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Load rec args #19

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d25628d
Allow collect_dots to accept non-concepts
prockenschaub Sep 29, 2022
1b57417
Pass arguments to lower-level concepts
prockenschaub Sep 29, 2022
253e418
Use named args in tests to pass
prockenschaub Sep 29, 2022
4a9f169
Remove unneeded keep_components from sep3
prockenschaub Oct 10, 2022
1225437
Merge branch 'main' into load-rec-args
prockenschaub Oct 4, 2023
f582793
Remove unneeded keep_components from sep3
prockenschaub Oct 10, 2022
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30 changes: 3 additions & 27 deletions R/callback-cncpt.R
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Original file line number Diff line number Diff line change
Expand Up @@ -4,37 +4,11 @@ collect_dots <- function(concepts, interval, ..., merge_dat = FALSE) {

dots <- list(...)

if (length(concepts) == 1L) {

assert_that(identical(length(dots), 1L))

res <- dots[[1L]]

if (is_ts_tbl(res)) {
ival <- coalesce(interval, interval(res))
assert_that(has_interval(res, ival))
} else {
assert_that(is_df(res))
}

return(res)
}

if (length(dots) == 1L) {
dots <- dots[[1L]]
}

if (is.null(names(dots))) {
names(dots) <- concepts
}

if (not_null(names(concepts))) {
concepts <- chr_ply(concepts, grep, names(dots), value = TRUE,
use_names = TRUE)
}

assert_that(setequal(names(dots), concepts))

res <- dots[concepts]

assert_that(all_map(has_col, res, concepts))
Expand All @@ -45,7 +19,9 @@ collect_dots <- function(concepts, interval, ..., merge_dat = FALSE) {

ival <- check_interval(res, interval)

if (merge_dat) {
if (length(res) == 1) {
res <- res[[1]]
} else if (merge_dat) {
res <- reduce(merge, res, all = TRUE)
} else {
attr(res, "ival_checked") <- ival
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4 changes: 1 addition & 3 deletions R/concept-load.R
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Expand Up @@ -547,7 +547,7 @@ load_concepts.rec_cncpt <- function(x, aggregate = NULL, patient_ids = NULL,

ext <- list(patient_ids = patient_ids, id_type = id_type,
interval = coalesce(x[["interval"]], interval),
progress = progress)
..., progress = progress)

sub <- x[["items"]]
agg <- x[["aggregate"]]
Expand Down Expand Up @@ -606,8 +606,6 @@ load_concepts.item <- function(x, patient_ids = NULL, id_type = "icustay",
load_concepts.itm <- function(x, patient_ids = NULL, id_type = "icustay",
interval = hours(1L), ...) {

warn_dots(..., ok_args = "keep_components")

res <- do_itm_load(x, id_type, interval = interval)
res <- merge_patid(res, patient_ids)
res <- do_callback(x, res)
Expand Down
1 change: 0 additions & 1 deletion inst/extdata/config/concept-dict.R
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Expand Up @@ -2769,7 +2769,6 @@ cfg <- list(
omopid = 132797L,
category = "outcome",
callback = "sep3",
keep_components = c(FALSE, TRUE),
class = "rec_cncpt"
),
bnd = list(
Expand Down
1 change: 0 additions & 1 deletion inst/extdata/config/concept-dict.json
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Expand Up @@ -5254,7 +5254,6 @@
"omopid": 132797,
"category": "outcome",
"callback": "sep3",
"keep_components": [false, true],
"class": "rec_cncpt"
},
"sex": {
Expand Down
2 changes: 1 addition & 1 deletion tests/testthat/test-callback.R
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Expand Up @@ -272,5 +272,5 @@ test_that("susp_inf", {
57, 61, 70)), susp_inf = rep(TRUE, 6L), interval = hours(1L)
)

expect_identical(susp_inf(abx, samp), expected)
expect_identical(susp_inf(abx = abx, samp = samp), expected)
})
2 changes: 1 addition & 1 deletion tests/testthat/test-scores.R
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Expand Up @@ -42,7 +42,7 @@ test_that("suspicion of infection", {
expect_equal(interval(si_ei), hours(1L))
})

sep3 <- sep3(so_mi, si_mi)
sep3 <- sep3(sofa = so_mi, susp_inf = si_mi)

test_that("sepsis 3", {

Expand Down