Nothing
skip_if_srcs_missing(c("mimic_demo", "eicu_demo"))
test_that("stay windows", {
wins <- stay_windows(c("mimic_demo", "eicu_demo"))
expect_s3_class(wins, "id_tbl")
expect_length(id_vars(wins), 2L)
expect_true("source" %in% id_vars(wins))
expect_setequal(data_vars(wins), c("start", "end"))
skip_if_not_installed("mockthat")
hrd <- mockthat::with_mock(
load_src = function(x, src, ...) {
if (identical(x, "observations")) {
data.table::data.table(
patientid = rep(seq_len(5L), each = 2L),
datetime = as.POSIXct(runif(10L, 1e4, 1e6), origin = "2100-01-01")
)
} else {
data.table::data.table(
patientid = rep(seq_len(5L), each = 2L) + 1L,
admissiontime = as.POSIXct(runif(10L, 0, 1e5), origin = "2100-01-01")
)
}
},
id_windows("hirid")
)
expect_s3_class(hrd, "id_tbl")
expect_identical(nrow(hrd), 8L)
expect_identical(id_vars(hrd), "patientid")
expect_setequal(data_vars(hrd), c("patientid_start", "patientid_end"))
aum <- mockthat::with_mock(
as_src_tbl = function(...) {
data.table::data.table(
patientid = integer(0L), admissionid = integer(0L),
admittedat = numeric(0L), dischargedat = numeric(0L),
dateofdeath = numeric(0L)
)
},
load_src = function(...) {
data.table::data.table(
admissionid = seq_len(10L),
patientid = seq_len(10L),
admittedat = rep(0, 10L),
dischargedat = runif(10L, 1e8, 1e9),
dateofdeath = sample(c(rep(NA_real_, 4L), runif(6L, 1e8, 1e9)))
)
},
id_windows("aumc")
)
expect_s3_class(aum, "id_tbl")
expect_identical(nrow(aum), 10L)
expect_identical(id_vars(aum), "patientid")
expect_setequal(data_vars(aum),
c("admissionid", "admissionid_start", "patientid_start", "admissionid_end",
"patientid_end")
)
})
test_that("id up/downgrades", {
tbl <- as_src_tbl("labevents", "mimic_demo")
alb <- load_ts(tbl, is_val(itemid, 50862L), "value",
"icustay_id", "charttime")
expect_s3_class(alb, "ts_tbl")
tbl <- as_src_tbl("lab", "eicu_demo")
alb <- load_ts(tbl, is_val(labname, "albumin"), "labresult",
"patienthealthsystemstayid", "labresultoffset")
expect_s3_class(alb, "ts_tbl")
tbl <- as_src_tbl("patients", "mimic_demo")
sex <- load_id(tbl, cols = "gender", id_var = "hadm_id")
expect_s3_class(sex, "id_tbl")
})
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