diff --git a/inst/extdata/config/data-sources.json b/inst/extdata/config/data-sources.json index b8548290..59e1a469 100644 --- a/inst/extdata/config/data-sources.json +++ b/inst/extdata/config/data-sources.json @@ -7039,7 +7039,7 @@ }, { "name": "miiv", - "url": "https://physionet.org/files/mimiciv/1.0", + "url": "https://physionet.org/files/mimiciv/2.2", "id_cfg": { "patient": { "id": "subject_id", @@ -7065,12 +7065,12 @@ }, "tables": { "admissions": { - "files": "core/admissions.csv.gz", + "files": "hosp/admissions.csv.gz", "defaults": { "val_var": "admission_type", "time_vars": ["admittime", "dischtime", "deathtime", "edregtime", "edouttime"] }, - "num_rows": 523740, + "num_rows": 431231, "cols": { "subject_id": { "name": "subject_id", @@ -7136,15 +7136,19 @@ "hospital_expire_flag": { "name": "hospital_expire_flag", "spec": "col_integer" + }, + "admit_provider_id": { + "name": "admit_provider_id", + "spec": "col_character" } } }, "patients": { - "files": "core/patients.csv.gz", + "files": "hosp/patients.csv.gz", "defaults": { "time_vars": "dod" }, - "num_rows": 382278, + "num_rows": 299712, "cols": { "subject_id": { "name": "subject_id", @@ -7174,7 +7178,7 @@ } }, "omr" : { - "files": "core/omr.csv.gz", + "files": "hosp/omr.csv.gz", "defaults": { "time_vars": ["chartdate"], "val_var": "result_value" @@ -7205,7 +7209,7 @@ } }, "transfers": { - "files": "core/transfers.csv.gz", + "files": "hosp/transfers.csv.gz", "defaults": { "time_vars": ["intime", "outtime"] }, @@ -7243,6 +7247,19 @@ } } }, + "caregiver": { + "files": "icu/caregiver.csv.gz", + "defaults": { + "val_var": "caregiver_id" + }, + "num_rows": 15468, + "cols": { + "code": { + "name": "caregiver_id", + "spec": "col_integer" + } + } + }, "d_hcpcs": { "files": "hosp/d_hcpcs.csv.gz", "defaults": { @@ -7556,7 +7573,7 @@ "index_var": "charttime", "time_vars": ["charttime", "scheduletime", "storetime"] }, - "num_rows": 27464367, + "num_rows": 16806014, "cols": { "subject_id": { "name": "subject_id", @@ -7604,6 +7621,10 @@ "name": "storetime", "spec": "col_datetime", "format": "%Y-%m-%d %H:%M:%S" + }, + "enter_provider_id": { + "name": "enter_provider_id", + "spec": "col_character" } } }, @@ -7613,7 +7634,7 @@ "index_var": "chartdate", "time_vars": "chartdate" }, - "num_rows": 160727, + "num_rows": 150771, "cols": { "subject_id": { "name": "subject_id", @@ -7650,7 +7671,7 @@ "unit_var": "valueuom", "time_vars": ["charttime", "storetime"] }, - "num_rows": 122103667, + "num_rows": 86300637, "cols": { "labevent_id": { "name": "labevent_id", @@ -7713,6 +7734,10 @@ "comments": { "name": "comments", "spec": "col_character" + }, + "order_provider_id": { + "name": "order_provider_id", + "spec": "col_character" } }, "partitioning": { @@ -7727,7 +7752,7 @@ "val_var": "isolate_num", "time_vars": ["chartdate", "charttime", "storedate", "storetime"] }, - "num_rows": 3397914, + "num_rows": 3228713, "cols": { "microevent_id": { "name": "microevent_id", @@ -7828,6 +7853,10 @@ "comments": { "name": "comments", "spec": "col_character" + }, + "order_provider_id": { + "name": "order_provider_id", + "spec": "col_character" } } }, @@ -7840,7 +7869,7 @@ "unit_var": "duration_interval", "time_vars": ["starttime", "stoptime", "entertime", "verifiedtime", "expirationdate"] }, - "num_rows": 14736386, + "num_rows": 13584514, "cols": { "subject_id": { "name": "subject_id", @@ -7962,7 +7991,7 @@ "defaults": { "id_var": "poe_id" }, - "num_rows": 3256358, + "num_rows": 3879418, "cols": { "poe_id": { "name": "poe_id", @@ -7992,7 +8021,7 @@ "index_var": "ordertime", "time_vars": "ordertime" }, - "num_rows": 42483962, + "num_rows": 39366291, "cols": { "poe_id": { "name": "poe_id", @@ -8043,6 +8072,10 @@ "partitioning": { "col": "subject_id", "breaks": [12017899, 13999829, 15979442, 17994364] + }, + "order_provider_id": { + "name": "order_provider_id", + "spec": "col_character" } }, "prescriptions": { @@ -8053,7 +8086,7 @@ "unit_var": "dose_unit_rx", "time_vars": ["starttime", "stoptime"] }, - "num_rows": 17008053, + "num_rows": 15416708, "cols": { "subject_id": { "name": "subject_id", @@ -8124,6 +8157,14 @@ "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" } } }, @@ -8134,7 +8175,7 @@ "val_var": "icd_code", "time_vars": "chartdate" }, - "num_rows": 779625, + "num_rows": 669186, "cols": { "subject_id": { "name": "subject_id", @@ -8170,7 +8211,7 @@ "val_var": "curr_service", "time_vars": "transfertime" }, - "num_rows": 562892, + "num_rows": 468029, "cols": { "subject_id": { "name": "subject_id", @@ -8203,7 +8244,7 @@ "unit_var": "valueuom", "time_vars": ["charttime", "storetime"] }, - "num_rows": 329499788, + "num_rows": 313645063, "cols": { "subject_id": { "name": "subject_id", @@ -8246,6 +8287,10 @@ "warning": { "name": "warning", "spec": "col_integer" + }, + "caregiver_id": { + "name": "caregiver_id", + "spec": "col_integer" } }, "partitioning": { @@ -8260,7 +8305,7 @@ "val_var": "itemid", "time_vars": ["charttime", "storetime", "value"] }, - "num_rows": 7495712, + "num_rows": 7112999, "cols": { "subject_id": { "name": "subject_id", @@ -8300,6 +8345,10 @@ "warning": { "name": "warning", "spec": "col_integer" + }, + "caregiver_id": { + "name": "caregiver_id", + "spec": "col_integer" } } }, @@ -8309,7 +8358,7 @@ "id_var": "itemid", "val_var": "label" }, - "num_rows": 3861, + "num_rows": 4014, "cols": { "itemid": { "name": "itemid", @@ -8356,7 +8405,7 @@ "val_var": "last_careunit", "time_vars": ["intime", "outtime"] }, - "num_rows": 76540, + "num_rows": 73181, "cols": { "subject_id": { "name": "subject_id", @@ -8402,7 +8451,7 @@ "unit_var": "rateuom", "time_vars": ["starttime", "endtime", "storetime"] }, - "num_rows": 9460658, + "num_rows": 8978893, "cols": { "subject_id": { "name": "subject_id", @@ -8416,6 +8465,10 @@ "name": "stay_id", "spec": "col_integer" }, + "caregiver_id": { + "name": "caregiver_id", + "spec": "col_integer" + }, "starttime": { "name": "starttime", "spec": "col_datetime", @@ -8463,10 +8516,6 @@ "name": "ordercategoryname", "spec": "col_character" }, - "secondaryordercategoryname": { - "name": "secondaryordercategoryname", - "spec": "col_character" - }, "ordercomponenttypedescription": { "name": "ordercomponenttypedescription", "spec": "col_character" @@ -8479,14 +8528,6 @@ "name": "patientweight", "spec": "col_double" }, - "totalamount": { - "name": "totalamount", - "spec": "col_double" - }, - "totalamountuom": { - "name": "totalamountuom", - "spec": "col_character" - }, "isopenbag": { "name": "isopenbag", "spec": "col_integer" @@ -8495,8 +8536,87 @@ "name": "continueinnextdept", "spec": "col_integer" }, - "cancelreason": { - "name": "cancelreason", + "statusdescription": { + "name": "statusdescription", + "spec": "col_character" + }, + "originalamount": { + "name": "originalamount", + "spec": "col_double" + }, + "originalrate": { + "name": "originalrate", + "spec": "col_double" + } + } + }, + "ingredientevents": { + "files": "icu/ingredientevents.csv.gz", + "defaults": { + "index_var": "starttime", + "val_var": "rate", + "unit_var": "rateuom", + "time_vars": ["starttime", "endtime", "storetime"] + }, + "num_rows": 11627821, + "cols": { + "subject_id": { + "name": "subject_id", + "spec": "col_integer" + }, + "hadm_id": { + "name": "hadm_id", + "spec": "col_integer" + }, + "stay_id": { + "name": "stay_id", + "spec": "col_integer" + }, + "caregiver_id": { + "name": "caregiver_id", + "spec": "col_integer" + }, + "starttime": { + "name": "starttime", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "endtime": { + "name": "endtime", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "storetime": { + "name": "storetime", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "itemid": { + "name": "itemid", + "spec": "col_integer" + }, + "amount": { + "name": "amount", + "spec": "col_double" + }, + "amountuom": { + "name": "amountuom", + "spec": "col_character" + }, + "rate": { + "name": "rate", + "spec": "col_double" + }, + "rateuom": { + "name": "rateuom", + "spec": "col_character" + }, + "orderid": { + "name": "orderid", + "spec": "col_integer" + }, + "linkorderid": { + "name": "linkorderid", "spec": "col_integer" }, "statusdescription": { @@ -8521,7 +8641,7 @@ "unit_var": "valueuom", "time_vars": ["charttime", "storetime"] }, - "num_rows": 4457381, + "num_rows": 4234967, "cols": { "subject_id": { "name": "subject_id", @@ -8556,7 +8676,11 @@ "valueuom": { "name": "valueuom", "spec": "col_character" - } + }, + "caregiver_id": { + "name": "caregiver_id", + "spec": "col_integer" + } } }, "procedureevents": { @@ -8567,7 +8691,7 @@ "unit_var": "valueuom", "time_vars": ["starttime", "endtime", "storetime", "comments_date"] }, - "num_rows": 731247, + "num_rows": 696092, "cols": { "subject_id": { "name": "subject_id", @@ -8640,14 +8764,6 @@ "name": "patientweight", "spec": "col_double" }, - "totalamount": { - "name": "totalamount", - "spec": "col_double" - }, - "totalamountuom": { - "name": "totalamountuom", - "spec": "col_character" - }, "isopenbag": { "name": "isopenbag", "spec": "col_integer" @@ -8656,19 +8772,10 @@ "name": "continueinnextdept", "spec": "col_integer" }, - "cancelreason": { - "name": "cancelreason", - "spec": "col_integer" - }, "statusdescription": { "name": "statusdescription", "spec": "col_character" }, - "comments_date": { - "name": "comments_date", - "spec": "col_datetime", - "format": "%Y-%m-%d %H:%M:%S" - }, "originalamount": { "name": "originalamount", "spec": "col_double" @@ -8676,6 +8783,10 @@ "originalrate": { "name": "originalrate", "spec": "col_double" + }, + "caregiver_id": { + "name": "caregiver_id", + "spec": "col_integer" } } }