Nothing
skip_on_cran()
test_that("load hirid items", {
skip_if_not_installed("mockthat")
gluc <- mockthat::with_mock(
get_hirid_ids = id_tbl(id = c(20005110L, 24000523L, 24000585L),
unit = rep("mmol/l", 3L)),
as_src_tbl = structure(list(),
class = c("hirid_tbl", "src_tbl"),
col_cfg = new_col_cfg("hirid", "observations", index_var = "datetime",
time_vars = c("datetime", "entertime"),
val_var = "value")
),
parse_dictionary(read_dictionary("concept-dict"), "hirid", "glu")
)
expect_identical(n_tick(gluc), 2L)
gluc <- as_item(gluc)[[1L]]
gluc <- try_add_vars(gluc, id_var = "patientid", index_var = "datetime",
type = "meta_vars")
dat <- mockthat::with_mock(
load_ts = ts_tbl(
patientid = rep(seq_len(2L), each = 10L),
datetime = hours(rep(seq_len(10L), 2L)),
variableid = rep(24000585L, 20L),
value = rnorm(20L)
),
do_itm_load(gluc)
)
expect_s3_class(dat, "ts_tbl")
expect_true(is_ts_tbl(dat))
expect_identical(data_vars(dat), c("variableid", "value", "unit"))
expect_equal(interval(dat), hours(1L))
expect_identical(id_vars(gluc), id_vars(dat))
expect_identical(index_var(gluc), index_var(dat))
expect_identical(meta_vars(gluc), meta_vars(dat))
expect_identical(dat, do_callback(gluc, dat))
})
skip_if_srcs_missing("mimic_demo")
test_that("load concepts", {
gluc <- concept("gluc",
item("mimic_demo", "labevents", "itemid", list(c(50809L, 50931L)))
)
dat1 <- load_concepts(gluc, verbose = FALSE)
expect_s3_class(dat1, "ts_tbl")
expect_true(is_ts_tbl(dat1))
expect_identical(colnames(dat1), c("icustay_id", "charttime", "gluc"))
expect_equal(interval(dat1), hours(1L))
expect_snapshot(print(gluc))
albu <- concept("albu", item("mimic_demo", "labevents", "itemid", 50862L))
glal <- c(albu, gluc)
dat2 <- load_concepts(glal, verbose = FALSE)
expect_setequal(data_vars(dat2), c("gluc", "albu"))
expect_snapshot(print(albu))
expect_snapshot(print(glal))
dat3 <- load_concepts(gluc, merge_data = FALSE, verbose = FALSE)
expect_type(dat3, "list")
expect_length(dat3, 1L)
dat3 <- dat3[[1L]]
expect_true(is_ts_tbl(dat3))
expect_identical(colnames(dat3), c("icustay_id", "charttime", "gluc"))
expect_equal(interval(dat3), hours(1L))
dat4 <- load_concepts(gluc, aggregate = FALSE, merge_data = FALSE,
verbose = FALSE)
expect_type(dat4, "list")
expect_length(dat4, 1L)
dat4 <- dat4[[1L]]
expect_true(is_ts_tbl(dat4))
expect_identical(colnames(dat4), c("icustay_id", "charttime", "gluc"))
expect_gt(nrow(dat4), nrow(dat3))
expect_identical(dat3,
dat4[, list(gluc = median(gluc)), by = c(meta_vars(dat4))]
)
dat5 <- load_concepts(gluc, aggregate = identity, merge_data = FALSE,
verbose = FALSE)
expect_type(dat5, "list")
expect_length(dat5, 1L)
expect_identical(dat4, dat5[[1L]], ignore_attr = TRUE)
expect_error(
load_concepts(gluc, aggregate = "identity", verbose = FALSE)
)
static <- load_concepts(c("sex", "age"), "mimic_demo", verbose = FALSE)
expect_s3_class(static, "id_tbl")
expect_true(is_id_tbl(static))
expect_setequal(colnames(static), c("icustay_id", "sex", "age"))
expect_type(static[["age"]], "double")
expect_type(static[["sex"]], "character")
expect_error(
concept("gluc",
item("mimic_demo", "labevents", "itemid", c(50809L, 50931L))
)
)
gluc2 <- concept("gluc",
list(item("mimic_demo", "labevents", "itemid", c(50809L, 50931L)))
)
dat6 <- load_concepts(gluc2, verbose = FALSE)
expect_identical(dat1, dat6, ignore_attr = TRUE)
gcs_con <- load_dictionary(concepts = "gcs")
gcs_raw <- concept("gcs_raw", gcs_con, sed_impute = "none",
class = "rec_cncpt")
dat7 <- load_concepts(gcs_raw, "mimic_demo", verbose = FALSE)
expect_s3_class(dat7, "ts_tbl")
expect_true(is_ts_tbl(dat7))
expect_identical(colnames(dat7), c("icustay_id", "charttime", "gcs_raw"))
expect_equal(interval(dat7), hours(1L))
expect_snapshot(print(gcs_con))
expect_snapshot(print(gcs_raw))
})
test_that("load concepts", {
dat1 <- load_concepts(4144235L, "mimic_demo", verbose = FALSE)
expect_s3_class(dat1, "ts_tbl")
expect_true(is_ts_tbl(dat1))
expect_identical(colnames(dat1),
c("icustay_id", "charttime", "omop_4144235"))
expect_equal(interval(dat1), hours(1L))
dat2 <- load_concepts(c(4144235, 4017497), "mimic_demo", verbose = FALSE)
expect_s3_class(dat2, "ts_tbl")
expect_true(is_ts_tbl(dat2))
expect_identical(
colnames(dat2),
c("icustay_id", "charttime", "omop_4144235", "omop_4017497")
)
expect_equal(interval(dat2), hours(1L))
expect_warning(
load_concepts(c(4144235, 123), "mimic_demo", verbose = FALSE),
class = "omop_miss_id"
)
})
skip_if_srcs_missing("eicu_demo")
test_that("load concepts multi src", {
ids <- list(eicu_demo = c(141765, 143870),
mimic_demo = c(293280, 298685))
dat <- load_concepts("glu", c("mimic_demo", "eicu_demo"),
patient_ids = ids, verbose = FALSE)
expect_s3_class(dat, "ts_tbl")
expect_true(is_ts_tbl(dat))
expect_length(id_vars(dat), 2L)
uqe <- unique(dat[, id_vars(dat), with = FALSE])
expect_identical(nrow(uqe), 4L)
expect_identical(dat,
load_concepts("glu", c("mimic_demo", "eicu_demo"), patient_ids = uqe,
verbose = FALSE)
)
uqe <- as.data.frame(uqe)
expect_identical(dat,
load_concepts("glu", c("mimic_demo", "eicu_demo"), patient_ids = uqe,
verbose = FALSE)
)
})
test_that("load external dictionary", {
srcs <- c("mimic_demo", "eicu_demo")
conc <- c("age", "alb", "glu", "gcs", "esr", "fgn")
dict <- load_dictionary(srcs, conc)
expect_s3_class(dict, "concept")
expect_length(dict, 6L)
expect_named(dict, conc)
expect_snapshot(print(dict))
itms <- as_item(dict)
expect_s3_class(itms, "item")
expect_length(itms, 21L)
expect_setequal(names(itms), srcs)
expect_snapshot(print(itms))
avail <- concept_availability(dict)
expect_snapshot_value(avail, style = "json2")
expect_snapshot_value(concept_availability(dict, include_rec = TRUE),
style = "json2")
expect_snapshot_value(explain_dictionary(dict), style = "json2")
conc <- c("age", "esr", "fgn", "foo")
extr <- load_dictionary(srcs, conc,
cfg_dirs = system.file("testdata", package = "ricu"))
expect_s3_class(extr, "concept")
expect_length(extr, 4L)
expect_named(extr, conc)
expect_false(avail["esr", "eicu_demo"])
expect_true(concept_availability(extr)["esr", "eicu_demo"])
itms <- as_item(extr["foo"])
expect_s3_class(itms, "item")
expect_length(itms, 2L)
expect_named(itms, srcs, ignore.order = TRUE)
expect_snapshot(print(itms))
itm <- subset_src(as_item(extr["fgn"]), "mimic_demo")
tmp <- item("mimic_demo", "labevents", "itemid", 12345L,
unit_var = "valueuom", target = "ts_tbl")
expect_s3_class(itm, "item")
expect_length(itm, 1L)
expect_named(itm, "mimic_demo")
expect_identical(itm, tmp)
expect_snapshot(print(itm))
})
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