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": 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"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", 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"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": 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"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, 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+ "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": "age", "spec": "col_integer"}, "discharge_status": {"name": "discharge_status", "spec": "col_character"}}, "num_rows": 33905, "zip_file": "reference_data.tar.gz"}, "observations": {"files": ["observation_tables/csv/part-0.csv", "observation_tables/csv/part-1.csv", "observation_tables/csv/part-2.csv", "observation_tables/csv/part-3.csv", "observation_tables/csv/part-4.csv", "observation_tables/csv/part-5.csv", "observation_tables/csv/part-6.csv", "observation_tables/csv/part-7.csv", "observation_tables/csv/part-8.csv", "observation_tables/csv/part-9.csv", 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"additional_information": {"name": "Additional information", "spec": "col_character"}}, "num_rows": 712, "zip_file": "reference_data.tar.gz"}}}] \ No newline at end of file +[ + { + "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": "age", + "spec": "col_integer" + }, + "discharge_status": { + "name": "discharge_status", + "spec": "col_character" + } + }, + "num_rows": 33905, + "zip_file": "reference_data.tar.gz" + }, + "observations": 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"spec": "col_integer" + } + }, + "num_rows": 776921131, + "zip_file": "raw_stage/observation_tables_csv.tar.gz", + "partitioning": { + "col": "variableid", + "breaks": [ + 110, + 120, + 200, + 210, + 211, + 300, + 620, + 2010, + 2610, + 3110, + 4000, + 5685, + 15001565, + 30005075 + ] + } + }, + "ordinal": { + "files": "ordinal_vars_ref.csv", + "defaults": { + "id_var": "variableid" + }, + "cols": { + "variableid": { + "name": "variableid", + "spec": "col_integer" + }, + "code": { + "name": "code", + "spec": "col_integer" + }, + "stringvalue": { + "name": "stringvalue", + "spec": "col_character" + } + }, + "num_rows": 72, + "zip_file": "reference_data.tar.gz" + }, + "pharma": { + "files": [ + "pharma_records/csv/part-0.csv", + "pharma_records/csv/part-1.csv", + "pharma_records/csv/part-2.csv", + "pharma_records/csv/part-3.csv", + "pharma_records/csv/part-4.csv", + "pharma_records/csv/part-5.csv", + "pharma_records/csv/part-6.csv", + "pharma_records/csv/part-7.csv", + 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"pharma_records/csv/part-62.csv", + "pharma_records/csv/part-63.csv", + "pharma_records/csv/part-64.csv", + "pharma_records/csv/part-65.csv", + "pharma_records/csv/part-66.csv", + "pharma_records/csv/part-67.csv", + "pharma_records/csv/part-68.csv", + "pharma_records/csv/part-69.csv", + "pharma_records/csv/part-70.csv", + "pharma_records/csv/part-71.csv", + "pharma_records/csv/part-72.csv", + "pharma_records/csv/part-73.csv", + "pharma_records/csv/part-74.csv", + "pharma_records/csv/part-75.csv", + "pharma_records/csv/part-76.csv", + "pharma_records/csv/part-77.csv", + "pharma_records/csv/part-78.csv", + "pharma_records/csv/part-79.csv", + "pharma_records/csv/part-80.csv", + "pharma_records/csv/part-81.csv", + "pharma_records/csv/part-82.csv", + "pharma_records/csv/part-83.csv", + "pharma_records/csv/part-84.csv", + "pharma_records/csv/part-85.csv", + "pharma_records/csv/part-86.csv", + "pharma_records/csv/part-87.csv", + "pharma_records/csv/part-88.csv", + 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"pharma_records/csv/part-170.csv", + "pharma_records/csv/part-171.csv", + "pharma_records/csv/part-172.csv", + "pharma_records/csv/part-173.csv", + "pharma_records/csv/part-174.csv", + "pharma_records/csv/part-175.csv", + "pharma_records/csv/part-176.csv", + "pharma_records/csv/part-177.csv", + "pharma_records/csv/part-178.csv", + "pharma_records/csv/part-179.csv", + "pharma_records/csv/part-180.csv", + "pharma_records/csv/part-181.csv", + "pharma_records/csv/part-182.csv", + "pharma_records/csv/part-183.csv", + "pharma_records/csv/part-184.csv", + "pharma_records/csv/part-185.csv", + "pharma_records/csv/part-186.csv", + "pharma_records/csv/part-187.csv", + "pharma_records/csv/part-188.csv", + "pharma_records/csv/part-189.csv", + "pharma_records/csv/part-190.csv", + "pharma_records/csv/part-191.csv", + "pharma_records/csv/part-192.csv", + "pharma_records/csv/part-193.csv", + "pharma_records/csv/part-194.csv", + "pharma_records/csv/part-195.csv", + "pharma_records/csv/part-196.csv", + "pharma_records/csv/part-197.csv", + "pharma_records/csv/part-198.csv", + "pharma_records/csv/part-199.csv", + "pharma_records/csv/part-200.csv", + "pharma_records/csv/part-201.csv", + "pharma_records/csv/part-202.csv", + "pharma_records/csv/part-203.csv", + "pharma_records/csv/part-204.csv", + "pharma_records/csv/part-205.csv", + "pharma_records/csv/part-206.csv", + "pharma_records/csv/part-207.csv", + "pharma_records/csv/part-208.csv", + "pharma_records/csv/part-209.csv", + "pharma_records/csv/part-210.csv", + "pharma_records/csv/part-211.csv", + "pharma_records/csv/part-212.csv", + "pharma_records/csv/part-213.csv", + "pharma_records/csv/part-214.csv", + "pharma_records/csv/part-215.csv", + "pharma_records/csv/part-216.csv", + "pharma_records/csv/part-217.csv", + "pharma_records/csv/part-218.csv", + "pharma_records/csv/part-219.csv", + "pharma_records/csv/part-220.csv", + "pharma_records/csv/part-221.csv", + "pharma_records/csv/part-222.csv", + "pharma_records/csv/part-223.csv", + "pharma_records/csv/part-224.csv", + "pharma_records/csv/part-225.csv", + "pharma_records/csv/part-226.csv", + "pharma_records/csv/part-227.csv", + "pharma_records/csv/part-228.csv", + "pharma_records/csv/part-229.csv", + "pharma_records/csv/part-230.csv", + "pharma_records/csv/part-231.csv", + "pharma_records/csv/part-232.csv", + "pharma_records/csv/part-233.csv", + "pharma_records/csv/part-234.csv", + "pharma_records/csv/part-235.csv", + "pharma_records/csv/part-236.csv", + "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" + }, + "givendose": { + "name": "givendose", + "spec": "col_double" + }, + "cumulativedose": { + "name": "cumulativedose", + "spec": "col_double" + }, + "fluidamount_calc": { + "name": "fluidamount_calc", + "spec": "col_double" + }, + "cumulfluidamount_calc": { + "name": "cumulfluidamount_calc", + "spec": "col_double" + }, + "doseunit": { + "name": "doseunit", + "spec": "col_character" + }, + "route": { + "name": "route", + "spec": "col_character" + }, + "infusionid": { + "name": "infusionid", + "spec": "col_integer" + }, + "typeid": { + "name": "typeid", + "spec": "col_integer" + }, + "subtypeid": { + "name": "subtypeid", + "spec": "col_double" + }, + "recordstatus": { + "name": "recordstatus", + "spec": "col_integer" + } + }, + "num_rows": 16270399, + "zip_file": "raw_stage/pharma_records_csv.tar.gz", + "partitioning": { + "col": "pharmaid", + "breaks": 431 + } + }, + "variables": { + "files": "hirid_variable_reference.csv", + "defaults": { + "id_var": "id" + }, + "cols": { + "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": "admissions"}, "icustay": {"id": "stay_id", "position": 3, "start": "intime", "end": "outtime", "table": "icustays"}}, "tables": {"admissions": {"files": "hosp/admissions.csv.gz", "defaults": {"val_var": "admission_type", "time_vars": ["admittime", "dischtime", "deathtime", "edregtime", "edouttime"]}, "num_rows": 431231, "cols": {"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 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"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": 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