diff --git a/inst/extdata/config/data-sources.json b/inst/extdata/config/data-sources.json index a7ceea6e..4b48f224 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", @@ -7099,6 +7099,10 @@ "name": "admission_type", "spec": "col_character" }, + "admit_provider_id": { + "name": "admit_provider_id", + "spec": "col_character" + }, "admission_location": { "name": "admission_location", "spec": "col_character" @@ -7139,79 +7143,6 @@ } } }, - "patients": { - "files": "core/patients.csv.gz", - "defaults": { - "time_vars": "dod" - }, - "num_rows": 382278, - "cols": { - "subject_id": { - "name": "subject_id", - "spec": "col_integer" - }, - "gender": { - "name": "gender", - "spec": "col_character" - }, - "anchor_age": { - "name": "anchor_age", - "spec": "col_integer" - }, - "anchor_year": { - "name": "anchor_year", - "spec": "col_integer" - }, - "anchor_year_group": { - "name": "anchor_year_group", - "spec": "col_character" - }, - "dod": { - "name": "dod", - "spec": "col_datetime", - "format": "%Y-%m-%d" - } - } - }, - "transfers": { - "files": "core/transfers.csv.gz", - "defaults": { - "time_vars": ["intime", "outtime"] - }, - "num_rows": 2189535, - "cols": { - "subject_id": { - "name": "subject_id", - "spec": "col_integer" - }, - "hadm_id": { - "name": "hadm_id", - "spec": "col_integer" - }, - "transfer_id": { - "name": "transfer_id", - "spec": "col_integer" - }, - "eventtype": { - "name": "eventtype", - "spec": "col_character" - }, - "careunit": { - "name": "careunit", - "spec": "col_character" - }, - "intime": { - "name": "intime", - "spec": "col_datetime", - "format": "%Y-%m-%d %H:%M:%S" - }, - "outtime": { - "name": "outtime", - "spec": "col_datetime", - "format": "%Y-%m-%d %H:%M:%S" - } - } - }, "d_hcpcs": { "files": "hosp/d_hcpcs.csv.gz", "defaults": { @@ -7238,35 +7169,6 @@ } } }, - "diagnoses_icd": { - "files": "hosp/diagnoses_icd.csv.gz", - "defaults": { - "val_var": "icd_code" - }, - "num_rows": 5280351, - "cols": { - "subject_id": { - "name": "subject_id", - "spec": "col_integer" - }, - "hadm_id": { - "name": "hadm_id", - "spec": "col_integer" - }, - "seq_num": { - "name": "seq_num", - "spec": "col_integer" - }, - "icd_code": { - "name": "icd_code", - "spec": "col_character" - }, - "icd_version": { - "name": "icd_version", - "spec": "col_integer" - } - } - }, "d_icd_diagnoses": { "files": "hosp/d_icd_diagnoses.csv.gz", "defaults": { @@ -7317,7 +7219,7 @@ "id_var": "itemid", "val_var": "label" }, - "num_rows": 1630, + "num_rows": 1622, "cols": { "itemid": { "name": "itemid", @@ -7334,10 +7236,35 @@ "category": { "name": "category", "spec": "col_character" + } + } + }, + "diagnoses_icd": { + "files": "hosp/diagnoses_icd.csv.gz", + "defaults": { + "val_var": "icd_code" + }, + "num_rows": 4756326, + "cols": { + "subject_id": { + "name": "subject_id", + "spec": "col_integer" }, - "loinc_code": { - "name": "loinc_code", + "hadm_id": { + "name": "hadm_id", + "spec": "col_integer" + }, + "seq_num": { + "name": "seq_num", + "spec": "col_integer" + }, + "icd_code": { + "name": "icd_code", "spec": "col_character" + }, + "icd_version": { + "name": "icd_version", + "spec": "col_integer" } } }, @@ -7346,7 +7273,7 @@ "defaults": { "val_var": "drg_code" }, - "num_rows": 769622, + "num_rows": 604377, "cols": { "subject_id": { "name": "subject_id", @@ -7383,7 +7310,7 @@ "defaults": { "id_var": "emar_id" }, - "num_rows": 55947921, + "num_rows": 54744789, "cols": { "subject_id": { "name": "subject_id", @@ -7525,7 +7452,7 @@ "index_var": "charttime", "time_vars": ["charttime", "scheduletime", "storetime"] }, - "num_rows": 27464367, + "num_rows": 26850359, "cols": { "subject_id": { "name": "subject_id", @@ -7551,6 +7478,10 @@ "name": "pharmacy_id", "spec": "col_integer" }, + "enter_provider_id": { + "name": "enter_provider_id", + "spec": "col_character" + }, "charttime": { "name": "charttime", "spec": "col_datetime", @@ -7582,7 +7513,7 @@ "index_var": "chartdate", "time_vars": "chartdate" }, - "num_rows": 160727, + "num_rows": 150771, "cols": { "subject_id": { "name": "subject_id", @@ -7619,7 +7550,7 @@ "unit_var": "valueuom", "time_vars": ["charttime", "storetime"] }, - "num_rows": 122103667, + "num_rows": 118171367, "cols": { "labevent_id": { "name": "labevent_id", @@ -7641,6 +7572,10 @@ "name": "itemid", "spec": "col_integer" }, + "order_provider_id": { + "name": "order_provider_id", + "spec": "col_character" + }, "charttime": { "name": "charttime", "spec": "col_datetime", @@ -7696,7 +7631,7 @@ "val_var": "isolate_num", "time_vars": ["chartdate", "charttime", "storedate", "storetime"] }, - "num_rows": 3397914, + "num_rows": 3228713, "cols": { "microevent_id": { "name": "microevent_id", @@ -7714,6 +7649,10 @@ "name": "micro_specimen_id", "spec": "col_integer" }, + "order_provider_id": { + "name": "order_provider_id", + "spec": "col_character" + }, "chartdate": { "name": "chartdate", "spec": "col_datetime", @@ -7800,6 +7739,71 @@ } } }, + "omr" : { + "files": "hosp/omr.csv.gz", + "defaults": { + "time_vars": ["chartdate"], + "val_var": "result_value" + }, + "num_rows": 6439169, + "cols" : { + "subject_id": { + "name": "subject_id", + "spec": "col_integer" + }, + "chartdate": { + "name": "chartdate", + "spec": "col_datetime", + "format": "%Y-%m-%d" + }, + "seq_num": { + "name": "seq_num", + "spec": "col_integer" + }, + "result_name": { + "name": "result_name", + "spec": "col_character" + }, + "result_value": { + "name": "result_value", + "spec": "col_character" + } + } + }, + "patients": { + "files": "hosp/patients.csv.gz", + "defaults": { + "time_vars": "dod" + }, + "num_rows": 299712, + "cols": { + "subject_id": { + "name": "subject_id", + "spec": "col_integer" + }, + "gender": { + "name": "gender", + "spec": "col_character" + }, + "anchor_age": { + "name": "anchor_age", + "spec": "col_integer" + }, + "anchor_year": { + "name": "anchor_year", + "spec": "col_integer" + }, + "anchor_year_group": { + "name": "anchor_year_group", + "spec": "col_character" + }, + "dod": { + "name": "dod", + "spec": "col_datetime", + "format": "%Y-%m-%d" + } + } + }, "pharmacy": { "files": "hosp/pharmacy.csv.gz", "defaults": { @@ -7809,7 +7813,7 @@ "unit_var": "duration_interval", "time_vars": ["starttime", "stoptime", "entertime", "verifiedtime", "expirationdate"] }, - "num_rows": 14736386, + "num_rows": 13584514, "cols": { "subject_id": { "name": "subject_id", @@ -7931,7 +7935,7 @@ "defaults": { "id_var": "poe_id" }, - "num_rows": 3256358, + "num_rows": 3879418, "cols": { "poe_id": { "name": "poe_id", @@ -7961,7 +7965,7 @@ "index_var": "ordertime", "time_vars": "ordertime" }, - "num_rows": 42483962, + "num_rows": 39366291, "cols": { "poe_id": { "name": "poe_id", @@ -8004,6 +8008,10 @@ "name": "discontinued_by_poe_id", "spec": "col_character" }, + "order_provider_id": { + "name": "order_provider_id", + "spec": "col_character" + }, "order_status": { "name": "order_status", "spec": "col_character" @@ -8022,7 +8030,7 @@ "unit_var": "dose_unit_rx", "time_vars": ["starttime", "stoptime"] }, - "num_rows": 17008053, + "num_rows": 15416708, "cols": { "subject_id": { "name": "subject_id", @@ -8036,6 +8044,18 @@ "name": "pharmacy_id", "spec": "col_integer" }, + "poe_id": { + "name": "poe_id", + "spec": "col_character" + }, + "poe_seq": { + "name": "poe_seq", + "spec": "col_integer" + }, + "order_provider_id": { + "name": "order_provider_id", + "spec": "col_character" + }, "starttime": { "name": "starttime", "spec": "col_datetime", @@ -8054,6 +8074,10 @@ "name": "drug", "spec": "col_character" }, + "formulary_drug_cd": { + "name": "formulary_drug_cd", + "spec": "col_character" + }, "gsn": { "name": "gsn", "spec": "col_character" @@ -8103,7 +8127,7 @@ "val_var": "icd_code", "time_vars": "chartdate" }, - "num_rows": 779625, + "num_rows": 669186, "cols": { "subject_id": { "name": "subject_id", @@ -8132,6 +8156,16 @@ } } }, + "provider": { + "files": "hosp/provider.csv.gz", + "num_rows": 40508, + "cols": { + "caregiver_id": { + "name": "caregiver_id", + "spec": "col_integer" + } + } + }, "services": { "files": "hosp/services.csv.gz", "defaults": { @@ -8139,7 +8173,7 @@ "val_var": "curr_service", "time_vars": "transfertime" }, - "num_rows": 562892, + "num_rows": 468029, "cols": { "subject_id": { "name": "subject_id", @@ -8164,15 +8198,12 @@ } } }, - "chartevents": { - "files": "icu/chartevents.csv.gz", + "transfers": { + "files": "hosp/transfers.csv.gz", "defaults": { - "index_var": "charttime", - "val_var": "valuenum", - "unit_var": "valueuom", - "time_vars": ["charttime", "storetime"] + "time_vars": ["intime", "outtime"] }, - "num_rows": 329499788, + "num_rows": 1890972, "cols": { "subject_id": { "name": "subject_id", @@ -8182,54 +8213,52 @@ "name": "hadm_id", "spec": "col_integer" }, - "stay_id": { - "name": "stay_id", + "transfer_id": { + "name": "transfer_id", "spec": "col_integer" }, - "charttime": { - "name": "charttime", + "eventtype": { + "name": "eventtype", + "spec": "col_character" + }, + "careunit": { + "name": "careunit", + "spec": "col_character" + }, + "intime": { + "name": "intime", "spec": "col_datetime", "format": "%Y-%m-%d %H:%M:%S" }, - "storetime": { - "name": "storetime", + "outtime": { + "name": "outtime", "spec": "col_datetime", "format": "%Y-%m-%d %H:%M:%S" - }, - "itemid": { - "name": "itemid", - "spec": "col_integer" - }, - "value": { - "name": "value", - "spec": "col_character" - }, - "valuenum": { - "name": "valuenum", - "spec": "col_double" - }, - "valueuom": { - "name": "valueuom", - "spec": "col_character" - }, - "warning": { - "name": "warning", - "spec": "col_integer" } + } + }, + "caregiver": { + "files": "icu/caregiver.csv.gz", + "defaults": { + "val_var": "caregiver_id" }, - "partitioning": { - "col": "itemid", - "breaks": [220048, 220059, 220181, 220228, 220615, 223782, 223835, 223905, 223962, 223990, 224015, 224055, 224082, 224093, 224328, 224650, 224701, 224850, 225072, 226104, 227240, 227467, 227950, 227960, 228004, 228397, 228594, 228924, 229124] + "num_rows": 15468, + "cols": { + "caregiver_id": { + "name": "caregiver_id", + "spec": "col_integer" + } } }, - "datetimeevents": { - "files": "icu/datetimeevents.csv.gz", + "chartevents": { + "files": "icu/chartevents.csv.gz", "defaults": { "index_var": "charttime", - "val_var": "itemid", - "time_vars": ["charttime", "storetime", "value"] + "val_var": "valuenum", + "unit_var": "valueuom", + "time_vars": ["charttime", "storetime"] }, - "num_rows": 7495712, + "num_rows": 313645063, "cols": { "subject_id": { "name": "subject_id", @@ -8243,6 +8272,10 @@ "name": "stay_id", "spec": "col_integer" }, + "caregiver_id": { + "name": "caregiver_id", + "spec": "col_integer" + }, "charttime": { "name": "charttime", "spec": "col_datetime", @@ -8259,8 +8292,11 @@ }, "value": { "name": "value", - "spec": "col_datetime", - "format": "%Y-%m-%d %H:%M:%S" + "spec": "col_character" + }, + "valuenum": { + "name": "valuenum", + "spec": "col_double" }, "valueuom": { "name": "valueuom", @@ -8270,6 +8306,10 @@ "name": "warning", "spec": "col_integer" } + }, + "partitioning": { + "col": "itemid", + "breaks": [220048, 220059, 220181, 220228, 220615, 223782, 223835, 223905, 223962, 223990, 224015, 224055, 224082, 224093, 224328, 224650, 224701, 224850, 225072, 226104, 227240, 227467, 227950, 227960, 228004, 228397, 228594, 228924, 229124] } }, "d_items": { @@ -8278,7 +8318,7 @@ "id_var": "itemid", "val_var": "label" }, - "num_rows": 3861, + "num_rows": 4014, "cols": { "itemid": { "name": "itemid", @@ -8318,6 +8358,60 @@ } } }, + "datetimeevents": { + "files": "icu/datetimeevents.csv.gz", + "defaults": { + "index_var": "charttime", + "val_var": "itemid", + "time_vars": ["charttime", "storetime", "value"] + }, + "num_rows": 7112999, + "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" + }, + "charttime": { + "name": "charttime", + "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" + }, + "value": { + "name": "value", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "valueuom": { + "name": "valueuom", + "spec": "col_character" + }, + "warning": { + "name": "warning", + "spec": "col_integer" + } + } + }, "icustays": { "files": "icu/icustays.csv.gz", "defaults": { @@ -8325,7 +8419,7 @@ "val_var": "last_careunit", "time_vars": ["intime", "outtime"] }, - "num_rows": 76540, + "num_rows": 73181, "cols": { "subject_id": { "name": "subject_id", @@ -8363,6 +8457,89 @@ } } }, + "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": { + "name": "statusdescription", + "spec": "col_character" + }, + "originalamount": { + "name": "originalamount", + "spec": "col_double" + }, + "originalrate": { + "name": "originalrate", + "spec": "col_double" + } + } + }, "inputevents": { "files": "icu/inputevents.csv.gz", "defaults": { @@ -8371,7 +8548,7 @@ "unit_var": "rateuom", "time_vars": ["starttime", "endtime", "storetime"] }, - "num_rows": 9460658, + "num_rows": 8978893, "cols": { "subject_id": { "name": "subject_id", @@ -8385,6 +8562,10 @@ "name": "stay_id", "spec": "col_integer" }, + "caregiver_id": { + "name": "caregiver_id", + "spec": "col_integer" + }, "starttime": { "name": "starttime", "spec": "col_datetime", @@ -8464,10 +8645,6 @@ "name": "continueinnextdept", "spec": "col_integer" }, - "cancelreason": { - "name": "cancelreason", - "spec": "col_integer" - }, "statusdescription": { "name": "statusdescription", "spec": "col_character" @@ -8490,7 +8667,7 @@ "unit_var": "valueuom", "time_vars": ["charttime", "storetime"] }, - "num_rows": 4457381, + "num_rows": 4234967, "cols": { "subject_id": { "name": "subject_id", @@ -8504,6 +8681,10 @@ "name": "stay_id", "spec": "col_integer" }, + "caregiver_id": { + "name": "caregiver_id", + "spec": "col_integer" + }, "charttime": { "name": "charttime", "spec": "col_datetime", @@ -8534,9 +8715,9 @@ "index_var": "starttime", "val_var": "value", "unit_var": "valueuom", - "time_vars": ["starttime", "endtime", "storetime", "comments_date"] + "time_vars": ["starttime", "endtime", "storetime"] }, - "num_rows": 731247, + "num_rows": 696092, "cols": { "subject_id": { "name": "subject_id", @@ -8550,6 +8731,10 @@ "name": "stay_id", "spec": "col_integer" }, + "caregiver_id": { + "name": "caregiver_id", + "spec": "col_integer" + }, "starttime": { "name": "starttime", "spec": "col_datetime", @@ -8597,10 +8782,6 @@ "name": "ordercategoryname", "spec": "col_character" }, - "secondaryordercategoryname": { - "name": "secondaryordercategoryname", - "spec": "col_character" - }, "ordercategorydescription": { "name": "ordercategorydescription", "spec": "col_character" @@ -8609,14 +8790,6 @@ "name": "patientweight", "spec": "col_double" }, - "totalamount": { - "name": "totalamount", - "spec": "col_double" - }, - "totalamountuom": { - "name": "totalamountuom", - "spec": "col_character" - }, "isopenbag": { "name": "isopenbag", "spec": "col_integer" @@ -8625,19 +8798,10 @@ "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"