
ageGroup = NULL))
expect_error(summariseCodeUse(list(cs = 123),
cdm = cdm,
byYear = FALSE,
bySex = "Maybe",
ageGroup = NULL))
expect_error(summariseCodeUse(list(cs = 123),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = 25))
expect_error(summariseCodeUse(list(cs = 123),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = list(c(18,17))))
expect_error(summariseCodeUse(list(cs = 123),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = list(c(0,17),
c(15,20))))
CDMConnector::cdmDisconnect(cdm)
})
oxford-pharmacoepi/CodelistGenerator documentation built on April 12, 2024, 9:30 a.m.
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test_that("summarise code use - eunomia", {
skip_on_cran()
if (Sys.getenv("EUNOMIA_DATA_FOLDER") == "") {
Sys.setenv("EUNOMIA_DATA_FOLDER" = tempdir())
}
if (!dir.exists(Sys.getenv("EUNOMIA_DATA_FOLDER"))) {
dir.create(Sys.getenv("EUNOMIA_DATA_FOLDER"))
}
if (!CDMConnector::eunomia_is_available()) {
invisible(utils::capture.output(CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER"))))
}
con <- DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir())
cdm <- CDMConnector::cdm_from_con(con, cdm_schem = "main", write_schema = "main")
acetiminophen <- c(1125315, 1127433, 40229134,
40231925, 40162522, 19133768, 1127078)
poliovirus_vaccine <- c(40213160)
cs <- list(acetiminophen = acetiminophen,
poliovirus_vaccine = poliovirus_vaccine)
results <- summariseCodeUse(cs,
cdm = cdm,
byYear = TRUE,
bySex = TRUE,
ageGroup = list(c(0,17),
c(18,65),
c(66, 100)))
# column names
expect_true(tibble::is_tibble(results))
expect_equal(colnames(results),
c("group_name", "group_level",
"strata_name", "strata_level",
"variable_name", "variable_level",
"variable_type",
"estimate_type", "estimate",
"estimate_suppressed",
"standard_concept_name",
"standard_concept_id",
"source_concept_name",
"source_concept_id",
"domain_id",
"codelist_name",
"cohort_name"))
# overall record count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Overall" &
strata_level == "Overall" &
codelist_name == "acetiminophen" &
variable_name == "Record count") %>%
dplyr::pull("estimate") ==
cdm$drug_exposure %>%
dplyr::filter(drug_concept_id %in% acetiminophen) %>%
dplyr::tally() %>%
dplyr::pull("n"))
# overall person count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Overall" &
strata_level == "Overall" &
codelist_name == "acetiminophen" &
variable_name == "Person count") %>%
dplyr::pull("estimate") ==
cdm$drug_exposure %>%
dplyr::filter(drug_concept_id %in% acetiminophen) %>%
dplyr::select("person_id") %>%
dplyr::distinct() %>%
dplyr::tally() %>%
dplyr::pull("n"))
# by year
# overall record count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Year" &
strata_level == "2008" &
codelist_name == "acetiminophen" &
variable_name == "Record count") %>%
dplyr::pull("estimate") ==
cdm$drug_exposure %>%
dplyr::filter(drug_concept_id %in% acetiminophen) %>%
dplyr::filter(year(drug_exposure_start_date) == 2008) %>%
dplyr::tally() %>%
dplyr::pull("n"))
# overall person count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Year" &
strata_level == "2008" &
codelist_name == "acetiminophen" &
variable_name == "Person count") %>%
dplyr::pull("estimate") ==
cdm$drug_exposure %>%
dplyr::filter(drug_concept_id %in% acetiminophen) %>%
dplyr::filter(year(drug_exposure_start_date) == 2008) %>%
dplyr::select("person_id") %>%
dplyr::distinct() %>%
dplyr::tally() %>%
dplyr::pull("n"))
# by age group and sex
# overall record count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Sex" &
strata_level == "Male" &
codelist_name == "acetiminophen" &
variable_name == "Record count") %>%
dplyr::pull("estimate") ==
cdm$drug_exposure %>%
dplyr::filter(drug_concept_id %in% acetiminophen) %>%
PatientProfiles::addSex(cdm) %>%
dplyr::filter(sex == "Male") %>%
dplyr::tally() %>%
dplyr::pull("n"))
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Age group and sex" &
strata_level == "18 to 65 and Male" &
codelist_name == "acetiminophen" &
variable_name == "Record count") %>%
dplyr::pull("estimate") ==
cdm$drug_exposure %>%
dplyr::filter(drug_concept_id %in% acetiminophen) %>%
PatientProfiles::addAge(cdm,
indexDate = "drug_exposure_start_date") %>%
PatientProfiles::addSex(cdm) %>%
dplyr::filter(sex == "Male" &
age >= "18" &
age <= "65") %>%
dplyr::tally() %>%
dplyr::pull("n"))
# overall person count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Age group and sex" &
strata_level == "18 to 65 and Male" &
codelist_name == "acetiminophen" &
variable_name == "Person count") %>%
dplyr::pull("estimate") ==
cdm$drug_exposure %>%
dplyr::filter(drug_concept_id %in% acetiminophen) %>%
PatientProfiles::addAge(cdm,
indexDate = "drug_exposure_start_date") %>%
PatientProfiles::addSex(cdm) %>%
dplyr::filter(sex == "Male" &
age >= "18" &
age <= "65") %>%
dplyr::select("person_id") %>%
dplyr::distinct() %>%
dplyr::tally() %>%
dplyr::pull("n"))
results <- summariseCodeUse(list("acetiminophen" = acetiminophen),
cdm = cdm, countBy = "person",
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL)
expect_true(nrow(results %>%
dplyr::filter(variable_name == "Person count")) > 0)
expect_true(nrow(results %>%
dplyr::filter(variable_name == "Record count")) == 0)
results <- summariseCodeUse(list("acetiminophen" = acetiminophen),
cdm = cdm, countBy = "record",
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL)
expect_true(nrow(results %>%
dplyr::filter(variable_name == "Person count")) == 0)
expect_true(nrow(results %>%
dplyr::filter(variable_name == "Record count")) > 0)
# check min cell count
results <- summariseCodeUse(list("acetiminophen" = acetiminophen),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL,
minCellCount = 75)
expect_true(max(results$estimate, na.rm = TRUE) >=75)
# domains covered
# condition
expect_true(nrow(summariseCodeUse(list(cs= c(4112343)),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# visit
expect_true(nrow(summariseCodeUse(list(cs= c(9201)),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# drug
expect_true(nrow(summariseCodeUse(list(cs= c(40213160)),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# measurement
expect_true(nrow(summariseCodeUse(list(cs= c(3006322)),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# procedure and condition
expect_true(nrow(summariseCodeUse(list(cs= c(4107731,4112343)),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# no records
expect_message(results <- summariseCodeUse(list(cs= c(999999)),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))
expect_true(nrow(results) == 0)
# expected errors
expect_error(summariseCodeUse("not a concept",
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))
expect_error(summariseCodeUse("123",
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))
expect_error(summariseCodeUse(list("123"), # not named
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))
expect_error(summariseCodeUse(list(a = 123),
cdm = "not a cdm",
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))
expect_error(summariseCodeUse(list(a = 123),
cdm = cdm,
byYear = "Maybe",
bySex = FALSE,
ageGroup = NULL))
expect_error(summariseCodeUse(list(a = 123),
cdm = cdm,
byYear = FALSE,
bySex = "Maybe",
ageGroup = NULL))
expect_error(summariseCodeUse(list(a = 123),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = 25))
expect_error(summariseCodeUse(list(a = 123),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = list(c(18,17))))
expect_error(summariseCodeUse(list(a = 123),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = list(c(0,17),
c(15,20))))
CDMConnector::cdmDisconnect(cdm)
})
test_that("summarise cohort code use - eunomia", {
skip_on_cran()
if (Sys.getenv("EUNOMIA_DATA_FOLDER") == "") {
Sys.setenv("EUNOMIA_DATA_FOLDER" = tempdir())
}
if (!dir.exists(Sys.getenv("EUNOMIA_DATA_FOLDER"))) {
dir.create(Sys.getenv("EUNOMIA_DATA_FOLDER"))
}
if (!CDMConnector::eunomia_is_available()) {
invisible(utils::capture.output(CDMConnector::downloadEunomiaData(pathToData = Sys.getenv("EUNOMIA_DATA_FOLDER"))))
}
con <- DBI::dbConnect(duckdb::duckdb(), dbdir = CDMConnector::eunomia_dir())
cdm <- CDMConnector::cdm_from_con(con, cdm_schem = "main", write_schema = "main")
pharyngitis <- c(4112343)
cdm <- CDMConnector::generateConceptCohortSet(cdm = cdm,
conceptSet = list(pharyngitis = pharyngitis),
name = "pharyngitis",
end = "observation_period_end_date",
overwrite = TRUE)
# any
results_all <- summariseCodeUse(list(cs = 4134304),
cdm = cdm, minCellCount = 0)
results_cohort <- summariseCohortCodeUse(list(cs = 4134304),
cdm = cdm,
cohortTable = "pharyngitis",
timing = "any", minCellCount = 0)
expect_true(tibble::is_tibble(results_cohort))
expect_true(all(colnames(results_cohort) %in%
c("group_name", "group_level",
"strata_name", "strata_level",
"variable_name", "variable_level",
"variable_type",
"estimate_type", "estimate",
"estimate_suppressed",
"standard_concept_name",
"standard_concept_id",
"source_concept_name",
"source_concept_id",
"domain_id",
"codelist_name",
"cohort_name")
))
expect_true(results_cohort %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Overall" &
strata_level == "Overall" &
variable_name == "Person count") %>%
dplyr::pull("estimate") <
results_all %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Overall" &
strata_level == "Overall" &
variable_name == "Person count") %>%
dplyr::pull("estimate"))
# at entry - everyone in the cohort should have the code
results_cohort <- summariseCohortCodeUse(list(pharyngitis = pharyngitis),
cdm = cdm,
cohortTable = "pharyngitis",
timing = "entry",
minCellCount = 0)
results_cohort %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Overall" &
strata_level == "Overall" &
variable_name == "Person count") %>%
dplyr::pull("estimate") ==
CDMConnector::cohortCount(cdm$pharyngitis) %>%
dplyr::pull("number_subjects")
# 260139
# on index
index_260139 <- cdm$pharyngitis %>%
dplyr::left_join(cdm$condition_occurrence,
by=c("subject_id"="person_id")) %>%
dplyr::filter(condition_start_date == cohort_start_date) %>%
dplyr::filter(condition_concept_id == 260139) %>%
dplyr::select("subject_id") %>%
dplyr::distinct() %>%
dplyr::count() %>%
dplyr::pull()
results_cohort_260139 <- summariseCohortCodeUse(list(cs = 260139),
cdm = cdm,
cohortTable = "pharyngitis",
timing = "entry",
minCellCount = 0)
expect_equal(results_cohort_260139 %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Overall" &
strata_level == "Overall" &
variable_name == "Person count") %>%
dplyr::pull("estimate"), index_260139)
# 260139 or 19133873 or 1127433
# on index
index_260139_19133873_1127433 <- dplyr::union_all(
cdm$pharyngitis %>%
dplyr::left_join(cdm$condition_occurrence,
by=c("subject_id"="person_id")) %>%
dplyr::filter(condition_start_date == cohort_start_date) %>%
dplyr::filter(condition_concept_id == 260139) %>%
dplyr::select("subject_id"),
cdm$pharyngitis %>%
dplyr::left_join(cdm$drug_exposure,
by=c("subject_id"="person_id")) %>%
dplyr::filter(drug_exposure_start_date == cohort_start_date) %>%
dplyr::filter(drug_concept_id %in% c(19133873,1127433)) %>%
dplyr::select("subject_id")) %>%
dplyr::count() %>%
dplyr::pull()
results_cohort_260139_19133873_1127433<- summariseCohortCodeUse(list(cs = c(260139,19133873,1127433)),
cdm = cdm,
cohortTable = "pharyngitis",
timing = "entry",
minCellCount = 0)
expect_equal(results_cohort_260139_19133873_1127433 %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Overall" &
strata_level == "Overall" &
variable_name == "Record count") %>%
dplyr::pull("estimate"),
index_260139_19133873_1127433)
expect_equal(results_cohort_260139_19133873_1127433 %>%
dplyr::filter(stringr::str_detect(group_level, "Acute bronchitis")) %>%
dplyr::filter(strata_name == "Overall" &
strata_level == "Overall" &
variable_name == "Person count") %>%
dplyr::pull("estimate"),
index_260139)
# multiple cohorts
cdm <- CDMConnector::generateConceptCohortSet(cdm = cdm,
conceptSet = list(a = 260139,
b = 1127433 ),
name = "cohorts",
end = "observation_period_end_date",
overwrite = TRUE)
results_cohort_mult <- summariseCohortCodeUse(list(cs = c(260139,19133873,1127433)),
cdm = cdm,
cohortTable = "cohorts",
timing = "entry",
minCellCount = 0)
expect_true(nrow(results_cohort_mult %>%
dplyr::filter(stringr::str_detect(group_level, "Acute bronchitis")) %>%
dplyr::filter(strata_name == "Overall" &
strata_level == "Overall" &
variable_name == "Person count")) == 2)
expect_equal(c("a", "b"), results_cohort_mult %>%
dplyr::filter(stringr::str_detect(group_level, "Acute bronchitis")) %>%
dplyr::filter(strata_name == "Overall" &
strata_level == "Overall" &
variable_name == "Person count") %>%
dplyr::pull("cohort_name"))
# empty cohort - no results
cdm$pharyngitis <- cdm$pharyngitis %>%
dplyr::filter(cohort_definition_id == 99)
expect_true(nrow(summariseCohortCodeUse(list(cs = 4134304),
cdm = cdm,
cohortTable = "pharyngitis",
timing = "any", minCellCount = 0)) == 0)
# expected errors
expect_error(summariseCohortCodeUse(4134304,
cdm = cdm,
cohortTable = "not_a_cohort",
timing = "any"))
expect_error(summariseCohortCodeUse(list(4134304),
cdm = cdm,
cohortTable = "not_a_cohort",
timing = "any"))
expect_error(summariseCohortCodeUse(list(cs = 4134304),
cdm = cdm,
cohortTable = "not_a_cohort",
timing = "any"))
expect_error(summariseCohortCodeUse(list(cs = 4134304),
cdm = cdm,
cohortTable = "pharyngitis",
timing = "not_a_option"))
expect_error(summariseCohortCodeUse(list(cs = 4134304),
cdm = cdm,
cohortTable = "pharyngitis",
timing = c("any", "entry")))
CDMConnector::cdmDisconnect(cdm)
})
test_that("summarise code use - redshift", {
testthat::skip_if(Sys.getenv("CDM5_REDSHIFT_DBNAME") == "")
db <- DBI::dbConnect(RPostgres::Redshift(),
dbname = Sys.getenv("CDM5_REDSHIFT_DBNAME"),
host = Sys.getenv("CDM5_REDSHIFT_HOST"),
port = Sys.getenv("CDM5_REDSHIFT_PORT"),
user = Sys.getenv("CDM5_REDSHIFT_USER"),
password = Sys.getenv("CDM5_REDSHIFT_PASSWORD"))
cdm <- CDMConnector::cdm_from_con(con = db,
cdm_schema = Sys.getenv("CDM5_REDSHIFT_CDM_SCHEMA"),
write_schema = Sys.getenv("CDM5_REDSHIFT_SCRATCH_SCHEMA"))
asthma <- list(asthma = c(317009, 257581))
results <- summariseCodeUse(asthma,
cdm = cdm,
byYear = TRUE,
bySex = TRUE,
ageGroup = list(c(0,17),
c(18,65),
c(66, 100)))
# column names
expect_true(tibble::is_tibble(results))
expect_true(all(colnames(results) %in%
c("group_name", "group_level",
"strata_name", "strata_level",
"variable_name", "variable_level",
"variable_type",
"estimate_type", "estimate",
"estimate_suppressed",
"standard_concept_name",
"standard_concept_id",
"source_concept_name",
"source_concept_id",
"domain_id",
"codelist_name",
"cohort_name")
))
# overall record count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Overall" &
strata_level == "Overall",
variable_name == "Record count") %>%
dplyr::pull("estimate") ==
cdm$condition_occurrence %>%
dplyr::filter(condition_concept_id %in% !!asthma[[1]]) %>%
dplyr::tally() %>%
dplyr::pull("n"))
# overall person count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Overall" &
strata_level == "Overall" &
variable_name == "Person count") %>%
dplyr::pull("estimate") ==
cdm$condition_occurrence %>%
dplyr::filter(condition_concept_id %in% !!asthma[[1]]) %>%
dplyr::select("person_id") %>%
dplyr::distinct() %>%
dplyr::tally() %>%
dplyr::pull("n"))
# by year
# overall record count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Year" &
strata_level == "2008",
variable_name == "Record count") %>%
dplyr::pull("estimate") ==
cdm$condition_occurrence %>%
dplyr::filter(condition_concept_id %in% !!asthma[[1]]) %>%
dplyr::filter(year(condition_start_date) == 2008) %>%
dplyr::tally() %>%
dplyr::pull("n"))
# overall person count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Year" &
strata_level == "2008",
variable_name == "Person count") %>%
dplyr::pull("estimate") ==
cdm$condition_occurrence %>%
dplyr::filter(condition_concept_id %in% !!asthma[[1]]) %>%
dplyr::filter(year(condition_start_date) == 2008) %>%
dplyr::select("person_id") %>%
dplyr::distinct() %>%
dplyr::tally() %>%
dplyr::pull("n"))
# by age group and sex
# overall record count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Sex" &
strata_level == "Male",
variable_name == "Record count") %>%
dplyr::pull("estimate") ==
cdm$condition_occurrence %>%
dplyr::filter(condition_concept_id %in% !!asthma[[1]]) %>%
PatientProfiles::addSex(cdm) %>%
dplyr::filter(sex == "Male") %>%
dplyr::tally() %>%
dplyr::pull("n"))
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Age group and sex" &
strata_level == "18 to 65 and Male",
variable_name == "Record count") %>%
dplyr::pull("estimate") ==
cdm$condition_occurrence %>%
dplyr::filter(condition_concept_id %in% !!asthma[[1]]) %>%
PatientProfiles::addAge(cdm,
indexDate = "condition_start_date") %>%
PatientProfiles::addSex(cdm) %>%
dplyr::filter(sex == "Male" &
age >= "18" &
age <= "65") %>%
dplyr::tally() %>%
dplyr::pull("n"))
# overall person count
expect_true(results %>%
dplyr::filter(group_name == "Codelist" &
strata_name == "Age group and sex" &
strata_level == "18 to 65 and Male",
variable_name == "Person count") %>%
dplyr::pull("estimate") ==
cdm$condition_occurrence %>%
dplyr::filter(condition_concept_id %in% !!asthma[[1]]) %>%
PatientProfiles::addAge(cdm,
indexDate = "condition_start_date") %>%
PatientProfiles::addSex(cdm) %>%
dplyr::filter(sex == "Male" &
age >= "18" &
age <= "65") %>%
dplyr::select("person_id") %>%
dplyr::distinct() %>%
dplyr::tally() %>%
dplyr::pull("n"))
results <- summariseCodeUse(asthma,
cdm = cdm, countBy = "person",
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL)
expect_true(nrow(results %>%
dplyr::filter(variable_name == "Person count")) > 0)
expect_true(nrow(results %>%
dplyr::filter(variable_name == "Record count")) == 0)
results <- summariseCodeUse(asthma,
cdm = cdm, countBy = "record",
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL)
expect_true(nrow(results %>%
dplyr::filter(variable_name == "Person count")) == 0)
expect_true(nrow(results %>%
dplyr::filter(variable_name == "Record count")) > 0)
# check min cell count
results <- summariseCodeUse(asthma,
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL,
minCellCount = 75)
expect_true(max(results$estimate, na.rm = TRUE) >=75)
# domains covered
# condition
expect_true(nrow(summariseCodeUse(list(cs = c(317009)),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# visit
expect_true(nrow(summariseCodeUse(list(cs = 9201),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# drug
expect_true(nrow(summariseCodeUse(list(cs = 19071493),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# measurement
expect_true(nrow(summariseCodeUse(list(cs = 2212542),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# procedure and condition
expect_true(nrow(summariseCodeUse(list(cs = c(4261206,317009)),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))>1)
# no records
expect_message(results <- summariseCodeUse(list(cs = c(999999)),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))
expect_true(nrow(results) == 0)
# expected errors
expect_error(summariseCodeUse(list(cs = "not a concept"),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))
expect_error(summariseCodeUse(list(cs = 123),
cdm = "not a cdm",
byYear = FALSE,
bySex = FALSE,
ageGroup = NULL))
expect_error(summariseCodeUse(list(cs = 123),
cdm = cdm,
byYear = "Maybe",
bySex = FALSE,
ageGroup = NULL))
expect_error(summariseCodeUse(list(cs = 123),
cdm = cdm,
byYear = FALSE,
bySex = "Maybe",
ageGroup = NULL))
expect_error(summariseCodeUse(list(cs = 123),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = 25))
expect_error(summariseCodeUse(list(cs = 123),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = list(c(18,17))))
expect_error(summariseCodeUse(list(cs = 123),
cdm = cdm,
byYear = FALSE,
bySex = FALSE,
ageGroup = list(c(0,17),
c(15,20))))
CDMConnector::cdmDisconnect(cdm)
})
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