From c1206dabedd6655bb98ab9fd2a4ba24b98f4aa37 Mon Sep 17 00:00:00 2001 From: Drago Plecko Date: Tue, 4 Jun 2024 17:32:01 +0200 Subject: [PATCH] ricu 0.6.1 --- DESCRIPTION | 2 +- NEWS.md | 5 ++- inst/extdata/config/data-sources.R | 35 +++++++++++------ inst/extdata/config/data-sources.json | 54 ++++++++++++++++++++++++++- 4 files changed, 82 insertions(+), 14 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index c04c3c3e..400b3a99 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -6,7 +6,7 @@ Description: Focused on (but not exclusive to) data sets hosted on PhysioNet functions for running arbitrary queries against available data sets, a system for defining clinical concepts and encoding their representations in tabular ICU data is presented. -Version: 0.6.0 +Version: 0.6.1 Authors@R: c( person(given = "Nicolas", family = "Bennett", diff --git a/NEWS.md b/NEWS.md index b0dda77e..a05dfed1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# ricu 0.6.1 + +* fixing the data-sources specification for MIMIC-IV (`miiv`) + # ricu 0.6.0 * Salzburg database (SICdb, `sic` in `ricu`) added as a data source with 64 concepts available @@ -7,7 +11,6 @@ # ricu 0.5.6 * maintenance release: fixes non-character numeric version input issues ->>>>>>> 3c72261c4f049b49e7040a588b28eeb974a2f177 # ricu 0.5.5 diff --git a/inst/extdata/config/data-sources.R b/inst/extdata/config/data-sources.R index 1a578b1e..fcf5963d 100644 --- a/inst/extdata/config/data-sources.R +++ b/inst/extdata/config/data-sources.R @@ -831,7 +831,8 @@ miiv_tbl_cfg <- function() { ethnicity = list(spec = "col_character"), edregtime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"), edouttime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"), - hospital_expire_flag = list(spec = "col_integer") + hospital_expire_flag = list(spec = "col_integer"), + admit_provider_id = list(spec = "col_character") ), patients = list( subject_id = list(spec = "col_integer"), @@ -935,7 +936,8 @@ miiv_tbl_cfg <- function() { medication = list(spec = "col_character"), event_txt = list(spec = "col_character"), scheduletime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"), - storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S") + storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"), + enter_provider_id = list(spec = "col_character") ), hcpcsevents = list( subject_id = list(spec = "col_integer"), @@ -960,7 +962,8 @@ miiv_tbl_cfg <- function() { ref_range_upper = list(spec = "col_double"), flag = list(spec = "col_character"), priority = list(spec = "col_character"), - comments = list(spec = "col_character") + comments = list(spec = "col_character"), + order_provider_id = list(spec = "col_character") ), microbiologyevents = list( microevent_id = list(spec = "col_integer"), @@ -986,7 +989,8 @@ miiv_tbl_cfg <- function() { dilution_comparison = list(spec = "col_character"), dilution_value = list(spec = "col_double"), interpretation = list(spec = "col_character"), - comments = list(spec = "col_character") + comments = list(spec = "col_character"), + order_provider_id = list(spec = "col_character") ), pharmacy = list( subject_id = list(spec = "col_integer"), @@ -1036,7 +1040,8 @@ miiv_tbl_cfg <- function() { transaction_type = list(spec = "col_character"), discontinue_of_poe_id = list(spec = "col_character"), discontinued_by_poe_id = list(spec = "col_character"), - order_status = list(spec = "col_character") + order_status = list(spec = "col_character"), + order_provider_id = list(spec = "col_character") ), prescriptions = list( subject_id = list(spec = "col_integer"), @@ -1055,7 +1060,9 @@ miiv_tbl_cfg <- function() { form_val_disp = list(spec = "col_character"), form_unit_disp = list(spec = "col_character"), doses_per_24_hrs = list(spec = "col_double"), - route = list(spec = "col_character") + route = list(spec = "col_character"), + order_provider_id = list(spec = "col_character"), + formulary_drug_cd = list(spec = "col_character") ), procedures_icd = list( subject_id = list(spec = "col_integer"), @@ -1082,7 +1089,8 @@ miiv_tbl_cfg <- function() { value = list(spec = "col_character"), valuenum = list(spec = "col_double"), valueuom = list(spec = "col_character"), - warning = list(spec = "col_integer") + warning = list(spec = "col_integer"), + caregiver_id = list(spec = "col_integer") ), datetimeevents = list( subject_id = list(spec = "col_integer"), @@ -1093,7 +1101,8 @@ miiv_tbl_cfg <- function() { itemid = list(spec = "col_integer"), value = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"), valueuom = list(spec = "col_character"), - warning = list(spec = "col_integer") + warning = list(spec = "col_integer"), + caregiver_id = list(spec = "col_integer") ), d_items = list( itemid = list(spec = "col_integer"), @@ -1120,6 +1129,7 @@ miiv_tbl_cfg <- function() { subject_id = list(spec = "col_integer"), hadm_id = list(spec = "col_integer"), stay_id = list(spec = "col_integer"), + caregiver_id = list(spec = "col_integer"), starttime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"), endtime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"), storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"), @@ -1152,7 +1162,8 @@ miiv_tbl_cfg <- function() { storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"), itemid = list(spec = "col_integer"), value = list(spec = "col_double"), - valueuom = list(spec = "col_character") + valueuom = list(spec = "col_character"), + caregiver_id = list(spec = "col_integer") ), procedureevents = list( subject_id = list(spec = "col_integer"), @@ -1181,7 +1192,8 @@ miiv_tbl_cfg <- function() { comments_date = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"), originalamount = list(spec = "col_double"), - originalrate = list(spec = "col_double") + originalrate = list(spec = "col_double"), + caregiver_id = list(spec = "col_integer") ), omr = list( subject_id = list(spec = "col_integer"), @@ -1200,6 +1212,7 @@ miiv_tbl_cfg <- function() { subject_id = list(spec = "col_integer"), hadm_id = list(spec = "col_integer"), stay_id = list(spec = "col_integer"), + caregiver_id = list(spec = "col_integer"), starttime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"), endtime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"), storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"), @@ -1406,7 +1419,7 @@ miiv_tbl_cfg <- function() { outputevents = "icu/outputevents.csv.gz", procedureevents = "icu/procedureevents.csv.gz", omr = "hosp/omr.csv.gz", - caregiver = "hosp/caregiver.csv.gz", + caregiver = "icu/caregiver.csv.gz", provider = "hosp/provider.csv.gz", ingredientevents = "icu/ingredientevents.csv.gz" ) diff --git a/inst/extdata/config/data-sources.json b/inst/extdata/config/data-sources.json index ff8f94f3..e31b3232 100644 --- a/inst/extdata/config/data-sources.json +++ b/inst/extdata/config/data-sources.json @@ -7136,6 +7136,10 @@ "hospital_expire_flag": { "name": "hospital_expire_flag", "spec": "col_integer" + }, + "admit_provider_id": { + "name": "admit_provider_id", + "spec": "col_character" } } }, @@ -7573,6 +7577,10 @@ "name": "storetime", "spec": "col_datetime", "format": "%Y-%m-%d %H:%M:%S" + }, + "enter_provider_id": { + "name": "enter_provider_id", + "spec": "col_character" } } }, @@ -7682,6 +7690,10 @@ "comments": { "name": "comments", "spec": "col_character" + }, + "order_provider_id": { + "name": "order_provider_id", + "spec": "col_character" } }, "partitioning": { @@ -7797,6 +7809,10 @@ "comments": { "name": "comments", "spec": "col_character" + }, + "order_provider_id": { + "name": "order_provider_id", + "spec": "col_character" } } }, @@ -8007,6 +8023,10 @@ "order_status": { "name": "order_status", "spec": "col_character" + }, + "order_provider_id": { + "name": "order_provider_id", + "spec": "col_character" } }, "partitioning": { @@ -8093,6 +8113,14 @@ "route": { "name": "route", "spec": "col_character" + }, + "order_provider_id": { + "name": "order_provider_id", + "spec": "col_character" + }, + "formulary_drug_cd": { + "name": "formulary_drug_cd", + "spec": "col_character" } } }, @@ -8215,6 +8243,10 @@ "warning": { "name": "warning", "spec": "col_integer" + }, + "caregiver_id": { + "name": "caregiver_id", + "spec": "col_integer" } }, "partitioning": { @@ -8269,6 +8301,10 @@ "warning": { "name": "warning", "spec": "col_integer" + }, + "caregiver_id": { + "name": "caregiver_id", + "spec": "col_integer" } } }, @@ -8385,6 +8421,10 @@ "name": "stay_id", "spec": "col_integer" }, + "caregiver_id": { + "name": "caregiver_id", + "spec": "col_integer" + }, "starttime": { "name": "starttime", "spec": "col_datetime", @@ -8525,6 +8565,10 @@ "valueuom": { "name": "valueuom", "spec": "col_character" + }, + "caregiver_id": { + "name": "caregiver_id", + "spec": "col_integer" } } }, @@ -8645,6 +8689,10 @@ "originalrate": { "name": "originalrate", "spec": "col_double" + }, + "caregiver_id": { + "name": "caregiver_id", + "spec": "col_integer" } } }, @@ -8681,7 +8729,7 @@ } }, "caregiver": { - "files": "hosp/caregiver.csv.gz", + "files": "icu/caregiver.csv.gz", "defaults": [], "num_rows": 15468, "cols": { @@ -8724,6 +8772,10 @@ "name": "stay_id", "spec": "col_integer" }, + "caregiver_id": { + "name": "caregiver_id", + "spec": "col_integer" + }, "starttime": { "name": "starttime", "spec": "col_datetime",