From 8aa77b9112d0dac258f64a1a453e8ff0f2676105 Mon Sep 17 00:00:00 2001 From: Malte Londschien Date: Mon, 4 Mar 2024 12:36:10 +0100 Subject: [PATCH] format jsons. --- inst/extdata/config/data-sources/aumc.json | 562 ++++- inst/extdata/config/data-sources/eicu.json | 1987 ++++++++++++++++- .../config/data-sources/eicu_demo.json | 1944 +++++++++++++++- inst/extdata/config/data-sources/hirid.json | 749 ++++++- inst/extdata/config/data-sources/miiv.json | 1850 ++++++++++++++- inst/extdata/config/data-sources/mimic.json | 1731 +++++++++++++- .../config/data-sources/mimic_demo.json | 1631 +++++++++++++- inst/extdata/config/data-sources/sic.json | 454 +++- 8 files changed, 10900 insertions(+), 8 deletions(-) diff --git a/inst/extdata/config/data-sources/aumc.json b/inst/extdata/config/data-sources/aumc.json index aa5aabb5..576df56e 100644 --- a/inst/extdata/config/data-sources/aumc.json +++ b/inst/extdata/config/data-sources/aumc.json @@ -1 +1,561 @@ -[{"name": "aumc", "id_cfg": {"patient": {"id": "patientid", "position": 1, "start": "firstadmittedat", "end": "dateofdeath", "table": "admissions"}, "icustay": {"id": "admissionid", "position": 2, "start": "admittedat", "end": "dischargedat", "table": "admissions"}}, "unit_mapping": [{"symbol": "uur", "def": "1 hour"}, {"symbol": "dag", "def": "1 day"}], "tables": {"admissions": {"files": "admissions.csv", "defaults": {"index_var": "admittedat", "time_vars": ["admittedat", "dischargedat", "dateofdeath"]}, "num_rows": 23106, "cols": {"patientid": {"name": "patientid", "spec": "col_integer"}, "admissionid": {"name": "admissionid", "spec": "col_integer"}, "admissioncount": {"name": "admissioncount", "spec": "col_integer"}, "location": {"name": "location", "spec": "col_character"}, "urgency": {"name": "urgency", "spec": "col_logical"}, "origin": {"name": "origin", "spec": "col_character"}, "admittedat": {"name": "admittedat", "spec": "col_double"}, "admissionyeargroup": {"name": "admissionyeargroup", "spec": "col_character"}, "dischargedat": {"name": "dischargedat", "spec": "col_double"}, "lengthofstay": {"name": "lengthofstay", "spec": "col_integer"}, "destination": {"name": "destination", "spec": "col_character"}, "gender": {"name": "gender", "spec": "col_character"}, "agegroup": {"name": "agegroup", "spec": "col_character"}, "dateofdeath": {"name": "dateofdeath", "spec": "col_double"}, "weightgroup": {"name": "weightgroup", "spec": "col_character"}, "weightsource": {"name": "weightsource", "spec": "col_character"}, "specialty": {"name": "specialty", "spec": "col_character"}}}, "drugitems": {"files": "drugitems.csv", "defaults": {"index_var": "start", "val_var": "dose", "unit_var": "doseunit", "time_vars": ["start", "stop"]}, "num_rows": 4907269, "cols": {"admissionid": {"name": "admissionid", "spec": "col_integer"}, "orderid": {"name": "orderid", "spec": "col_integer"}, "ordercategoryid": {"name": "ordercategoryid", "spec": "col_integer"}, "ordercategory": {"name": "ordercategory", "spec": "col_character"}, "itemid": {"name": "itemid", "spec": "col_integer"}, "item": {"name": "item", "spec": "col_character"}, "isadditive": {"name": "isadditive", "spec": "col_logical"}, "isconditional": {"name": "isconditional", "spec": "col_logical"}, "rate": {"name": "rate", "spec": "col_double"}, "rateunit": {"name": "rateunit", "spec": "col_character"}, "rateunitid": {"name": "rateunitid", "spec": "col_integer"}, "ratetimeunitid": {"name": "ratetimeunitid", "spec": "col_integer"}, "doserateperkg": {"name": "doserateperkg", "spec": "col_logical"}, "dose": {"name": "dose", "spec": "col_double"}, "doseunit": {"name": "doseunit", "spec": "col_character"}, "doserateunit": {"name": "doserateunit", "spec": "col_character"}, "doseunitid": {"name": "doseunitid", "spec": "col_integer"}, "doserateunitid": {"name": "doserateunitid", "spec": "col_integer"}, "administered": {"name": "administered", "spec": "col_double"}, "administeredunit": {"name": "administeredunit", "spec": "col_character"}, "administeredunitid": {"name": "administeredunitid", "spec": "col_integer"}, "action": {"name": "action", "spec": "col_character"}, "start": {"name": "start", "spec": "col_double"}, "stop": {"name": "stop", "spec": "col_double"}, "duration": {"name": "duration", "spec": "col_integer"}, "solutionitemid": {"name": "solutionitemid", "spec": "col_integer"}, "solutionitem": {"name": "solutionitem", "spec": "col_character"}, "solutionadministered": {"name": "solutionadministered", "spec": "col_double"}, "solutionadministeredunit": {"name": "solutionadministeredunit", "spec": "col_character"}, "fluidin": {"name": "fluidin", "spec": "col_double"}, "iscontinuous": {"name": "iscontinuous", "spec": "col_logical"}}}, "freetextitems": {"files": "freetextitems.csv", "defaults": {"index_var": "measuredat", "id_var": "value", "time_vars": ["measuredat", "registeredat", "updatedat"]}, "num_rows": 651248, "cols": {"admissionid": {"name": "admissionid", "spec": "col_integer"}, "itemid": {"name": "itemid", "spec": "col_integer"}, "item": {"name": "item", "spec": "col_character"}, "value": {"name": "value", "spec": "col_character"}, "comment": {"name": "comment", "spec": "col_character"}, "measuredat": {"name": "measuredat", "spec": "col_double"}, "registeredat": {"name": "registeredat", "spec": "col_double"}, "registeredby": {"name": "registeredby", "spec": "col_character"}, "updatedat": {"name": "updatedat", "spec": "col_double"}, "updatedby": {"name": "updatedby", "spec": "col_character"}, "islabresult": {"name": "islabresult", "spec": "col_logical"}}}, "listitems": {"files": "listitems.csv", "defaults": {"index_var": "measuredat", "val_var": "value", "time_vars": ["measuredat", "registeredat", "updatedat"]}, "num_rows": 30744065, "cols": {"admissionid": {"name": "admissionid", "spec": "col_integer"}, "itemid": {"name": "itemid", "spec": "col_integer"}, "item": {"name": "item", "spec": "col_character"}, "valueid": {"name": "valueid", "spec": "col_integer"}, "value": {"name": "value", "spec": "col_character"}, "measuredat": {"name": "measuredat", "spec": "col_double"}, "registeredat": {"name": "registeredat", "spec": "col_double"}, "registeredby": {"name": "registeredby", "spec": "col_character"}, "updatedat": {"name": "updatedat", "spec": "col_double"}, "updatedby": {"name": "updatedby", "spec": "col_character"}, "islabresult": {"name": "islabresult", "spec": "col_logical"}}, "partitioning": {"col": "itemid", "breaks": 12290}}, "numericitems": {"files": "numericitems.csv", "defaults": {"index_var": "measuredat", "val_var": "value", "unit_var": "unit", "time_vars": ["measuredat", "registeredat", "updatedat"]}, "num_rows": 977625612, "cols": {"admissionid": {"name": "admissionid", "spec": "col_integer"}, "itemid": {"name": "itemid", "spec": "col_integer"}, "item": {"name": "item", "spec": "col_character"}, "tag": {"name": "tag", "spec": "col_character"}, "value": {"name": "value", "spec": "col_double"}, "unitid": {"name": "unitid", "spec": "col_integer"}, "unit": {"name": "unit", "spec": "col_character"}, "comment": {"name": "comment", "spec": "col_character"}, "measuredat": {"name": "measuredat", "spec": "col_double"}, "registeredat": {"name": "registeredat", "spec": "col_double"}, "registeredby": {"name": "registeredby", "spec": "col_character"}, "updatedat": {"name": "updatedat", "spec": "col_double"}, "updatedby": {"name": "updatedby", "spec": "col_character"}, "islabresult": {"name": "islabresult", "spec": "col_logical"}, "fluidout": {"name": "fluidout", "spec": "col_double"}}, "partitioning": {"col": "itemid", "breaks": [6641, 6642, 6643, 6664, 6666, 6667, 6669, 6672, 6673, 6675, 6707, 6709, 8874, 12270, 12275, 12278, 12281, 12286, 12303, 12561, 12576, 12804, 14841]}}, "procedureorderitems": {"files": "procedureorderitems.csv", "defaults": {"index_var": "registeredat", "val_var": "item", "time_vars": "registeredat"}, "num_rows": 2188626, "cols": {"admissionid": {"name": "admissionid", "spec": "col_integer"}, "orderid": {"name": "orderid", "spec": "col_integer"}, "ordercategoryid": {"name": "ordercategoryid", "spec": "col_integer"}, "ordercategoryname": {"name": "ordercategoryname", "spec": "col_character"}, "itemid": {"name": "itemid", "spec": "col_integer"}, "item": {"name": "item", "spec": "col_character"}, "registeredat": {"name": "registeredat", "spec": "col_double"}, "registeredby": {"name": "registeredby", "spec": "col_character"}}}, "processitems": {"files": "processitems.csv", "defaults": {"index_var": "start", "val_var": "item", "time_vars": ["start", "stop"]}, "num_rows": 256715, "cols": {"admissionid": {"name": "admissionid", "spec": "col_integer"}, "itemid": {"name": "itemid", "spec": "col_integer"}, "item": {"name": "item", "spec": "col_character"}, "start": {"name": "start", "spec": "col_double"}, "stop": {"name": "stop", "spec": "col_double"}, "duration": {"name": "duration", "spec": "col_integer"}}}}}] \ No newline at end of file +[ + { + "name": "aumc", + "id_cfg": { + "patient": { + "id": "patientid", + "position": 1, + "start": "firstadmittedat", + "end": "dateofdeath", + "table": "admissions" + }, + "icustay": { + "id": "admissionid", + "position": 2, + "start": "admittedat", + "end": "dischargedat", + "table": "admissions" + } + }, + "unit_mapping": [ + { + "symbol": "uur", + "def": "1 hour" + }, + { + "symbol": "dag", + "def": "1 day" + } + ], + "tables": { + "admissions": { + "files": "admissions.csv", + "defaults": { + "index_var": "admittedat", + "time_vars": [ + "admittedat", + "dischargedat", + "dateofdeath" + ] + }, + "num_rows": 23106, + "cols": { + "patientid": { + "name": "patientid", + "spec": "col_integer" + }, + "admissionid": { + "name": "admissionid", + "spec": "col_integer" + }, + "admissioncount": { + "name": "admissioncount", + "spec": "col_integer" + }, + "location": { + "name": "location", + "spec": "col_character" + }, + "urgency": { + "name": "urgency", + "spec": "col_logical" + }, + "origin": { + "name": "origin", + "spec": "col_character" + }, + "admittedat": { + "name": "admittedat", + "spec": "col_double" + }, + "admissionyeargroup": { + "name": "admissionyeargroup", + "spec": "col_character" + }, + "dischargedat": { + "name": "dischargedat", + "spec": "col_double" + }, + "lengthofstay": { + "name": "lengthofstay", + "spec": "col_integer" + }, + "destination": { + "name": "destination", + "spec": "col_character" + }, + "gender": { + "name": "gender", + "spec": "col_character" + }, + "agegroup": { + "name": "agegroup", + "spec": "col_character" + }, + "dateofdeath": { + "name": "dateofdeath", + "spec": "col_double" + }, + "weightgroup": { + "name": "weightgroup", + "spec": "col_character" + }, + "weightsource": { + "name": "weightsource", + "spec": "col_character" + }, + "specialty": { + "name": "specialty", + "spec": "col_character" + } + } + }, + "drugitems": { + "files": "drugitems.csv", + "defaults": { + "index_var": "start", + "val_var": "dose", + "unit_var": "doseunit", + "time_vars": [ + "start", + "stop" + ] + }, + "num_rows": 4907269, + "cols": { + "admissionid": { + "name": "admissionid", + "spec": "col_integer" + }, + "orderid": { + "name": "orderid", + "spec": "col_integer" + }, + "ordercategoryid": { + "name": "ordercategoryid", + "spec": "col_integer" + }, + "ordercategory": { + "name": "ordercategory", + "spec": "col_character" + }, + "itemid": { + "name": "itemid", + "spec": "col_integer" + }, + "item": { + "name": "item", + "spec": "col_character" + }, + "isadditive": { + "name": "isadditive", + "spec": "col_logical" + }, + "isconditional": { + "name": "isconditional", + "spec": "col_logical" + }, + "rate": { + "name": "rate", + "spec": "col_double" + }, + "rateunit": { + "name": "rateunit", + "spec": "col_character" + }, + "rateunitid": { + "name": "rateunitid", + "spec": "col_integer" + }, + "ratetimeunitid": { + "name": "ratetimeunitid", + "spec": "col_integer" + }, + "doserateperkg": { + "name": "doserateperkg", + "spec": "col_logical" + }, + "dose": { + "name": "dose", + "spec": "col_double" + }, + "doseunit": { + "name": "doseunit", + "spec": "col_character" + }, + "doserateunit": { + "name": "doserateunit", + "spec": "col_character" + }, + "doseunitid": { + "name": "doseunitid", + "spec": "col_integer" + }, + "doserateunitid": { + "name": "doserateunitid", + "spec": "col_integer" + }, + "administered": { + "name": "administered", + "spec": "col_double" + }, + "administeredunit": { + "name": "administeredunit", + "spec": "col_character" + }, + "administeredunitid": { + "name": "administeredunitid", + "spec": "col_integer" + }, + "action": { + "name": "action", + "spec": "col_character" + }, + "start": { + "name": "start", + "spec": "col_double" + }, + "stop": { + "name": "stop", + "spec": "col_double" + }, + "duration": { + "name": "duration", + "spec": "col_integer" + }, + "solutionitemid": { + "name": "solutionitemid", + "spec": "col_integer" + }, + "solutionitem": { + "name": "solutionitem", + "spec": "col_character" + }, + "solutionadministered": { + "name": "solutionadministered", + "spec": "col_double" + }, + "solutionadministeredunit": { + "name": "solutionadministeredunit", + "spec": "col_character" + }, + "fluidin": { + "name": "fluidin", + "spec": "col_double" + }, + "iscontinuous": { + "name": "iscontinuous", + "spec": "col_logical" + } + } + }, + "freetextitems": { + "files": "freetextitems.csv", + "defaults": { + "index_var": "measuredat", + "id_var": "value", + "time_vars": [ + "measuredat", + "registeredat", + "updatedat" + ] + }, + "num_rows": 651248, + "cols": { + "admissionid": { + "name": "admissionid", + "spec": "col_integer" + }, + "itemid": { + "name": "itemid", + "spec": "col_integer" + }, + "item": { + "name": "item", + "spec": "col_character" + }, + "value": { + "name": "value", + "spec": "col_character" + }, + "comment": { + "name": "comment", + "spec": "col_character" + }, + "measuredat": { + "name": "measuredat", + "spec": "col_double" + }, + "registeredat": { + "name": "registeredat", + "spec": "col_double" + }, + "registeredby": { + "name": "registeredby", + "spec": "col_character" + }, + "updatedat": { + "name": "updatedat", + "spec": "col_double" + }, + "updatedby": { + "name": "updatedby", + "spec": "col_character" + }, + "islabresult": { + "name": "islabresult", + "spec": "col_logical" + } + } + }, + "listitems": { + "files": "listitems.csv", + "defaults": { + "index_var": "measuredat", + "val_var": "value", + "time_vars": [ + "measuredat", + "registeredat", + "updatedat" + ] + }, + "num_rows": 30744065, + "cols": { + "admissionid": { + "name": "admissionid", + "spec": "col_integer" + }, + "itemid": { + "name": "itemid", + "spec": "col_integer" + }, + "item": { + "name": "item", + "spec": "col_character" + }, + "valueid": { + "name": "valueid", + "spec": "col_integer" + }, + "value": { + "name": "value", + "spec": "col_character" + }, + "measuredat": { + "name": "measuredat", + "spec": "col_double" + }, + "registeredat": { + "name": "registeredat", + "spec": "col_double" + }, + "registeredby": { + "name": "registeredby", + "spec": "col_character" + }, + "updatedat": { + "name": "updatedat", + "spec": "col_double" + }, + "updatedby": { + "name": "updatedby", + "spec": "col_character" + }, + "islabresult": { + "name": "islabresult", + "spec": "col_logical" + } + }, + "partitioning": { + "col": "itemid", + "breaks": 12290 + } + }, + "numericitems": { + "files": "numericitems.csv", + "defaults": { + "index_var": "measuredat", + "val_var": "value", + "unit_var": "unit", + "time_vars": [ + "measuredat", + "registeredat", + "updatedat" + ] + }, + "num_rows": 977625612, + "cols": { + "admissionid": { + "name": "admissionid", + "spec": "col_integer" + }, + "itemid": { + "name": "itemid", + "spec": "col_integer" + }, + "item": { + "name": "item", + "spec": "col_character" + }, + "tag": { + "name": "tag", + "spec": "col_character" + }, + "value": { + "name": "value", + "spec": "col_double" + }, + "unitid": { + "name": "unitid", + "spec": "col_integer" + }, + "unit": { + "name": "unit", + "spec": "col_character" + }, + "comment": { + "name": "comment", + "spec": "col_character" + }, + "measuredat": { + "name": "measuredat", + "spec": "col_double" + }, + "registeredat": { + "name": "registeredat", + "spec": "col_double" + }, + "registeredby": { + "name": "registeredby", + "spec": "col_character" + }, + "updatedat": { + "name": "updatedat", + "spec": "col_double" + }, + "updatedby": { + "name": "updatedby", + "spec": "col_character" + }, + "islabresult": { + "name": "islabresult", + "spec": "col_logical" + }, + "fluidout": { + "name": "fluidout", + "spec": "col_double" + } + }, + "partitioning": { + "col": "itemid", + "breaks": [ + 6641, + 6642, + 6643, + 6664, + 6666, + 6667, + 6669, + 6672, + 6673, + 6675, + 6707, + 6709, + 8874, + 12270, + 12275, + 12278, + 12281, + 12286, + 12303, + 12561, + 12576, + 12804, + 14841 + ] + } + }, + "procedureorderitems": { + "files": "procedureorderitems.csv", + "defaults": { + "index_var": "registeredat", + "val_var": "item", + "time_vars": "registeredat" + }, + "num_rows": 2188626, + "cols": { + "admissionid": { + "name": "admissionid", + "spec": "col_integer" + }, + "orderid": { + "name": "orderid", + "spec": "col_integer" + }, + "ordercategoryid": { + "name": "ordercategoryid", + "spec": "col_integer" + }, + "ordercategoryname": { + "name": "ordercategoryname", + "spec": "col_character" + }, + "itemid": { + "name": "itemid", + "spec": "col_integer" + }, + "item": { + "name": "item", + "spec": "col_character" + }, + "registeredat": { + "name": "registeredat", + "spec": "col_double" + }, + "registeredby": { + "name": "registeredby", + "spec": "col_character" + } + } + }, + "processitems": { + "files": "processitems.csv", + "defaults": { + "index_var": "start", + "val_var": "item", + "time_vars": [ + "start", + "stop" + ] + }, + "num_rows": 256715, + "cols": { + "admissionid": { + "name": "admissionid", + "spec": "col_integer" + }, + "itemid": { + "name": "itemid", + "spec": "col_integer" + }, + "item": { + "name": "item", + "spec": "col_character" + }, + "start": { + "name": "start", + "spec": "col_double" + }, + "stop": { + "name": "stop", + "spec": "col_double" + }, + "duration": { + "name": "duration", + "spec": "col_integer" + } + } + } + } + } +] \ No newline at end of file diff --git a/inst/extdata/config/data-sources/eicu.json b/inst/extdata/config/data-sources/eicu.json index 0383a095..19b41d13 100644 --- a/inst/extdata/config/data-sources/eicu.json +++ b/inst/extdata/config/data-sources/eicu.json @@ -1 +1,1986 @@ -[{"name": "eicu", "url": "https://physionet.org/files/eicu-crd/2.0", "id_cfg": {"hadm": {"id": "patienthealthsystemstayid", "position": 1, "start": "hospitaladmitoffset", "end": "hospitaldischargeoffset", "table": "patient"}, "icustay": {"id": "patientunitstayid", "position": 2, "start": "unitadmitoffset", "end": "unitdischargeoffset", "table": "patient"}}, "tables": {"admissiondrug": {"files": "admissionDrug.csv.gz", "defaults": {"index_var": "drugoffset", 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"respchartoffset": { + "name": "respchartoffset", + "spec": "col_integer" + }, + "respchartentryoffset": { + "name": "respchartentryoffset", + "spec": "col_integer" + }, + "respcharttypecat": { + "name": "respcharttypecat", + "spec": "col_character" + }, + "respchartvaluelabel": { + "name": "respchartvaluelabel", + "spec": "col_character" + }, + "respchartvalue": { + "name": "respchartvalue", + "spec": "col_character" + } + } + }, + "treatment": { + "files": "treatment.csv.gz", + "defaults": { + "index_var": "treatmentoffset", + "val_var": "treatmentstring", + "time_vars": "treatmentoffset" + }, + "num_rows": 3688745, + "cols": { + "treatmentid": { + "name": "treatmentid", + "spec": "col_integer" + }, + "patientunitstayid": { + "name": "patientunitstayid", + "spec": "col_integer" + }, + "treatmentoffset": { + "name": "treatmentoffset", + "spec": "col_integer" + }, + "treatmentstring": { + "name": "treatmentstring", + "spec": "col_character" + }, + "activeupondischarge": { + "name": "activeupondischarge", + "spec": "col_character" + } + } + }, + "vitalaperiodic": { + "files": "vitalAperiodic.csv.gz", + "defaults": { + "index_var": "observationoffset", + "time_vars": "observationoffset" + }, + "num_rows": 25075074, + "cols": { + "vitalaperiodicid": { + "name": "vitalaperiodicid", + "spec": "col_integer" + }, + "patientunitstayid": { + "name": "patientunitstayid", + "spec": "col_integer" + }, + "observationoffset": { + "name": "observationoffset", + "spec": "col_integer" + }, + "noninvasivesystolic": { + "name": "noninvasivesystolic", + "spec": "col_double" + }, + "noninvasivediastolic": { + "name": "noninvasivediastolic", + "spec": "col_double" + }, + "noninvasivemean": { + "name": "noninvasivemean", + "spec": "col_double" + }, + "paop": { + "name": "paop", + "spec": "col_double" + }, + "cardiacoutput": { + "name": "cardiacoutput", + "spec": "col_double" + }, + "cardiacinput": { + "name": "cardiacinput", + "spec": "col_double" + }, + "svr": { + "name": "svr", + "spec": "col_double" + }, + "svri": { + "name": "svri", + "spec": "col_double" + }, + "pvr": { + "name": "pvr", + "spec": "col_double" + }, + "pvri": { + "name": "pvri", + "spec": "col_double" + } + } + }, + "vitalperiodic": { + "files": "vitalPeriodic.csv.gz", + "defaults": { + "index_var": "observationoffset", + "time_vars": "observationoffset" + }, + "num_rows": 146671642, + "cols": { + "vitalperiodicid": { + "name": "vitalperiodicid", + "spec": "col_double" + }, + "patientunitstayid": { + "name": "patientunitstayid", + "spec": "col_integer" + }, + "observationoffset": { + "name": "observationoffset", + "spec": "col_integer" + }, + "temperature": { + "name": "temperature", + "spec": "col_double" + }, + "sao2": { + "name": "sao2", + "spec": "col_integer" + }, + "heartrate": { + "name": "heartrate", + "spec": "col_integer" + }, + "respiration": { + "name": "respiration", + "spec": "col_integer" + }, + "cvp": { + "name": "cvp", + "spec": "col_integer" + }, + "etco2": { + "name": "etco2", + "spec": "col_integer" + }, + "systemicsystolic": { + "name": "systemicsystolic", + "spec": "col_integer" + }, + "systemicdiastolic": { + "name": "systemicdiastolic", + "spec": "col_integer" + }, + "systemicmean": { + "name": "systemicmean", + "spec": "col_integer" + }, + "pasystolic": { + "name": "pasystolic", + "spec": "col_integer" + }, + "padiastolic": { + "name": "padiastolic", + "spec": "col_integer" + }, + "pamean": { + "name": "pamean", + "spec": "col_integer" + }, + "st1": { + "name": "st1", + "spec": "col_double" + }, + "st2": { + "name": "st2", + "spec": "col_double" + }, + "st3": { + "name": "st3", + "spec": "col_double" + }, + "icp": { + "name": "icp", + "spec": "col_integer" + } + }, + "partitioning": { + "col": "patientunitstayid", + "breaks": [ + 514528, + 1037072, + 1453997, + 1775421, + 2499831, + 2937948, + 3213286 + ] + } + } + } + } +] \ No newline at end of file diff --git a/inst/extdata/config/data-sources/eicu_demo.json b/inst/extdata/config/data-sources/eicu_demo.json index e8a1b4c8..7f96f442 100644 --- a/inst/extdata/config/data-sources/eicu_demo.json +++ b/inst/extdata/config/data-sources/eicu_demo.json @@ -1 +1,1943 @@ -[{"name": "eicu_demo", "class_prefix": ["eicu_demo", "eicu"], "url": "https://physionet.org/files/eicu-crd-demo/2.0.1", "id_cfg": {"hadm": {"id": "patienthealthsystemstayid", "position": 1, "start": "hospitaladmitoffset", "end": "hospitaldischargeoffset", "table": "patient"}, "icustay": {"id": "patientunitstayid", "position": 2, "start": "unitadmitoffset", "end": "unitdischargeoffset", "table": "patient"}}, "tables": {"admissiondrug": {"files": "admissiondrug.csv.gz", "defaults": {"index_var": "drugoffset", "val_var": "drugdosage", "unit_var": "drugunit", "time_vars": ["drugoffset", "drugenteredoffset"]}, "cols": {"admissiondrugid": {"name": "admissiondrugid", "spec": "col_integer"}, "patientunitstayid": {"name": "patientunitstayid", "spec": "col_integer"}, "drugoffset": {"name": 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"pasthistoryid", + "spec": "col_integer" + }, + "patientunitstayid": { + "name": "patientunitstayid", + "spec": "col_integer" + }, + "pasthistoryoffset": { + "name": "pasthistoryoffset", + "spec": "col_integer" + }, + "pasthistoryenteredoffset": { + "name": "pasthistoryenteredoffset", + "spec": "col_integer" + }, + "pasthistorynotetype": { + "name": "pasthistorynotetype", + "spec": "col_character" + }, + "pasthistorypath": { + "name": "pasthistorypath", + "spec": "col_character" + }, + "pasthistoryvalue": { + "name": "pasthistoryvalue", + "spec": "col_character" + }, + "pasthistoryvaluetext": { + "name": "pasthistoryvaluetext", + "spec": "col_character" + } + } + }, + "patient": { + "files": "patient.csv.gz", + "defaults": { + "val_var": "unitdischargestatus", + "time_vars": [ + "hospitaladmitoffset", + "hospitaldischargeoffset", + "unitdischargeoffset" + ] + }, + "cols": { + "patientunitstayid": { + "name": "patientunitstayid", + "spec": "col_integer" + }, + "patienthealthsystemstayid": { + "name": "patienthealthsystemstayid", + "spec": "col_integer" + }, + "gender": { + "name": "gender", + "spec": "col_character" + }, + "age": { + "name": "age", + "spec": "col_character" + }, + "ethnicity": { + "name": "ethnicity", + "spec": "col_character" + }, + "hospitalid": { + "name": "hospitalid", + "spec": "col_integer" + }, + "wardid": { + "name": "wardid", + "spec": "col_integer" + }, + "apacheadmissiondx": { + "name": "apacheadmissiondx", + "spec": "col_character" + }, + "admissionheight": { + "name": "admissionheight", + "spec": "col_double" + }, + "hospitaladmittime24": { + "name": "hospitaladmittime24", + "spec": "col_character" + }, + "hospitaladmitoffset": { + "name": "hospitaladmitoffset", + "spec": "col_integer" + }, + "hospitaladmitsource": { + "name": "hospitaladmitsource", + "spec": "col_character" + }, + "hospitaldischargeyear": { + "name": "hospitaldischargeyear", + "spec": "col_integer" + }, + "hospitaldischargetime24": { + "name": "hospitaldischargetime24", + "spec": "col_character" + }, + "hospitaldischargeoffset": { + "name": "hospitaldischargeoffset", + "spec": "col_integer" + }, + "hospitaldischargelocation": { + "name": "hospitaldischargelocation", + "spec": "col_character" + }, + "hospitaldischargestatus": { + "name": "hospitaldischargestatus", + "spec": "col_character" + }, + "unittype": { + "name": "unittype", + "spec": "col_character" + }, + "unitadmittime24": { + "name": "unitadmittime24", + "spec": "col_character" + }, + "unitadmitsource": { + "name": "unitadmitsource", + "spec": "col_character" + }, + "unitvisitnumber": { + "name": "unitvisitnumber", + "spec": "col_integer" + }, + "unitstaytype": { + "name": "unitstaytype", + "spec": "col_character" + }, + "admissionweight": { + "name": "admissionweight", + "spec": "col_double" + }, + "dischargeweight": { + "name": "dischargeweight", + "spec": "col_double" + }, + "unitdischargetime24": { + "name": "unitdischargetime24", + "spec": "col_character" + }, + "unitdischargeoffset": { + "name": "unitdischargeoffset", + "spec": "col_integer" + }, + "unitdischargelocation": { + "name": "unitdischargelocation", + "spec": "col_character" + }, + "unitdischargestatus": { + "name": "unitdischargestatus", + "spec": "col_character" + }, + "uniquepid": { + "name": "uniquepid", + "spec": "col_character" + } + } + }, + "physicalexam": { + "files": "physicalExam.csv.gz", + "defaults": { + "index_var": "physicalexamoffset", + "val_var": "physicalexamvalue", + "time_vars": "physicalexamoffset" + }, + "cols": { + "physicalexamid": { + "name": "physicalexamid", + "spec": "col_integer" + }, + "patientunitstayid": { + "name": "patientunitstayid", + "spec": "col_integer" + }, + "physicalexamoffset": { + "name": "physicalexamoffset", + "spec": "col_integer" + }, + "physicalexampath": { + "name": "physicalexampath", + "spec": "col_character" + }, + "physicalexamvalue": { + "name": "physicalexamvalue", + "spec": "col_character" + }, + "physicalexamtext": { + "name": "physicalexamtext", + "spec": "col_character" + } + } + }, + "respiratorycare": { + "files": "respiratoryCare.csv.gz", + "defaults": { + "index_var": "respcarestatusoffset", + "time_vars": [ + "respcarestatusoffset", + "ventstartoffset", + "ventendoffset", + "priorventstartoffset", + "priorventendoffset" + ] + }, + "cols": { + "respcareid": { + "name": "respcareid", + "spec": "col_integer" + }, + "patientunitstayid": { + "name": "patientunitstayid", + "spec": "col_integer" + }, + "respcarestatusoffset": { + "name": "respcarestatusoffset", + "spec": "col_integer" + }, + "currenthistoryseqnum": { + "name": "currenthistoryseqnum", + "spec": "col_integer" + }, + "airwaytype": { + "name": "airwaytype", + "spec": "col_character" + }, + "airwaysize": { + "name": "airwaysize", + "spec": "col_character" + }, + "airwayposition": { + "name": "airwayposition", + "spec": "col_character" + }, + "cuffpressure": { + "name": "cuffpressure", + "spec": "col_double" + }, + "ventstartoffset": { + "name": "ventstartoffset", + "spec": "col_integer" + }, + "ventendoffset": { + "name": "ventendoffset", + "spec": "col_integer" + }, + "priorventstartoffset": { + "name": "priorventstartoffset", + "spec": "col_integer" + }, + "priorventendoffset": { + "name": "priorventendoffset", + "spec": "col_integer" + }, + "apneaparams": { + "name": "apneaparams", + "spec": "col_character" + }, + "lowexhmvlimit": { + "name": "lowexhmvlimit", + "spec": "col_double" + }, + "hiexhmvlimit": { + "name": "hiexhmvlimit", + "spec": "col_double" + }, + "lowexhtvlimit": { + "name": "lowexhtvlimit", + "spec": "col_double" + }, + "hipeakpreslimit": { + "name": "hipeakpreslimit", + "spec": "col_double" + }, + "lowpeakpreslimit": { + "name": "lowpeakpreslimit", + "spec": "col_double" + }, + "hirespratelimit": { + "name": "hirespratelimit", + "spec": "col_double" + }, + "lowrespratelimit": { + "name": "lowrespratelimit", + "spec": "col_double" + }, + "sighpreslimit": { + "name": "sighpreslimit", + "spec": "col_double" + }, + "lowironoxlimit": { + "name": "lowironoxlimit", + "spec": "col_double" + }, + "highironoxlimit": { + "name": "highironoxlimit", + "spec": "col_double" + }, + "meanairwaypreslimit": { + "name": "meanairwaypreslimit", + "spec": "col_double" + }, + "peeplimit": { + "name": "peeplimit", + "spec": "col_double" + }, + "cpaplimit": { + "name": "cpaplimit", + "spec": "col_double" + }, + "setapneainterval": { + "name": "setapneainterval", + "spec": "col_character" + }, + "setapneatv": { + "name": "setapneatv", + "spec": "col_character" + }, + "setapneaippeephigh": { + "name": "setapneaippeephigh", + "spec": "col_character" + }, + "setapnearr": { + "name": "setapnearr", + "spec": "col_character" + }, + "setapneapeakflow": { + "name": "setapneapeakflow", + "spec": "col_character" + }, + "setapneainsptime": { + "name": "setapneainsptime", + "spec": "col_character" + }, + "setapneaie": { + "name": "setapneaie", + "spec": "col_character" + }, + "setapneafio2": { + "name": "setapneafio2", + "spec": "col_character" + } + } + }, + "respiratorycharting": { + "files": "respiratoryCharting.csv.gz", + "defaults": { + "index_var": "respchartoffset", + "val_var": "respchartvalue", + "time_vars": [ + "respchartoffset", + "respchartentryoffset" + ] + }, + "cols": { + "respchartid": { + "name": "respchartid", + "spec": "col_integer" + }, + "patientunitstayid": { + "name": "patientunitstayid", + "spec": "col_integer" + }, + "respchartoffset": { + "name": "respchartoffset", + "spec": "col_integer" + }, + "respchartentryoffset": { + "name": "respchartentryoffset", + "spec": "col_integer" + }, + "respcharttypecat": { + "name": "respcharttypecat", + "spec": "col_character" + }, + "respchartvaluelabel": { + "name": "respchartvaluelabel", + "spec": "col_character" + }, + "respchartvalue": { + "name": "respchartvalue", + "spec": "col_character" + } + } + }, + "treatment": { + "files": "treatment.csv.gz", + "defaults": { + "index_var": "treatmentoffset", + "val_var": "treatmentstring", + "time_vars": "treatmentoffset" + }, + "cols": { + "treatmentid": { + "name": "treatmentid", + "spec": "col_integer" + }, + "patientunitstayid": { + "name": "patientunitstayid", + "spec": "col_integer" + }, + "treatmentoffset": { + "name": "treatmentoffset", + "spec": "col_integer" + }, + "treatmentstring": { + "name": "treatmentstring", + "spec": "col_character" + }, + "activeupondischarge": { + "name": "activeupondischarge", + "spec": "col_character" + } + } + }, + "vitalaperiodic": { + "files": "vitalAperiodic.csv.gz", + "defaults": { + "index_var": "observationoffset", + "time_vars": "observationoffset" + }, + "cols": { + "vitalaperiodicid": { + "name": "vitalaperiodicid", + "spec": "col_integer" + }, + "patientunitstayid": { + "name": "patientunitstayid", + "spec": "col_integer" + }, + "observationoffset": { + "name": "observationoffset", + "spec": "col_integer" + }, + "noninvasivesystolic": { + "name": "noninvasivesystolic", + "spec": "col_double" + }, + "noninvasivediastolic": { + "name": "noninvasivediastolic", + "spec": "col_double" + }, + "noninvasivemean": { + "name": "noninvasivemean", + "spec": "col_double" + }, + "paop": { + "name": "paop", + "spec": "col_double" + }, + "cardiacoutput": { + "name": "cardiacoutput", + "spec": "col_double" + }, + "cardiacinput": { + "name": "cardiacinput", + "spec": "col_double" + }, + "svr": { + "name": "svr", + "spec": "col_double" + }, + "svri": { + "name": "svri", + "spec": "col_double" + }, + "pvr": { + "name": "pvr", + "spec": "col_double" + }, + "pvri": { + "name": "pvri", + "spec": "col_double" + } + } + }, + "vitalperiodic": { + "files": "vitalPeriodic.csv.gz", + "defaults": { + "index_var": "observationoffset", + "time_vars": "observationoffset" + }, + "cols": { + "vitalperiodicid": { + "name": "vitalperiodicid", + "spec": "col_double" + }, + "patientunitstayid": { + "name": "patientunitstayid", + "spec": "col_integer" + }, + "observationoffset": { + "name": "observationoffset", + "spec": "col_integer" + }, + "temperature": { + "name": "temperature", + "spec": "col_double" + }, + "sao2": { + "name": "sao2", + "spec": "col_integer" + }, + "heartrate": { + "name": "heartrate", + "spec": "col_integer" + }, + "respiration": { + "name": "respiration", + "spec": "col_integer" + }, + "cvp": { + "name": "cvp", + "spec": "col_integer" + }, + "etco2": { + "name": "etco2", + "spec": "col_integer" + }, + "systemicsystolic": { + "name": "systemicsystolic", + "spec": "col_integer" + }, + "systemicdiastolic": { + "name": "systemicdiastolic", + "spec": "col_integer" + }, + "systemicmean": { + "name": "systemicmean", + "spec": "col_integer" + }, + "pasystolic": { + "name": "pasystolic", + "spec": "col_integer" + }, + "padiastolic": { + "name": "padiastolic", + "spec": "col_integer" + }, + "pamean": { + "name": "pamean", + "spec": "col_integer" + }, + "st1": { + "name": "st1", + "spec": "col_double" + }, + "st2": { + "name": "st2", + "spec": "col_double" + }, + "st3": { + "name": "st3", + "spec": "col_double" + }, + "icp": { + "name": "icp", + "spec": "col_integer" + } + }, + "partitioning": { + "col": "patientunitstayid", + "breaks": 1775421 + } + } + } + } +] \ No newline at end of file diff --git a/inst/extdata/config/data-sources/hirid.json b/inst/extdata/config/data-sources/hirid.json index 31f5155c..04c67c10 100644 --- a/inst/extdata/config/data-sources/hirid.json +++ b/inst/extdata/config/data-sources/hirid.json @@ -1 +1,748 @@ -[{"name": "hirid", "url": "https://physionet.org/files/hirid/1.1.1", "id_cfg": {"icustay": {"id": "patientid", "position": 1, "start": "admissiontime", "table": "general"}}, "tables": {"general": {"files": "general_table.csv", "defaults": {"index_var": "admissiontime", "time_vars": "admissiontime"}, "cols": {"patientid": {"name": "patientid", "spec": "col_integer"}, "admissiontime": {"name": "admissiontime", "spec": "col_datetime", "format": "%Y-%m-%d %H:%M:%S"}, "sex": {"name": "sex", "spec": "col_character"}, "age": {"name": 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"pharma_records/csv/part-237.csv", + "pharma_records/csv/part-238.csv", + "pharma_records/csv/part-239.csv", + "pharma_records/csv/part-240.csv", + "pharma_records/csv/part-241.csv", + "pharma_records/csv/part-242.csv", + "pharma_records/csv/part-243.csv", + "pharma_records/csv/part-244.csv", + "pharma_records/csv/part-245.csv", + "pharma_records/csv/part-246.csv", + "pharma_records/csv/part-247.csv", + "pharma_records/csv/part-248.csv", + "pharma_records/csv/part-249.csv" + ], + "defaults": { + "index_var": "givenat", + "val_var": "givendose", + "unit_var": "doseunit", + "time_vars": [ + "givenat", + "enteredentryat" + ] + }, + "cols": { + "patientid": { + "name": "patientid", + "spec": "col_integer" + }, + "pharmaid": { + "name": "pharmaid", + "spec": "col_integer" + }, + "givenat": { + "name": "givenat", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "enteredentryat": { + "name": "enteredentryat", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + 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"source_table": { + "name": "Source Table", + "spec": "col_character" + }, + "id": { + "name": "ID", + "spec": "col_integer" + }, + "variable_name": { + "name": "Variable Name", + "spec": "col_character" + }, + "unit": { + "name": "Unit", + "spec": "col_character" + }, + "additional_information": { + "name": "Additional information", + "spec": "col_character" + } + }, + "num_rows": 712, + "zip_file": "reference_data.tar.gz" + } + } + } +] \ No newline at end of file diff --git a/inst/extdata/config/data-sources/miiv.json b/inst/extdata/config/data-sources/miiv.json index 4ab8e0f9..35385795 100644 --- a/inst/extdata/config/data-sources/miiv.json +++ b/inst/extdata/config/data-sources/miiv.json @@ -1 +1,1849 @@ -[{"name": "miiv", "url": "https://physionet.org/files/mimiciv/2.2", "id_cfg": {"patient": {"id": "subject_id", "position": 1, "start": "anchor_year", "end": "dod", "table": "patients"}, "hadm": {"id": "hadm_id", "position": 2, "start": "admittime", "end": "dischtime", "table": 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"LOCATION", + "spec": "col_character" + }, + "locationcategory": { + "name": "LOCATIONCATEGORY", + "spec": "col_character" + }, + "storetime": { + "name": "STORETIME", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "cgid": { + "name": "CGID", + "spec": "col_integer" + }, + "orderid": { + "name": "ORDERID", + "spec": "col_integer" + }, + "linkorderid": { + "name": "LINKORDERID", + "spec": "col_integer" + }, + "ordercategoryname": { + "name": "ORDERCATEGORYNAME", + "spec": "col_character" + }, + "secondaryordercategoryname": { + "name": "SECONDARYORDERCATEGORYNAME", + "spec": "col_character" + }, + "ordercategorydescription": { + "name": "ORDERCATEGORYDESCRIPTION", + "spec": "col_character" + }, + "isopenbag": { + "name": "ISOPENBAG", + "spec": "col_integer" + }, + "continueinnextdept": { + "name": "CONTINUEINNEXTDEPT", + "spec": "col_integer" + }, + "cancelreason": { + "name": "CANCELREASON", + "spec": "col_integer" + }, + "statusdescription": { + "name": "STATUSDESCRIPTION", + "spec": "col_character" + }, + "comments_editedby": { + "name": "COMMENTS_EDITEDBY", + "spec": "col_character" + }, + "comments_canceledby": { + "name": "COMMENTS_CANCELEDBY", + "spec": "col_character" + }, + "comments_date": { + "name": "COMMENTS_DATE", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + } + } + }, + "procedures_icd": { + "files": "PROCEDURES_ICD.csv.gz", + "defaults": { + "val_var": "icd9_code" + }, + "num_rows": 240095, + "cols": { + "row_id": { + "name": "ROW_ID", + "spec": "col_integer" + }, + "subject_id": { + "name": "SUBJECT_ID", + "spec": "col_integer" + }, + "hadm_id": { + "name": "HADM_ID", + "spec": "col_integer" + }, + "seq_num": { + "name": "SEQ_NUM", + "spec": "col_integer" + }, + "icd9_code": { + "name": "ICD9_CODE", + "spec": "col_character" + } + } + }, + "services": { + "files": "SERVICES.csv.gz", + "defaults": { + "index_var": "transfertime", + "val_var": "curr_service", + "time_vars": "transfertime" + }, + "num_rows": 73343, + "cols": { + "row_id": { + "name": "ROW_ID", + "spec": "col_integer" + }, + "subject_id": { + "name": "SUBJECT_ID", + "spec": "col_integer" + }, + "hadm_id": { + "name": "HADM_ID", + "spec": "col_integer" + }, + "transfertime": { + "name": "TRANSFERTIME", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "prev_service": { + "name": "PREV_SERVICE", + "spec": "col_character" + }, + "curr_service": { + "name": "CURR_SERVICE", + "spec": "col_character" + } + } + }, + "transfers": { + "files": "TRANSFERS.csv.gz", + "defaults": { + "index_var": "intime", + "val_var": "curr_careunit", + "time_vars": [ + "intime", + "outtime" + ] + }, + "num_rows": 261897, + "cols": { + "row_id": { + "name": "ROW_ID", + "spec": "col_integer" + }, + "subject_id": { + "name": "SUBJECT_ID", + "spec": "col_integer" + }, + "hadm_id": { + "name": "HADM_ID", + "spec": "col_integer" + }, + "icustay_id": { + "name": "ICUSTAY_ID", + "spec": "col_integer" + }, + "dbsource": { + "name": "DBSOURCE", + "spec": "col_character" + }, + "eventtype": { + "name": "EVENTTYPE", + "spec": "col_character" + }, + "prev_careunit": { + "name": "PREV_CAREUNIT", + "spec": "col_character" + }, + "curr_careunit": { + "name": "CURR_CAREUNIT", + "spec": "col_character" + }, + "prev_wardid": { + "name": "PREV_WARDID", + "spec": "col_integer" + }, + "curr_wardid": { + "name": "CURR_WARDID", + "spec": "col_integer" + }, + "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" + }, + "los": { + "name": "LOS", + "spec": "col_double" + } + } + } + } + } +] \ No newline at end of file diff --git a/inst/extdata/config/data-sources/mimic_demo.json b/inst/extdata/config/data-sources/mimic_demo.json index ff197574..4779db98 100644 --- a/inst/extdata/config/data-sources/mimic_demo.json +++ b/inst/extdata/config/data-sources/mimic_demo.json @@ -1 +1,1630 @@ -[{"name": "mimic_demo", "class_prefix": ["mimic_demo", "mimic"], "url": "https://physionet.org/files/mimiciii-demo/1.4", "id_cfg": {"patient": {"id": "subject_id", "position": 1, "start": "dob", "end": "dod", "table": "patients"}, "hadm": {"id": "hadm_id", "position": 2, "start": "admittime", "end": "dischtime", "table": "admissions"}, "icustay": {"id": "icustay_id", "position": 3, "start": "intime", "end": "outtime", "table": "icustays"}}, "tables": {"admissions": {"files": "ADMISSIONS.csv", "defaults": {"val_var": "admission_type", "time_vars": ["admittime", "dischtime", "deathtime", "edregtime", "edouttime"]}, "cols": {"row_id": {"name": "row_id", "spec": "col_integer"}, "subject_id": {"name": "subject_id", "spec": "col_integer"}, "hadm_id": {"name": "hadm_id", "spec": "col_integer"}, "admittime": {"name": "admittime", "spec": "col_datetime", "format": "%Y-%m-%d %H:%M:%S"}, "dischtime": {"name": "dischtime", "spec": "col_datetime", "format": "%Y-%m-%d %H:%M:%S"}, "deathtime": {"name": "deathtime", "spec": "col_datetime", "format": "%Y-%m-%d %H:%M:%S"}, "admission_type": {"name": "admission_type", "spec": "col_character"}, "admission_location": {"name": "admission_location", "spec": "col_character"}, "discharge_location": {"name": "discharge_location", "spec": "col_character"}, "insurance": {"name": "insurance", "spec": "col_character"}, "language": {"name": "language", "spec": "col_character"}, "religion": {"name": "religion", "spec": "col_character"}, "marital_status": {"name": "marital_status", "spec": "col_character"}, "ethnicity": {"name": "ethnicity", "spec": "col_character"}, "edregtime": {"name": "edregtime", "spec": "col_datetime", "format": "%Y-%m-%d %H:%M:%S"}, "edouttime": {"name": "edouttime", "spec": "col_datetime", "format": "%Y-%m-%d %H:%M:%S"}, "diagnosis": {"name": "diagnosis", "spec": "col_character"}, "hospital_expire_flag": {"name": "hospital_expire_flag", "spec": "col_integer"}, "has_chartevents_data": {"name": "has_chartevents_data", "spec": "col_integer"}}}, "callout": {"files": "CALLOUT.csv", "defaults": {"index_var": "outcometime", "val_var": "callout_outcome", "time_vars": ["createtime", "updatetime", "acknowledgetime", "outcometime", "firstreservationtime", "currentreservationtime"]}, "cols": {"row_id": {"name": "row_id", "spec": "col_integer"}, "subject_id": {"name": "subject_id", "spec": "col_integer"}, "hadm_id": {"name": "hadm_id", "spec": "col_integer"}, "submit_wardid": {"name": "submit_wardid", "spec": "col_integer"}, "submit_careunit": {"name": "submit_careunit", "spec": "col_character"}, "curr_wardid": {"name": "curr_wardid", "spec": "col_integer"}, "curr_careunit": {"name": "curr_careunit", "spec": "col_character"}, "callout_wardid": {"name": "callout_wardid", "spec": "col_integer"}, "callout_service": {"name": "callout_service", "spec": "col_character"}, "request_tele": {"name": "request_tele", "spec": "col_integer"}, "request_resp": {"name": "request_resp", "spec": "col_integer"}, "request_cdiff": {"name": "request_cdiff", 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"col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "los": { + "name": "los", + "spec": "col_double" + } + } + }, + "inputevents_cv": { + "files": "INPUTEVENTS_CV.csv", + "defaults": { + "index_var": "charttime", + "val_var": "rate", + "unit_var": "rateuom", + "time_vars": [ + "charttime", + "storetime" + ] + }, + "cols": { + "row_id": { + "name": "row_id", + "spec": "col_integer" + }, + "subject_id": { + "name": "subject_id", + "spec": "col_integer" + }, + "hadm_id": { + "name": "hadm_id", + "spec": "col_integer" + }, + "icustay_id": { + "name": "icustay_id", + "spec": "col_integer" + }, + "charttime": { + "name": "charttime", + "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" + }, + "storetime": { + "name": "storetime", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "cgid": { + "name": "cgid", + "spec": "col_integer" + }, + "orderid": { + "name": "orderid", + "spec": "col_integer" + }, + "linkorderid": { + "name": "linkorderid", + "spec": "col_integer" + }, + "stopped": { + "name": "stopped", + "spec": "col_character" + }, + "newbottle": { + "name": "newbottle", + "spec": "col_integer" + }, + "originalamount": { + "name": "originalamount", + "spec": "col_double" + }, + "originalamountuom": { + "name": "originalamountuom", + "spec": "col_character" + }, + "originalroute": { + "name": "originalroute", + "spec": "col_character" + }, + "originalrate": { + "name": "originalrate", + "spec": "col_double" + }, + "originalrateuom": { + "name": "originalrateuom", + "spec": "col_character" + }, + "originalsite": { + "name": "originalsite", + "spec": "col_character" + } + } + }, + "inputevents_mv": { + "files": 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}, + "storetime": { + "name": "storetime", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "cgid": { + "name": "cgid", + "spec": "col_integer" + }, + "orderid": { + "name": "orderid", + "spec": "col_integer" + }, + "linkorderid": { + "name": "linkorderid", + "spec": "col_integer" + }, + "ordercategoryname": { + "name": "ordercategoryname", + "spec": "col_character" + }, + "secondaryordercategoryname": { + "name": "secondaryordercategoryname", + "spec": "col_character" + }, + "ordercomponenttypedescription": { + "name": "ordercomponenttypedescription", + "spec": "col_character" + }, + "ordercategorydescription": { + "name": "ordercategorydescription", + "spec": "col_character" + }, + "patientweight": { + "name": "patientweight", + "spec": "col_double" + }, + "totalamount": { + "name": "totalamount", + "spec": "col_double" + }, + "totalamountuom": { + "name": "totalamountuom", + "spec": "col_character" + }, + "isopenbag": { + "name": "isopenbag", + "spec": "col_integer" 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"spec": "col_integer" + }, + "hadm_id": { + "name": "hadm_id", + "spec": "col_integer" + }, + "itemid": { + "name": "itemid", + "spec": "col_integer" + }, + "charttime": { + "name": "charttime", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "value": { + "name": "value", + "spec": "col_character" + }, + "valuenum": { + "name": "valuenum", + "spec": "col_double" + }, + "valueuom": { + "name": "valueuom", + "spec": "col_character" + }, + "flag": { + "name": "flag", + "spec": "col_character" + } + } + }, + "microbiologyevents": { + "files": "MICROBIOLOGYEVENTS.csv", + "defaults": { + "index_var": "chartdate", + "val_var": "isolate_num", + "time_vars": [ + "chartdate", + "charttime" + ] + }, + "cols": { + "row_id": { + "name": "row_id", + "spec": "col_integer" + }, + "subject_id": { + "name": "subject_id", + "spec": "col_integer" + }, + "hadm_id": { + "name": "hadm_id", + "spec": "col_integer" + }, + "chartdate": { + "name": "chartdate", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "charttime": { + "name": "charttime", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "spec_itemid": { + "name": "spec_itemid", + "spec": "col_integer" + }, + "spec_type_desc": { + "name": "spec_type_desc", + "spec": "col_character" + }, + "org_itemid": { + "name": "org_itemid", + "spec": "col_integer" + }, + "org_name": { + "name": "org_name", + "spec": "col_character" + }, + "isolate_num": { + "name": "isolate_num", + "spec": "col_integer" + }, + "ab_itemid": { + "name": "ab_itemid", + "spec": "col_integer" + }, + "ab_name": { + "name": "ab_name", + "spec": "col_character" + }, + "dilution_text": { + "name": "dilution_text", + "spec": "col_character" + }, + "dilution_comparison": { + "name": "dilution_comparison", + "spec": "col_character" + }, + "dilution_value": { + "name": "dilution_value", + "spec": "col_double" + }, + "interpretation": { + "name": "interpretation", + "spec": "col_character" + } + } + }, + "outputevents": { + "files": "OUTPUTEVENTS.csv", + "defaults": { + "index_var": "charttime", + "val_var": "value", + "unit_var": "valueuom", + "time_vars": [ + "charttime", + "storetime" + ] + }, + "cols": { + "row_id": { + "name": "row_id", + "spec": "col_integer" + }, + "subject_id": { + "name": "subject_id", + "spec": "col_integer" + }, + "hadm_id": { + "name": "hadm_id", + "spec": "col_integer" + }, + "icustay_id": { + "name": "icustay_id", + "spec": "col_integer" + }, + "charttime": { + "name": "charttime", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "itemid": { + "name": "itemid", + "spec": "col_integer" + }, + "value": { + "name": "value", + "spec": "col_double" + }, + "valueuom": { + "name": "valueuom", + "spec": "col_character" + }, + "storetime": { + "name": "storetime", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "cgid": { + "name": "cgid", + "spec": "col_integer" + }, + "stopped": { + "name": "stopped", + "spec": "col_character" + }, + "newbottle": { + "name": "newbottle", + "spec": "col_character" + }, + "iserror": { + "name": "iserror", + "spec": "col_integer" + } + } + }, + "patients": { + "files": "PATIENTS.csv", + "defaults": { + "val_var": "expire_flag", + "time_vars": [ + "dob", + "dod", + "dod_hosp", + "dod_ssn" + ] + }, + "cols": { + "row_id": { + "name": "row_id", + "spec": "col_integer" + }, + "subject_id": { + "name": "subject_id", + "spec": "col_integer" + }, + "gender": { + "name": "gender", + "spec": "col_character" + }, + "dob": { + "name": "dob", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "dod": { + "name": "dod", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "dod_hosp": { + "name": "dod_hosp", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "dod_ssn": { + "name": "dod_ssn", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "expire_flag": { + "name": "expire_flag", + "spec": "col_integer" + } + } + }, + "prescriptions": { + "files": "PRESCRIPTIONS.csv", + "defaults": { + "index_var": "startdate", + "val_var": "dose_val_rx", + "unit_var": "dose_unit_rx", + "time_vars": [ + "startdate", + "enddate" + ] + }, + "cols": { + "row_id": { + "name": "row_id", + "spec": "col_integer" + }, + "subject_id": { + "name": "subject_id", + "spec": "col_integer" + }, + "hadm_id": { + "name": "hadm_id", + "spec": "col_integer" + }, + "icustay_id": { + "name": "icustay_id", + "spec": "col_integer" + }, + "startdate": { + "name": "startdate", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "enddate": { + "name": "enddate", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "drug_type": { + "name": "drug_type", + "spec": "col_character" + }, + "drug": { + "name": "drug", + "spec": "col_character" + }, + "drug_name_poe": { + "name": "drug_name_poe", + "spec": "col_character" + }, + "drug_name_generic": { + "name": "drug_name_generic", + "spec": "col_character" + }, + "formulary_drug_cd": { + "name": "formulary_drug_cd", + "spec": "col_character" + }, + "gsn": { + "name": "gsn", + "spec": "col_character" + }, + "ndc": { + "name": "ndc", + "spec": "col_character" + }, + "prod_strength": { + "name": "prod_strength", + "spec": "col_character" + }, + "dose_val_rx": { + "name": "dose_val_rx", + "spec": "col_character" + }, + "dose_unit_rx": { + "name": "dose_unit_rx", + "spec": "col_character" + }, + "form_val_disp": { + "name": "form_val_disp", + "spec": "col_character" + }, + "form_unit_disp": { + "name": "form_unit_disp", + "spec": "col_character" + }, + "route": { + "name": "route", + "spec": "col_character" + } + } + }, + "procedureevents_mv": { + "files": "PROCEDUREEVENTS_MV.csv", + "defaults": { + "index_var": "starttime", + "val_var": "value", + "unit_var": "valueuom", + "time_vars": [ + "starttime", + "endtime", + "storetime", + "comments_date" + ] + }, + "cols": { + "row_id": { + "name": "row_id", + "spec": "col_integer" + }, + "subject_id": { + "name": "subject_id", + "spec": "col_integer" + }, + "hadm_id": { + "name": "hadm_id", + "spec": "col_integer" + }, + "icustay_id": { + "name": "icustay_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" + }, + "itemid": { + "name": "itemid", + "spec": "col_integer" + }, + "value": { + "name": "value", + "spec": "col_double" + }, + "valueuom": { + "name": "valueuom", + "spec": "col_character" + }, + "location": { + "name": "location", + "spec": "col_character" + }, + "locationcategory": { + "name": "locationcategory", + "spec": "col_character" + }, + "storetime": { + "name": "storetime", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "cgid": { + "name": "cgid", + "spec": "col_integer" + }, + "orderid": { + "name": "orderid", + "spec": "col_integer" + }, + "linkorderid": { + "name": "linkorderid", + "spec": "col_integer" + }, + "ordercategoryname": { + "name": "ordercategoryname", + "spec": "col_character" + }, + "secondaryordercategoryname": { + "name": "secondaryordercategoryname", + "spec": "col_character" + }, + "ordercategorydescription": { + "name": "ordercategorydescription", + "spec": "col_character" + }, + "isopenbag": { + "name": "isopenbag", + "spec": "col_integer" + }, + "continueinnextdept": { + "name": "continueinnextdept", + "spec": "col_integer" + }, + "cancelreason": { + "name": "cancelreason", + "spec": "col_integer" + }, + "statusdescription": { + "name": "statusdescription", + "spec": "col_character" + }, + "comments_editedby": { + "name": "comments_editedby", + "spec": "col_character" + }, + "comments_canceledby": { + "name": "comments_canceledby", + "spec": "col_character" + }, + "comments_date": { + "name": "comments_date", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + } + } + }, + "procedures_icd": { + "files": "PROCEDURES_ICD.csv", + "defaults": { + "val_var": "icd9_code" + }, + "cols": { + "row_id": { + "name": "row_id", + "spec": "col_integer" + }, + "subject_id": { + "name": "subject_id", + "spec": "col_integer" + }, + "hadm_id": { + "name": "hadm_id", + "spec": "col_integer" + }, + "seq_num": { + "name": "seq_num", + "spec": "col_integer" + }, + "icd9_code": { + "name": "icd9_code", + "spec": "col_character" + } + } + }, + "services": { + "files": "SERVICES.csv", + "defaults": { + "index_var": "transfertime", + "val_var": "curr_service", + "time_vars": "transfertime" + }, + "cols": { + "row_id": { + "name": "row_id", + "spec": "col_integer" + }, + "subject_id": { + "name": "subject_id", + "spec": "col_integer" + }, + "hadm_id": { + "name": "hadm_id", + "spec": "col_integer" + }, + "transfertime": { + "name": "transfertime", + "spec": "col_datetime", + "format": "%Y-%m-%d %H:%M:%S" + }, + "prev_service": { + "name": "prev_service", + "spec": "col_character" + }, + "curr_service": { + "name": "curr_service", + "spec": "col_character" + } + } + }, + "transfers": { + "files": "TRANSFERS.csv", + "defaults": { + "index_var": "intime", + "val_var": "curr_careunit", + "time_vars": [ + "intime", + "outtime" + ] + }, + "cols": { + "row_id": { + "name": "row_id", + "spec": "col_integer" + }, + "subject_id": { + "name": "subject_id", + "spec": "col_integer" + }, + "hadm_id": { + "name": "hadm_id", + "spec": "col_integer" + }, + "icustay_id": { + "name": "icustay_id", + "spec": "col_integer" + }, + "dbsource": { + "name": "dbsource", + "spec": "col_character" + }, + "eventtype": { + "name": "eventtype", + "spec": "col_character" + }, + "prev_careunit": { + "name": "prev_careunit", + "spec": "col_character" + }, + "curr_careunit": { + "name": "curr_careunit", + "spec": "col_character" + }, + "prev_wardid": { + "name": "prev_wardid", + "spec": "col_integer" + }, + "curr_wardid": { + "name": "curr_wardid", + "spec": "col_integer" + }, + "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" + }, + "los": { + "name": "los", + "spec": "col_double" + } + } + } + } + } +] \ No newline at end of file diff --git a/inst/extdata/config/data-sources/sic.json b/inst/extdata/config/data-sources/sic.json index 0badb234..760b50fc 100644 --- a/inst/extdata/config/data-sources/sic.json +++ b/inst/extdata/config/data-sources/sic.json @@ -1 +1,453 @@ -[{"name": "sic", "url": "https://physionet.org/files/sicdb/1.0.6", "id_cfg": {"patient": {"id": "PatientID", "position": 1, "start": "ICUOffset", "end": "OffsetOfDeath", "table": "cases"}, "icustay": {"id": "CaseID", "position": 2, "start": "ICUOffset", "end": "TimeOfStay", "table": "cases"}}, "tables": {"cases": {"files": "cases.csv.gz", "defaults": {"index_var": "ICUOffset", "time_vars": ["ICUOffset", "OffsetOfDeath", "HeartSurgeryBeginOffset", "HeartSurgeryEndOffset", "OffsetAfterFirstAdmission"]}, "num_rows": 27386, "cols": {"caseid": {"name": 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