tests/testthat/test-timeline.R
In ramses-antibiotics/ramses-package: R Package for Antimicrobial Stewardship & Surveillance
test_that(".therapy_timeline_get_diagnoses (merge diagnoses)", {
db_conn <- DBI::dbConnect(duckdb::duckdb(), ":memory:", timezone_out = "UTC")
on.exit({DBI::dbDisconnect(db_conn, shutdown = TRUE)})
patients <- dplyr::tibble(patient_id = 99)
encounters <- dplyr::tibble(
patient_id = 99, encounter_id = 99,
admission_method = "2",
admission_date = structure(1438684036, tzone = "Europe/London", class = c("POSIXct", "POSIXt")),
discharge_date = structure(1439380488, tzone = "Europe/London", class = c("POSIXct", "POSIXt")),
episode_number = 1:5, last_episode_in_encounter = c("2", "2", "2", "2", "1"),
episode_start = structure(c(1438684036, 1438858149, 1439032262, 1439206375, 1439380488), tzone = "Europe/London", class = c("POSIXct", "POSIXt")),
episode_end = structure(c(1438858149, 1439032262, 1439206375, 1439380488, 1439380488), tzone = "Europe/London", class = c("POSIXct", "POSIXt"))
)
dplyr::copy_to(db_conn, patients, temporary = FALSE)
dplyr::copy_to(db_conn, encounters, name = "inpatient_episodes", temporary = FALSE)
expect_warning(
expect_equal(
.therapy_timeline_get_diagnoses(Patient(db_conn, 99)),
data.frame()
),
"^The following tables are missing from the Ramses database:"
)
load_inpatient_diagnoses(
conn = db_conn,
diagnoses_data = dplyr::tibble(
patient_id = 99,
encounter_id = 99,
episode_number = 1L,
icd_code = "N390",
diagnosis_position = 2L
),
diagnoses_lookup = dplyr::tibble(
icd_code = "N390", icd_display = "N39.0",
icd_description = "Urinary tract infection, site not specified",
category_code = "N39",
category_description = "Other disorders of urinary system"
)
)
expect_equal(
.therapy_timeline_get_diagnoses(Patient(db_conn, 99)),
data.frame(
id = NA,
content = "N39.0 – Urinary tract infection, site not specified",
title = "Urinary tract infection, site not specified",
start = structure(1438684036, class = c("POSIXct", "POSIXt"), tzone = "UTC"),
end = structure(1438858149, class = c("POSIXct", "POSIXt"), tzone = "UTC"),
group = 2, subgroup = "u03", type = "range",
style = "background-color: #97e2f8", className = "",
stringsAsFactors = FALSE
)
)
load_inpatient_diagnoses(
conn = db_conn,
diagnoses_data = dplyr::tibble(
patient_id = 99,
encounter_id = 99,
episode_number = c(1L, 3L, 4L),
icd_code = "N390",
diagnosis_position = 2L
),
diagnoses_lookup = dplyr::tibble(
icd_code = "N390", icd_display = "N39.0",
icd_description = "Urinary tract infection, site not specified",
category_code = "N39",
category_description = "Other disorders of urinary system"
),
overwrite = TRUE
)
expect_equal(
.therapy_timeline_get_diagnoses(Patient(db_conn, 99)),
data.frame(
id = NA,
content = "N39.0 – Urinary tract infection, site not specified",
title = "Urinary tract infection, site not specified",
start = structure(c(1438684036, 1439032262), class = c("POSIXct", "POSIXt"), tzone = "UTC"),
end = structure(c(1438858149, 1439380488), class = c("POSIXct", "POSIXt"), tzone = "UTC"),
group = 2, subgroup = "u03", type = "range",
style = "background-color: #97e2f8", className = "",
stringsAsFactors = FALSE
)
)
})
test_that(".therapy_timeline_get_diagnoses (use additional dates)", {
db_conn <- DBI::dbConnect(duckdb::duckdb(), ":memory:", timezone_out = "UTC")
on.exit({DBI::dbDisconnect(db_conn, shutdown = TRUE)})
patients <- dplyr::tibble(patient_id = 99)
encounters <- dplyr::tibble(
patient_id = 99, encounter_id = 99,
admission_method = "2",
admission_date = structure(1438684036, tzone = "Europe/London", class = c("POSIXct", "POSIXt")),
discharge_date = structure(1439380488, tzone = "Europe/London", class = c("POSIXct", "POSIXt")),
episode_number = 1:5, last_episode_in_encounter = c("2", "2", "2", "2", "1"),
episode_start = structure(c(1438684036, 1438858149, 1439032262, 1439206375, 1439380488), tzone = "Europe/London", class = c("POSIXct", "POSIXt")),
episode_end = structure(c(1438858149, 1439032262, 1439206375, 1439380488, 1439380488), tzone = "Europe/London", class = c("POSIXct", "POSIXt"))
)
dplyr::copy_to(db_conn, patients, temporary = FALSE)
dplyr::copy_to(db_conn, encounters, name = "inpatient_episodes", temporary = FALSE)
expect_warning(
expect_equal(
.therapy_timeline_get_diagnoses(Patient(db_conn, 99)),
data.frame()
),
"^The following tables are missing from the Ramses database:"
)
load_inpatient_diagnoses(
conn = db_conn,
diagnoses_data = dplyr::tibble(
patient_id = 99,
encounter_id = 99,
episode_number = 1L,
icd_code = "N390",
diagnosis_position = 2L,
diagnosis_start = structure(1438682036, tzone = "Europe/London", class = c("POSIXct", "POSIXt")),
diagnosis_end = structure(1438683036, tzone = "Europe/London", class = c("POSIXct", "POSIXt"))
),
diagnoses_lookup = dplyr::tibble(
icd_code = "N390", icd_display = "N39.0",
icd_description = "Urinary tract infection, site not specified",
category_code = "N39",
category_description = "Other disorders of urinary system"
)
)
expect_equal(
.therapy_timeline_get_diagnoses(Patient(db_conn, 99)),
data.frame(
id = NA,
content = "N39.0 – Urinary tract infection, site not specified",
title = "Urinary tract infection, site not specified",
start = structure(c(1438682036), class = c("POSIXct", "POSIXt"), tzone = "UTC"),
end = structure(c(1438683036), class = c("POSIXct", "POSIXt"), tzone = "UTC"),
group = 2, subgroup = "u03", type = "range",
style = "background-color: #97e2f8", className = "",
stringsAsFactors = FALSE
)
)
# missing diagnosis_end
load_inpatient_diagnoses(
conn = db_conn,
diagnoses_data = dplyr::tibble(
patient_id = 99,
encounter_id = 99,
episode_number = 1L,
icd_code = "N390",
diagnosis_position = 2L,
diagnosis_start = structure(1438682036, tzone = "Europe/London", class = c("POSIXct", "POSIXt"))
),
diagnoses_lookup = dplyr::tibble(
icd_code = "N390", icd_display = "N39.0",
icd_description = "Urinary tract infection, site not specified",
category_code = "N39",
category_description = "Other disorders of urinary system"
),
overwrite = TRUE
)
expect_equal(
.therapy_timeline_get_diagnoses(Patient(db_conn, 99)),
data.frame(
id = NA,
content = "N39.0 – Urinary tract infection, site not specified",
title = "Urinary tract infection, site not specified",
start = structure(c(1438684036), class = c("POSIXct", "POSIXt"), tzone = "UTC"),
end = structure(c(1438858149), class = c("POSIXct", "POSIXt"), tzone = "UTC"),
group = 2, subgroup = "u03", type = "range",
style = "background-color: #97e2f8", className = "",
stringsAsFactors = FALSE
)
)
})
test_that(".therapy_timeline_get_admissions", {
db_conn <- DBI::dbConnect(duckdb::duckdb(), ":memory:", timezone_out = "UTC")
on.exit({DBI::dbDisconnect(db_conn, shutdown = TRUE)})
patients <- dplyr::tibble(patient_id = 99,
date_of_birth = structure(-1248, class = "Date"),
date_of_death = structure(NA_real_, class = "Date"))
dplyr::copy_to(db_conn, patients, temporary = FALSE)
expect_warning(
expect_equal(
.therapy_timeline_get_admissions(Patient(db_conn, 99)),
data.frame()
),
"^The following tables are missing from the Ramses database:"
)
load_inpatient_episodes(
conn = db_conn,
patients_data = patients,
episodes_data = dplyr::tibble(
patient_id = 99,
encounter_id = 99,
admission_method = "2",
admission_date = structure(1438684036, tzone = "UTC", class = c("POSIXct", "POSIXt")),
discharge_date = structure(1439380488, tzone = "UTC", class = c("POSIXct", "POSIXt")),
episode_number = 1L,
last_episode_in_encounter = 2,
episode_start = structure(1438684036, tzone = "UTC", class = c("POSIXct", "POSIXt")),
episode_end = structure(1438858149, tzone = "UTC", class = c("POSIXct", "POSIXt")),
consultant_code = "C3400039",
main_specialty_code = "340"
),
overwrite = TRUE
)
expect_equal(
.therapy_timeline_get_admissions(Patient(db_conn, 99)),
data.frame(
id = NA_character_,
content = "Emergency admission",
start = structure(1438684036, class = c("POSIXct", "POSIXt"), tzone = "UTC"),
end = structure(1439380488, class = c("POSIXct", "POSIXt"), tzone = "UTC"),
type = "background", className = "admission-emergency",
stringsAsFactors = FALSE
)
)
})
test_that("therapy_timeline No drugs data", {
db_conn <- DBI::dbConnect(duckdb::duckdb(), ":memory:", timezone_out = "UTC")
on.exit({DBI::dbDisconnect(db_conn, shutdown = TRUE)})
patients <- dplyr::tibble(patient_id = 99,
date_of_birth = structure(-1248, class = "Date"),
date_of_death = structure(NA_real_, class = "Date"))
dplyr::copy_to(db_conn, patients, temporary = FALSE)
expect_error(
therapy_timeline(Patient(db_conn, 99)),
"^The Ramses database must contain a valid `drug_prescriptions` table."
)
})
test_that(".therapy_timeline_get_micro", {
db_conn <- DBI::dbConnect(duckdb::duckdb(), ":memory:", timezone_out = "UTC")
on.exit({DBI::dbDisconnect(db_conn, shutdown = TRUE)})
patients <- dplyr::tibble(patient_id = 99,
date_of_birth = structure(-1248, class = "Date"),
date_of_death = structure(NA_real_, class = "Date"))
dplyr::copy_to(db_conn, patients, temporary = FALSE)
expect_warning(
expect_equal(
.therapy_timeline_get_micro(Patient(db_conn, 99)),
data.frame()
),
"^The following tables are missing from the Ramses database:"
)
load_inpatient_microbiology(
conn = db_conn,
specimens = dplyr::tibble(
specimen_id = "CCC2",
patient_id = 99,
status = "available",
specimen_datetime = structure(1487030400, class = c("POSIXct", "POSIXt"), tzone = "UTC"),
specimen_type_code = "697989009",
specimen_type_name = "Anterior nares swab",
specimen_type_display = "MRSA Screen"
),
isolates = dplyr::tibble(
isolate_id = "2300967",
specimen_id = "CCC2",
patient_id = 99,
organism_code = NA_character_,
organism_name = NA_character_,
organism_display_name = "No growth",
isolation_datetime = structure(1487289600, class = c("POSIXct", "POSIXt"), tzone = "UTC")
),
susceptibilities = dplyr::tibble(
isolate_id = character(0), specimen_id = character(0),
patient_id = numeric(0), organism_code = character(0),
organism_name = character(0), organism_display_name = character(0),
agent_code = character(0), agent_name = character(0),
agent_display_name = character(0),
rsi_code = character(0), concept_code = character(0)
)
)
expect_equal(
.therapy_timeline_get_micro(Patient(db_conn, 99)),
dplyr::tibble(
specimen_id = "CCC2",
className = "micro-report-no-growth",
id = "Specimen ID:CCC2:report",
start = structure(1487289600, tzone = "UTC", class = c("POSIXct", "POSIXt")),
title = "MRSA Screen\nOrganisms: No growth\nSample received: 2017-02-14",
type = "point", group = 1, subgroup = "micro"
)
)
})
ramses-antibiotics/ramses-package documentation built on Feb. 13, 2024, 1:01 p.m.
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test_that(".therapy_timeline_get_diagnoses (merge diagnoses)", {
db_conn <- DBI::dbConnect(duckdb::duckdb(), ":memory:", timezone_out = "UTC")
on.exit({DBI::dbDisconnect(db_conn, shutdown = TRUE)})
patients <- dplyr::tibble(patient_id = 99)
encounters <- dplyr::tibble(
patient_id = 99, encounter_id = 99,
admission_method = "2",
admission_date = structure(1438684036, tzone = "Europe/London", class = c("POSIXct", "POSIXt")),
discharge_date = structure(1439380488, tzone = "Europe/London", class = c("POSIXct", "POSIXt")),
episode_number = 1:5, last_episode_in_encounter = c("2", "2", "2", "2", "1"),
episode_start = structure(c(1438684036, 1438858149, 1439032262, 1439206375, 1439380488), tzone = "Europe/London", class = c("POSIXct", "POSIXt")),
episode_end = structure(c(1438858149, 1439032262, 1439206375, 1439380488, 1439380488), tzone = "Europe/London", class = c("POSIXct", "POSIXt"))
)
dplyr::copy_to(db_conn, patients, temporary = FALSE)
dplyr::copy_to(db_conn, encounters, name = "inpatient_episodes", temporary = FALSE)
expect_warning(
expect_equal(
.therapy_timeline_get_diagnoses(Patient(db_conn, 99)),
data.frame()
),
"^The following tables are missing from the Ramses database:"
)
load_inpatient_diagnoses(
conn = db_conn,
diagnoses_data = dplyr::tibble(
patient_id = 99,
encounter_id = 99,
episode_number = 1L,
icd_code = "N390",
diagnosis_position = 2L
),
diagnoses_lookup = dplyr::tibble(
icd_code = "N390", icd_display = "N39.0",
icd_description = "Urinary tract infection, site not specified",
category_code = "N39",
category_description = "Other disorders of urinary system"
)
)
expect_equal(
.therapy_timeline_get_diagnoses(Patient(db_conn, 99)),
data.frame(
id = NA,
content = "N39.0 – Urinary tract infection, site not specified",
title = "Urinary tract infection, site not specified",
start = structure(1438684036, class = c("POSIXct", "POSIXt"), tzone = "UTC"),
end = structure(1438858149, class = c("POSIXct", "POSIXt"), tzone = "UTC"),
group = 2, subgroup = "u03", type = "range",
style = "background-color: #97e2f8", className = "",
stringsAsFactors = FALSE
)
)
load_inpatient_diagnoses(
conn = db_conn,
diagnoses_data = dplyr::tibble(
patient_id = 99,
encounter_id = 99,
episode_number = c(1L, 3L, 4L),
icd_code = "N390",
diagnosis_position = 2L
),
diagnoses_lookup = dplyr::tibble(
icd_code = "N390", icd_display = "N39.0",
icd_description = "Urinary tract infection, site not specified",
category_code = "N39",
category_description = "Other disorders of urinary system"
),
overwrite = TRUE
)
expect_equal(
.therapy_timeline_get_diagnoses(Patient(db_conn, 99)),
data.frame(
id = NA,
content = "N39.0 – Urinary tract infection, site not specified",
title = "Urinary tract infection, site not specified",
start = structure(c(1438684036, 1439032262), class = c("POSIXct", "POSIXt"), tzone = "UTC"),
end = structure(c(1438858149, 1439380488), class = c("POSIXct", "POSIXt"), tzone = "UTC"),
group = 2, subgroup = "u03", type = "range",
style = "background-color: #97e2f8", className = "",
stringsAsFactors = FALSE
)
)
})
test_that(".therapy_timeline_get_diagnoses (use additional dates)", {
db_conn <- DBI::dbConnect(duckdb::duckdb(), ":memory:", timezone_out = "UTC")
on.exit({DBI::dbDisconnect(db_conn, shutdown = TRUE)})
patients <- dplyr::tibble(patient_id = 99)
encounters <- dplyr::tibble(
patient_id = 99, encounter_id = 99,
admission_method = "2",
admission_date = structure(1438684036, tzone = "Europe/London", class = c("POSIXct", "POSIXt")),
discharge_date = structure(1439380488, tzone = "Europe/London", class = c("POSIXct", "POSIXt")),
episode_number = 1:5, last_episode_in_encounter = c("2", "2", "2", "2", "1"),
episode_start = structure(c(1438684036, 1438858149, 1439032262, 1439206375, 1439380488), tzone = "Europe/London", class = c("POSIXct", "POSIXt")),
episode_end = structure(c(1438858149, 1439032262, 1439206375, 1439380488, 1439380488), tzone = "Europe/London", class = c("POSIXct", "POSIXt"))
)
dplyr::copy_to(db_conn, patients, temporary = FALSE)
dplyr::copy_to(db_conn, encounters, name = "inpatient_episodes", temporary = FALSE)
expect_warning(
expect_equal(
.therapy_timeline_get_diagnoses(Patient(db_conn, 99)),
data.frame()
),
"^The following tables are missing from the Ramses database:"
)
load_inpatient_diagnoses(
conn = db_conn,
diagnoses_data = dplyr::tibble(
patient_id = 99,
encounter_id = 99,
episode_number = 1L,
icd_code = "N390",
diagnosis_position = 2L,
diagnosis_start = structure(1438682036, tzone = "Europe/London", class = c("POSIXct", "POSIXt")),
diagnosis_end = structure(1438683036, tzone = "Europe/London", class = c("POSIXct", "POSIXt"))
),
diagnoses_lookup = dplyr::tibble(
icd_code = "N390", icd_display = "N39.0",
icd_description = "Urinary tract infection, site not specified",
category_code = "N39",
category_description = "Other disorders of urinary system"
)
)
expect_equal(
.therapy_timeline_get_diagnoses(Patient(db_conn, 99)),
data.frame(
id = NA,
content = "N39.0 – Urinary tract infection, site not specified",
title = "Urinary tract infection, site not specified",
start = structure(c(1438682036), class = c("POSIXct", "POSIXt"), tzone = "UTC"),
end = structure(c(1438683036), class = c("POSIXct", "POSIXt"), tzone = "UTC"),
group = 2, subgroup = "u03", type = "range",
style = "background-color: #97e2f8", className = "",
stringsAsFactors = FALSE
)
)
# missing diagnosis_end
load_inpatient_diagnoses(
conn = db_conn,
diagnoses_data = dplyr::tibble(
patient_id = 99,
encounter_id = 99,
episode_number = 1L,
icd_code = "N390",
diagnosis_position = 2L,
diagnosis_start = structure(1438682036, tzone = "Europe/London", class = c("POSIXct", "POSIXt"))
),
diagnoses_lookup = dplyr::tibble(
icd_code = "N390", icd_display = "N39.0",
icd_description = "Urinary tract infection, site not specified",
category_code = "N39",
category_description = "Other disorders of urinary system"
),
overwrite = TRUE
)
expect_equal(
.therapy_timeline_get_diagnoses(Patient(db_conn, 99)),
data.frame(
id = NA,
content = "N39.0 – Urinary tract infection, site not specified",
title = "Urinary tract infection, site not specified",
start = structure(c(1438684036), class = c("POSIXct", "POSIXt"), tzone = "UTC"),
end = structure(c(1438858149), class = c("POSIXct", "POSIXt"), tzone = "UTC"),
group = 2, subgroup = "u03", type = "range",
style = "background-color: #97e2f8", className = "",
stringsAsFactors = FALSE
)
)
})
test_that(".therapy_timeline_get_admissions", {
db_conn <- DBI::dbConnect(duckdb::duckdb(), ":memory:", timezone_out = "UTC")
on.exit({DBI::dbDisconnect(db_conn, shutdown = TRUE)})
patients <- dplyr::tibble(patient_id = 99,
date_of_birth = structure(-1248, class = "Date"),
date_of_death = structure(NA_real_, class = "Date"))
dplyr::copy_to(db_conn, patients, temporary = FALSE)
expect_warning(
expect_equal(
.therapy_timeline_get_admissions(Patient(db_conn, 99)),
data.frame()
),
"^The following tables are missing from the Ramses database:"
)
load_inpatient_episodes(
conn = db_conn,
patients_data = patients,
episodes_data = dplyr::tibble(
patient_id = 99,
encounter_id = 99,
admission_method = "2",
admission_date = structure(1438684036, tzone = "UTC", class = c("POSIXct", "POSIXt")),
discharge_date = structure(1439380488, tzone = "UTC", class = c("POSIXct", "POSIXt")),
episode_number = 1L,
last_episode_in_encounter = 2,
episode_start = structure(1438684036, tzone = "UTC", class = c("POSIXct", "POSIXt")),
episode_end = structure(1438858149, tzone = "UTC", class = c("POSIXct", "POSIXt")),
consultant_code = "C3400039",
main_specialty_code = "340"
),
overwrite = TRUE
)
expect_equal(
.therapy_timeline_get_admissions(Patient(db_conn, 99)),
data.frame(
id = NA_character_,
content = "Emergency admission",
start = structure(1438684036, class = c("POSIXct", "POSIXt"), tzone = "UTC"),
end = structure(1439380488, class = c("POSIXct", "POSIXt"), tzone = "UTC"),
type = "background", className = "admission-emergency",
stringsAsFactors = FALSE
)
)
})
test_that("therapy_timeline No drugs data", {
db_conn <- DBI::dbConnect(duckdb::duckdb(), ":memory:", timezone_out = "UTC")
on.exit({DBI::dbDisconnect(db_conn, shutdown = TRUE)})
patients <- dplyr::tibble(patient_id = 99,
date_of_birth = structure(-1248, class = "Date"),
date_of_death = structure(NA_real_, class = "Date"))
dplyr::copy_to(db_conn, patients, temporary = FALSE)
expect_error(
therapy_timeline(Patient(db_conn, 99)),
"^The Ramses database must contain a valid `drug_prescriptions` table."
)
})
test_that(".therapy_timeline_get_micro", {
db_conn <- DBI::dbConnect(duckdb::duckdb(), ":memory:", timezone_out = "UTC")
on.exit({DBI::dbDisconnect(db_conn, shutdown = TRUE)})
patients <- dplyr::tibble(patient_id = 99,
date_of_birth = structure(-1248, class = "Date"),
date_of_death = structure(NA_real_, class = "Date"))
dplyr::copy_to(db_conn, patients, temporary = FALSE)
expect_warning(
expect_equal(
.therapy_timeline_get_micro(Patient(db_conn, 99)),
data.frame()
),
"^The following tables are missing from the Ramses database:"
)
load_inpatient_microbiology(
conn = db_conn,
specimens = dplyr::tibble(
specimen_id = "CCC2",
patient_id = 99,
status = "available",
specimen_datetime = structure(1487030400, class = c("POSIXct", "POSIXt"), tzone = "UTC"),
specimen_type_code = "697989009",
specimen_type_name = "Anterior nares swab",
specimen_type_display = "MRSA Screen"
),
isolates = dplyr::tibble(
isolate_id = "2300967",
specimen_id = "CCC2",
patient_id = 99,
organism_code = NA_character_,
organism_name = NA_character_,
organism_display_name = "No growth",
isolation_datetime = structure(1487289600, class = c("POSIXct", "POSIXt"), tzone = "UTC")
),
susceptibilities = dplyr::tibble(
isolate_id = character(0), specimen_id = character(0),
patient_id = numeric(0), organism_code = character(0),
organism_name = character(0), organism_display_name = character(0),
agent_code = character(0), agent_name = character(0),
agent_display_name = character(0),
rsi_code = character(0), concept_code = character(0)
)
)
expect_equal(
.therapy_timeline_get_micro(Patient(db_conn, 99)),
dplyr::tibble(
specimen_id = "CCC2",
className = "micro-report-no-growth",
id = "Specimen ID:CCC2:report",
start = structure(1487289600, tzone = "UTC", class = c("POSIXct", "POSIXt")),
title = "MRSA Screen\nOrganisms: No growth\nSample received: 2017-02-14",
type = "point", group = 1, subgroup = "micro"
)
)
})
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