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Finish PICdb integration #16

Merged
merged 8 commits into from
Apr 8, 2024
Merged

Finish PICdb integration #16

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0454bdb
No `ett_gcs`, no `mech_vent`
manuelburger Apr 5, 2024
e04530c
Checked `respiratory`
manuelburger Apr 5, 2024
42dc474
Update `hematology`
manuelburger Apr 5, 2024
047c099
Check `neuro`
manuelburger Apr 5, 2024
866f52b
Add surgery vitals
manuelburger Apr 5, 2024
9a91a7d
WIP picdb `death_icu`
manuelburger Apr 5, 2024
41ed665
`death_icu` implemented
manuelburger Apr 8, 2024
ec237c7
`los_` added
manuelburger Apr 8, 2024
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27 changes: 27 additions & 0 deletions R/callback-icu-mortality.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -61,3 +61,30 @@ miiv_death_icu <- function(x, env, ...){
mi_death_icu(x, transfers, icu_wards, ...)
}

picdb_death_icu <- function(x, env, ...){
#' Extract in-ICU mortality from PICdb
#'
#' We rely on a concept-dict config, which passes rows for each `icustay_id`
#' separately (e.g. the `icustays` table). As this table does not contain mortality
#' information we rely on a auxiliary column defined for all patients in PICdb in
#' the chosen table (e.g. `los`).
#' We extract the last ICU stay for each `hadm_id`. We reset the `los` column to be
#' FALSE for each `icustay_id` and set it to TRUE for the `icustay_id` of the last
#' ICU stay of each `hadm_id`, which is marked as deceased.

icu_stays <- load_ts(env[["icustays"]], id_var = "hadm_id", index_var = "intime", interval = mins(1L))
admissions <- load_id(env[["admissions"]], id_var = "hadm_id", cols = c("hospital_expire_flag"))

# For each "hadm_id" we find the "icustay_id" of the last ICU stay based on the "intime"
last_icu_stay <- icu_stays[, .(icustay_id = icustay_id[.N]), by = hadm_id]
deceased_hadm_id <- admissions[ricu:::is_true(hospital_expire_flag), .(hadm_id)]$hadm_id
deceased_icustay_id <- icu_stays[hadm_id %in% deceased_hadm_id, .(icustay_id)]$icustay_id

# For all `icustay_id` not in last_icu_stay, we set the value of the `hospital_expire_flag` variable to FALSE
# Patients only die in the last ICU stay
# `los` should be configured to be the target extraction column as a dummy column
# to put the value of the `hospital_expire_flag` variable
x[, los := FALSE]
x[icustay_id %in% deceased_icustay_id, los := TRUE]
x[!icustay_id %in% last_icu_stay$icustay_id, los := FALSE]
}
109 changes: 57 additions & 52 deletions inst/extdata/config/concept-dict/hematology.json
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Original file line number Diff line number Diff line change
Expand Up @@ -73,10 +73,14 @@
"picdb": [
{
"table": "labevents",
"ids": [
5492
],
"ids": 5492,
"sub_var": "itemid"
},
{
"table": "labevents",
"ids": 5493,
"sub_var": "itemid",
"callback": "blood_cell_ratio"
}
]
}
Expand Down Expand Up @@ -139,8 +143,7 @@
"table": "labevents",
"sub_var": "itemid"
}
],
"picdb": []
]
}
},
"eos": {
Expand Down Expand Up @@ -217,9 +220,7 @@
"picdb": [
{
"table": "labevents",
"ids": [
5002
],
"ids": 5002,
"sub_var": "itemid"
}
]
Expand Down Expand Up @@ -274,8 +275,7 @@
"table": "labevents",
"sub_var": "itemid"
}
],
"picdb": []
]
}
},
"fgn": {
Expand Down Expand Up @@ -350,7 +350,14 @@
"class": "sic_itm"
}
],
"picdb": []
"picdb": [
{
"table": "labevents",
"ids": 5164,
"sub_var": "itemid",
"callback": "convert_unit(binary_op(`*`, 100), 'mg/dL', 'g/L')"
}
]
}
},
"hba1c": {
Expand Down Expand Up @@ -398,7 +405,13 @@
"class": "sic_itm"
}
],
"picdb": []
"picdb": [
{
"table": "labevents",
"ids": [5628, 6070],
"sub_var": "itemid"
}
]
}
},
"hct": {
Expand Down Expand Up @@ -567,7 +580,8 @@
5099,
5257
],
"sub_var": "itemid"
"sub_var": "itemid",
"callback": "convert_unit(binary_op(`*`, 0.1), 'g/dL', 'g/L')"
}
]
}
Expand Down Expand Up @@ -626,8 +640,7 @@
"table": "labevents",
"sub_var": "itemid"
}
],
"picdb": []
]
}
},
"lymph": {
Expand Down Expand Up @@ -710,7 +723,19 @@
"class": "sic_itm"
}
],
"picdb": []
"picdb": [
{
"table": "labevents",
"ids": [5006, 5503, 5111, 5503],
"sub_var": "itemid"
},
{
"table": "labevents",
"ids": 5110,
"sub_var": "itemid",
"callback": "blood_cell_ratio"
}
]
}
},
"mch": {
Expand Down Expand Up @@ -782,9 +807,7 @@
"picdb": [
{
"table": "labevents",
"ids": [
5113
],
"ids": 5113,
"sub_var": "itemid"
}
]
Expand Down Expand Up @@ -862,10 +885,9 @@
"picdb": [
{
"table": "labevents",
"ids": [
5114
],
"sub_var": "itemid"
"ids": 5114,
"sub_var": "itemid",
"callback": "convert_unit(binary_op(`*`, 0.1), '%')"
}
]
}
Expand Down Expand Up @@ -939,9 +961,7 @@
"picdb": [
{
"table": "labevents",
"ids": [
5115
],
"ids": 5115,
"sub_var": "itemid"
}
]
Expand Down Expand Up @@ -1033,9 +1053,7 @@
"picdb": [
{
"table": "labevents",
"ids": [
5094
],
"ids": [5005, 5094, 5095, 5511],
"sub_var": "itemid"
}
]
Expand Down Expand Up @@ -1118,9 +1136,7 @@
"picdb": [
{
"table": "labevents",
"ids": [
5129
],
"ids": 5129,
"sub_var": "itemid"
}
]
Expand Down Expand Up @@ -1186,11 +1202,9 @@
"picdb": [
{
"table": "labevents",
"ids": [
5186,
6890
],
"sub_var": "itemid"
"ids": [5186, 6890],
"sub_var": "itemid",
"callback": "convert_unit(identity_callback, 'sec')"
}
]
}
Expand Down Expand Up @@ -1263,10 +1277,9 @@
"picdb": [
{
"table": "labevents",
"ids": [
5161
],
"sub_var": "itemid"
"ids": 5161,
"sub_var": "itemid",
"callback": "convert_unit(identity_callback, 'sec')"
}
]
}
Expand Down Expand Up @@ -1336,11 +1349,7 @@
"picdb": [
{
"table": "labevents",
"ids": [
5379,
5381,
6515
],
"ids": 5132,
"sub_var": "itemid"
}
]
Expand Down Expand Up @@ -1399,9 +1408,7 @@
"picdb": [
{
"table": "labevents",
"ids": [
5136
],
"ids": 5136,
"sub_var": "itemid"
}
]
Expand Down Expand Up @@ -1481,9 +1488,7 @@
"picdb": [
{
"table": "labevents",
"ids": [
6516
],
"ids": 5141,
"sub_var": "itemid"
}
]
Expand Down
15 changes: 5 additions & 10 deletions inst/extdata/config/concept-dict/neurological.json
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Original file line number Diff line number Diff line change
Expand Up @@ -76,8 +76,7 @@
"table": "chartevents",
"sub_var": "itemid"
}
],
"picdb": []
]
}
},
"gcs": {
Expand Down Expand Up @@ -170,8 +169,7 @@
"table": "chartevents",
"sub_var": "itemid"
}
],
"picdb": []
]
}
},
"rass": {
Expand Down Expand Up @@ -232,8 +230,7 @@
"table": "chartevents",
"sub_var": "itemid"
}
],
"picdb": []
]
}
},
"tgcs": {
Expand Down Expand Up @@ -270,8 +267,7 @@
"table": "chartevents",
"sub_var": "itemid"
}
],
"picdb": []
]
}
},
"vgcs": {
Expand Down Expand Up @@ -343,8 +339,7 @@
"table": "chartevents",
"sub_var": "itemid"
}
],
"picdb": []
]
}
}
}
34 changes: 32 additions & 2 deletions inst/extdata/config/concept-dict/outcome.json
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -141,6 +141,15 @@
"callback": "transform_fun(comp_na(`==`, 1L))",
"class": "col_itm"
}
],
"picdb": [
{
"table": "admissions",
"index_var": "deathtime",
"val_var": "hospital_expire_flag",
"callback": "transform_fun(comp_na(`==`, 1L))",
"class": "col_itm"
}
]
}
},
Expand Down Expand Up @@ -222,6 +231,15 @@
"callback": "sic_death",
"class": "col_itm"
}
],
"picdb": [
{
"table": "icustays",
"index_var": "intime",
"val_var": "los",
"callback": "picdb_death_icu",
"class": "col_itm"
}
]
}
},
Expand Down Expand Up @@ -297,7 +315,13 @@
"class": "fun_itm"
}
],
"picdb": []
"picdb": [
{
"callback": "los_callback",
"win_type": "hadm",
"class": "fun_itm"
}
]
}
},
"los_icu": {
Expand Down Expand Up @@ -364,7 +388,13 @@
"class": "col_itm"
}
],
"picdb": []
"picdb": [
{
"table": "icustays",
"val_var": "los",
"class": "col_itm"
}
]
}
},
"mews": {
Expand Down
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