From ead0d832b532e5a3fc470d0ae5a9957d48517a24 Mon Sep 17 00:00:00 2001
From: Malte Londschien <malte@londschien.de>
Date: Tue, 1 Aug 2023 11:21:06 +0200
Subject: [PATCH 1/3] Make new table miiv.json to prevent me losing my mind.

---
 inst/extdata/config/miiv.json | 1632 +++++++++++++++++++++++++++++++++
 1 file changed, 1632 insertions(+)
 create mode 100644 inst/extdata/config/miiv.json

diff --git a/inst/extdata/config/miiv.json b/inst/extdata/config/miiv.json
new file mode 100644
index 00000000..184dca0f
--- /dev/null
+++ b/inst/extdata/config/miiv.json
@@ -0,0 +1,1632 @@
+{
+    "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 %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"
+          },
+          "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"
+          },
+          "hospital_expire_flag": {
+            "name": "hospital_expire_flag",
+            "spec": "col_integer"
+          }
+        }
+      },
+      "patients": {
+        "files": "hosp/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"
+          }
+        }
+      },
+      "omr" : {
+        "files": "core/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"
+          }
+        }
+      },
+      "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": {
+          "id_var": "code",
+          "val_var": "short_description"
+        },
+        "num_rows": 89200,
+        "cols": {
+          "code": {
+            "name": "code",
+            "spec": "col_character"
+          },
+          "category": {
+            "name": "category",
+            "spec": "col_integer"
+          },
+          "long_description": {
+            "name": "long_description",
+            "spec": "col_character"
+          },
+          "short_description": {
+            "name": "short_description",
+            "spec": "col_character"
+          }
+        }
+      },
+      "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": {
+          "id_var": "icd_code",
+          "val_var": "long_title"
+        },
+        "num_rows": 109775,
+        "cols": {
+          "icd_code": {
+            "name": "icd_code",
+            "spec": "col_character"
+          },
+          "icd_version": {
+            "name": "icd_version",
+            "spec": "col_integer"
+          },
+          "long_title": {
+            "name": "long_title",
+            "spec": "col_character"
+          }
+        }
+      },
+      "d_icd_procedures": {
+        "files": "hosp/d_icd_procedures.csv.gz",
+        "defaults": {
+          "id_var": "icd_code",
+          "val_var": "long_title"
+        },
+        "num_rows": 85257,
+        "cols": {
+          "icd_code": {
+            "name": "icd_code",
+            "spec": "col_character"
+          },
+          "icd_version": {
+            "name": "icd_version",
+            "spec": "col_integer"
+          },
+          "long_title": {
+            "name": "long_title",
+            "spec": "col_character"
+          }
+        }
+      },
+      "d_labitems": {
+        "files": "hosp/d_labitems.csv.gz",
+        "defaults": {
+          "id_var": "itemid",
+          "val_var": "label"
+        },
+        "num_rows": 1630,
+        "cols": {
+          "itemid": {
+            "name": "itemid",
+            "spec": "col_integer"
+          },
+          "label": {
+            "name": "label",
+            "spec": "col_character"
+          },
+          "fluid": {
+            "name": "fluid",
+            "spec": "col_character"
+          },
+          "category": {
+            "name": "category",
+            "spec": "col_character"
+          },
+          "loinc_code": {
+            "name": "loinc_code",
+            "spec": "col_character"
+          }
+        }
+      },
+      "drgcodes": {
+        "files": "hosp/drgcodes.csv.gz",
+        "defaults": {
+          "val_var": "drg_code"
+        },
+        "num_rows": 769622,
+        "cols": {
+          "subject_id": {
+            "name": "subject_id",
+            "spec": "col_integer"
+          },
+          "hadm_id": {
+            "name": "hadm_id",
+            "spec": "col_integer"
+          },
+          "drg_type": {
+            "name": "drg_type",
+            "spec": "col_character"
+          },
+          "drg_code": {
+            "name": "drg_code",
+            "spec": "col_character"
+          },
+          "description": {
+            "name": "description",
+            "spec": "col_character"
+          },
+          "drg_severity": {
+            "name": "drg_severity",
+            "spec": "col_integer"
+          },
+          "drg_mortality": {
+            "name": "drg_mortality",
+            "spec": "col_integer"
+          }
+        }
+      },
+      "emar_detail": {
+        "files": "hosp/emar_detail.csv.gz",
+        "defaults": {
+          "id_var": "emar_id"
+        },
+        "num_rows": 55947921,
+        "cols": {
+          "subject_id": {
+            "name": "subject_id",
+            "spec": "col_integer"
+          },
+          "emar_id": {
+            "name": "emar_id",
+            "spec": "col_character"
+          },
+          "emar_seq": {
+            "name": "emar_seq",
+            "spec": "col_integer"
+          },
+          "parent_field_ordinal": {
+            "name": "parent_field_ordinal",
+            "spec": "col_double"
+          },
+          "administration_type": {
+            "name": "administration_type",
+            "spec": "col_character"
+          },
+          "pharmacy_id": {
+            "name": "pharmacy_id",
+            "spec": "col_integer"
+          },
+          "barcode_type": {
+            "name": "barcode_type",
+            "spec": "col_character"
+          },
+          "reason_for_no_barcode": {
+            "name": "reason_for_no_barcode",
+            "spec": "col_character"
+          },
+          "complete_dose_not_given": {
+            "name": "complete_dose_not_given",
+            "spec": "col_character"
+          },
+          "dose_due": {
+            "name": "dose_due",
+            "spec": "col_character"
+          },
+          "dose_due_unit": {
+            "name": "dose_due_unit",
+            "spec": "col_character"
+          },
+          "dose_given": {
+            "name": "dose_given",
+            "spec": "col_character"
+          },
+          "dose_given_unit": {
+            "name": "dose_given_unit",
+            "spec": "col_character"
+          },
+          "will_remainder_of_dose_be_given": {
+            "name": "will_remainder_of_dose_be_given",
+            "spec": "col_character"
+          },
+          "product_amount_given": {
+            "name": "product_amount_given",
+            "spec": "col_character"
+          },
+          "product_unit": {
+            "name": "product_unit",
+            "spec": "col_character"
+          },
+          "product_code": {
+            "name": "product_code",
+            "spec": "col_character"
+          },
+          "product_description": {
+            "name": "product_description",
+            "spec": "col_character"
+          },
+          "product_description_other": {
+            "name": "product_description_other",
+            "spec": "col_character"
+          },
+          "prior_infusion_rate": {
+            "name": "prior_infusion_rate",
+            "spec": "col_character"
+          },
+          "infusion_rate": {
+            "name": "infusion_rate",
+            "spec": "col_character"
+          },
+          "infusion_rate_adjustment": {
+            "name": "infusion_rate_adjustment",
+            "spec": "col_character"
+          },
+          "infusion_rate_adjustment_amount": {
+            "name": "infusion_rate_adjustment_amount",
+            "spec": "col_character"
+          },
+          "infusion_rate_unit": {
+            "name": "infusion_rate_unit",
+            "spec": "col_character"
+          },
+          "route": {
+            "name": "route",
+            "spec": "col_character"
+          },
+          "infusion_complete": {
+            "name": "infusion_complete",
+            "spec": "col_character"
+          },
+          "completion_interval": {
+            "name": "completion_interval",
+            "spec": "col_character"
+          },
+          "new_iv_bag_hung": {
+            "name": "new_iv_bag_hung",
+            "spec": "col_character"
+          },
+          "continued_infusion_in_other_location": {
+            "name": "continued_infusion_in_other_location",
+            "spec": "col_character"
+          },
+          "restart_interval": {
+            "name": "restart_interval",
+            "spec": "col_character"
+          },
+          "side": {
+            "name": "side",
+            "spec": "col_character"
+          },
+          "site": {
+            "name": "site",
+            "spec": "col_character"
+          },
+          "non_formulary_visual_verification": {
+            "name": "non_formulary_visual_verification",
+            "spec": "col_character"
+          }
+        }
+      },
+      "emar": {
+        "files": "hosp/emar.csv.gz",
+        "defaults": {
+          "index_var": "charttime",
+          "time_vars": ["charttime", "scheduletime", "storetime"]
+        },
+        "num_rows": 27464367,
+        "cols": {
+          "subject_id": {
+            "name": "subject_id",
+            "spec": "col_integer"
+          },
+          "hadm_id": {
+            "name": "hadm_id",
+            "spec": "col_integer"
+          },
+          "emar_id": {
+            "name": "emar_id",
+            "spec": "col_character"
+          },
+          "emar_seq": {
+            "name": "emar_seq",
+            "spec": "col_integer"
+          },
+          "poe_id": {
+            "name": "poe_id",
+            "spec": "col_character"
+          },
+          "pharmacy_id": {
+            "name": "pharmacy_id",
+            "spec": "col_integer"
+          },
+          "charttime": {
+            "name": "charttime",
+            "spec": "col_datetime",
+            "format": "%Y-%m-%d %H:%M:%S"
+          },
+          "medication": {
+            "name": "medication",
+            "spec": "col_character"
+          },
+          "event_txt": {
+            "name": "event_txt",
+            "spec": "col_character"
+          },
+          "scheduletime": {
+            "name": "scheduletime",
+            "spec": "col_datetime",
+            "format": "%Y-%m-%d %H:%M:%S"
+          },
+          "storetime": {
+            "name": "storetime",
+            "spec": "col_datetime",
+            "format": "%Y-%m-%d %H:%M:%S"
+          }
+        }
+      },
+      "hcpcsevents": {
+        "files": "hosp/hcpcsevents.csv.gz",
+        "defaults": {
+          "index_var": "chartdate",
+          "time_vars": "chartdate"
+        },
+        "num_rows": 160727,
+        "cols": {
+          "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"
+          },
+          "hcpcs_cd": {
+            "name": "hcpcs_cd",
+            "spec": "col_character"
+          },
+          "seq_num": {
+            "name": "seq_num",
+            "spec": "col_integer"
+          },
+          "short_description": {
+            "name": "short_description",
+            "spec": "col_character"
+          }
+        }
+      },
+      "labevents": {
+        "files": "hosp/labevents.csv.gz",
+        "defaults": {
+          "index_var": "charttime",
+          "val_var": "valuenum",
+          "unit_var": "valueuom",
+          "time_vars": ["charttime", "storetime"]
+        },
+        "num_rows": 122103667,
+        "cols": {
+          "labevent_id": {
+            "name": "labevent_id",
+            "spec": "col_integer"
+          },
+          "subject_id": {
+            "name": "subject_id",
+            "spec": "col_integer"
+          },
+          "hadm_id": {
+            "name": "hadm_id",
+            "spec": "col_integer"
+          },
+          "specimen_id": {
+            "name": "specimen_id",
+            "spec": "col_integer"
+          },
+          "itemid": {
+            "name": "itemid",
+            "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"
+          },
+          "value": {
+            "name": "value",
+            "spec": "col_character"
+          },
+          "valuenum": {
+            "name": "valuenum",
+            "spec": "col_double"
+          },
+          "valueuom": {
+            "name": "valueuom",
+            "spec": "col_character"
+          },
+          "ref_range_lower": {
+            "name": "ref_range_lower",
+            "spec": "col_double"
+          },
+          "ref_range_upper": {
+            "name": "ref_range_upper",
+            "spec": "col_double"
+          },
+          "flag": {
+            "name": "flag",
+            "spec": "col_character"
+          },
+          "priority": {
+            "name": "priority",
+            "spec": "col_character"
+          },
+          "comments": {
+            "name": "comments",
+            "spec": "col_character"
+          }
+        },
+        "partitioning": {
+          "col": "itemid",
+          "breaks": [50868, 50902, 50943, 50983, 51146, 51248, 51256, 51279, 51491]
+        }
+      },
+      "microbiologyevents": {
+        "files": "hosp/microbiologyevents.csv.gz",
+        "defaults": {
+          "index_var": "chartdate",
+          "val_var": "isolate_num",
+          "time_vars": ["chartdate", "charttime", "storedate", "storetime"]
+        },
+        "num_rows": 3397914,
+        "cols": {
+          "microevent_id": {
+            "name": "microevent_id",
+            "spec": "col_integer"
+          },
+          "subject_id": {
+            "name": "subject_id",
+            "spec": "col_integer"
+          },
+          "hadm_id": {
+            "name": "hadm_id",
+            "spec": "col_integer"
+          },
+          "micro_specimen_id": {
+            "name": "micro_specimen_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"
+          },
+          "test_seq": {
+            "name": "test_seq",
+            "spec": "col_integer"
+          },
+          "storedate": {
+            "name": "storedate",
+            "spec": "col_datetime",
+            "format": "%Y-%m-%d %H:%M:%S"
+          },
+          "storetime": {
+            "name": "storetime",
+            "spec": "col_datetime",
+            "format": "%Y-%m-%d %H:%M:%S"
+          },
+          "test_itemid": {
+            "name": "test_itemid",
+            "spec": "col_integer"
+          },
+          "test_name": {
+            "name": "test_name",
+            "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"
+          },
+          "quantity": {
+            "name": "quantity",
+            "spec": "col_character"
+          },
+          "ab_itemid": {
+            "name": "ab_itemid",
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+            "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"
+          },
+          "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"
+          },
+          "patientweight": {
+            "name": "patientweight",
+            "spec": "col_double"
+          },
+          "totalamount": {
+            "name": "totalamount",
+            "spec": "col_double"
+          },
+          "totalamountuom": {
+            "name": "totalamountuom",
+            "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_date": {
+            "name": "comments_date",
+            "spec": "col_datetime",
+            "format": "%Y-%m-%d %H:%M:%S"
+          },
+          "originalamount": {
+            "name": "originalamount",
+            "spec": "col_double"
+          },
+          "originalrate": {
+            "name": "originalrate",
+            "spec": "col_double"
+          }
+        }
+      }
+    }
+  }
\ No newline at end of file

From ade685a6f179951c5147bb4494ff9fdd00d3fdfa Mon Sep 17 00:00:00 2001
From: Malte Londschien <malte@londschien.de>
Date: Tue, 1 Aug 2023 21:11:25 +0200
Subject: [PATCH 2/3] Update data-sources.json.

---
 inst/extdata/config/data-sources.json | 223 +++++++++++++++++++-------
 1 file changed, 167 insertions(+), 56 deletions(-)

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

From 35ae3bf20704a4173a8702ba092b6bad5f283690 Mon Sep 17 00:00:00 2001
From: Malte Londschien <malte@londschien.de>
Date: Wed, 2 Aug 2023 12:11:25 +0200
Subject: [PATCH 3/3] Get rid of miiv.json.

---
 inst/extdata/config/miiv.json | 1632 ---------------------------------
 1 file changed, 1632 deletions(-)
 delete mode 100644 inst/extdata/config/miiv.json

diff --git a/inst/extdata/config/miiv.json b/inst/extdata/config/miiv.json
deleted file mode 100644
index 184dca0f..00000000
--- a/inst/extdata/config/miiv.json
+++ /dev/null
@@ -1,1632 +0,0 @@
-{
-    "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 %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"
-          },
-          "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"
-          },
-          "hospital_expire_flag": {
-            "name": "hospital_expire_flag",
-            "spec": "col_integer"
-          }
-        }
-      },
-      "patients": {
-        "files": "hosp/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"
-          }
-        }
-      },
-      "omr" : {
-        "files": "core/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"
-          }
-        }
-      },
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\ No newline at end of file