ricu 0.6.1

eth-mds · Jun 4, 2024 · c1206da · c1206da
1 parent 7f2cc42
commit c1206da
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Showing 4 changed files with 82 additions and 14 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -6,7 +6,7 @@ Description: Focused on (but not exclusive to) data sets hosted on PhysioNet
     functions for running arbitrary queries against available data sets, a
     system for defining clinical concepts and encoding their representations
     in tabular ICU data is presented.
-Version: 0.6.0
+Version: 0.6.1
 Authors@R: c(
     person(given = "Nicolas",
            family = "Bennett",

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# ricu 0.6.1
+
+* fixing the data-sources specification for MIMIC-IV (`miiv`)
+
 # ricu 0.6.0
 
 * Salzburg database (SICdb, `sic` in `ricu`) added as a data source with 64 concepts available
@@ -7,7 +11,6 @@
 # ricu 0.5.6
 
 * maintenance release: fixes non-character numeric version input issues
->>>>>>> 3c72261c4f049b49e7040a588b28eeb974a2f177
 
 # ricu 0.5.5
 

diff --git a/inst/extdata/config/data-sources.R b/inst/extdata/config/data-sources.R
@@ -831,7 +831,8 @@ miiv_tbl_cfg <- function() {
       ethnicity = list(spec = "col_character"),
       edregtime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
       edouttime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
-      hospital_expire_flag = list(spec = "col_integer")
+      hospital_expire_flag = list(spec = "col_integer"),
+      admit_provider_id = list(spec = "col_character")
     ),
     patients = list(
       subject_id = list(spec = "col_integer"),
@@ -935,7 +936,8 @@ miiv_tbl_cfg <- function() {
       medication = list(spec = "col_character"),
       event_txt = list(spec = "col_character"),
       scheduletime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
-      storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S")
+      storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
+      enter_provider_id = list(spec = "col_character")
     ),
     hcpcsevents = list(
       subject_id = list(spec = "col_integer"),
@@ -960,7 +962,8 @@ miiv_tbl_cfg <- function() {
       ref_range_upper = list(spec = "col_double"),
       flag = list(spec = "col_character"),
       priority = list(spec = "col_character"),
-      comments = list(spec = "col_character")
+      comments = list(spec = "col_character"),
+      order_provider_id = list(spec = "col_character")
     ),
     microbiologyevents = list(
       microevent_id = list(spec = "col_integer"),
@@ -986,7 +989,8 @@ miiv_tbl_cfg <- function() {
       dilution_comparison = list(spec = "col_character"),
       dilution_value = list(spec = "col_double"),
       interpretation = list(spec = "col_character"),
-      comments = list(spec = "col_character")
+      comments = list(spec = "col_character"),
+      order_provider_id = list(spec = "col_character")
     ),
     pharmacy = list(
       subject_id = list(spec = "col_integer"),
@@ -1036,7 +1040,8 @@ miiv_tbl_cfg <- function() {
       transaction_type = list(spec = "col_character"),
       discontinue_of_poe_id = list(spec = "col_character"),
       discontinued_by_poe_id = list(spec = "col_character"),
-      order_status = list(spec = "col_character")
+      order_status = list(spec = "col_character"),
+      order_provider_id = list(spec = "col_character")
     ),
     prescriptions = list(
       subject_id = list(spec = "col_integer"),
@@ -1055,7 +1060,9 @@ miiv_tbl_cfg <- function() {
       form_val_disp = list(spec = "col_character"),
       form_unit_disp = list(spec = "col_character"),
       doses_per_24_hrs = list(spec = "col_double"),
-      route = list(spec = "col_character")
+      route = list(spec = "col_character"),
+      order_provider_id = list(spec = "col_character"),
+      formulary_drug_cd = list(spec = "col_character")
     ),
     procedures_icd = list(
       subject_id = list(spec = "col_integer"),
@@ -1082,7 +1089,8 @@ miiv_tbl_cfg <- function() {
       value = list(spec = "col_character"),
       valuenum = list(spec = "col_double"),
       valueuom = list(spec = "col_character"),
-      warning = list(spec = "col_integer")
+      warning = list(spec = "col_integer"),
+      caregiver_id = list(spec = "col_integer")
     ),
     datetimeevents = list(
       subject_id = list(spec = "col_integer"),
@@ -1093,7 +1101,8 @@ miiv_tbl_cfg <- function() {
       itemid = list(spec = "col_integer"),
       value = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
       valueuom = list(spec = "col_character"),
-      warning = list(spec = "col_integer")
+      warning = list(spec = "col_integer"),
+      caregiver_id = list(spec = "col_integer")
     ),
     d_items = list(
       itemid = list(spec = "col_integer"),
@@ -1120,6 +1129,7 @@ miiv_tbl_cfg <- function() {
       subject_id = list(spec = "col_integer"),
       hadm_id = list(spec = "col_integer"),
       stay_id = list(spec = "col_integer"),
+      caregiver_id = list(spec = "col_integer"),
       starttime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
       endtime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
       storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
@@ -1152,7 +1162,8 @@ miiv_tbl_cfg <- function() {
       storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
       itemid = list(spec = "col_integer"),
       value = list(spec = "col_double"),
-      valueuom = list(spec = "col_character")
+      valueuom = list(spec = "col_character"),
+      caregiver_id = list(spec = "col_integer")
     ),
     procedureevents = list(
       subject_id = list(spec = "col_integer"),
@@ -1181,7 +1192,8 @@ miiv_tbl_cfg <- function() {
       comments_date = list(spec = "col_datetime",
                            format = "%Y-%m-%d %H:%M:%S"),
       originalamount = list(spec = "col_double"),
-      originalrate = list(spec = "col_double")
+      originalrate = list(spec = "col_double"),
+      caregiver_id = list(spec = "col_integer")
     ),
     omr = list(
       subject_id = list(spec = "col_integer"),
@@ -1200,6 +1212,7 @@ miiv_tbl_cfg <- function() {
       subject_id = list(spec = "col_integer"),
       hadm_id = list(spec = "col_integer"),
       stay_id = list(spec = "col_integer"),
+      caregiver_id = list(spec = "col_integer"),
       starttime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
       endtime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
       storetime = list(spec = "col_datetime", format = "%Y-%m-%d %H:%M:%S"),
@@ -1406,7 +1419,7 @@ miiv_tbl_cfg <- function() {
     outputevents = "icu/outputevents.csv.gz",
     procedureevents = "icu/procedureevents.csv.gz",
     omr = "hosp/omr.csv.gz",
-    caregiver = "hosp/caregiver.csv.gz",
+    caregiver = "icu/caregiver.csv.gz",
     provider = "hosp/provider.csv.gz",
     ingredientevents = "icu/ingredientevents.csv.gz"
   )

diff --git a/inst/extdata/config/data-sources.json b/inst/extdata/config/data-sources.json
@@ -7136,6 +7136,10 @@
           "hospital_expire_flag": {
             "name": "hospital_expire_flag",
             "spec": "col_integer"
+          },
+          "admit_provider_id": {
+            "name": "admit_provider_id",
+            "spec": "col_character"
           }
         }
       },
@@ -7573,6 +7577,10 @@
             "name": "storetime",
             "spec": "col_datetime",
             "format": "%Y-%m-%d %H:%M:%S"
+          },
+          "enter_provider_id": {
+            "name": "enter_provider_id",
+            "spec": "col_character"
           }
         }
       },
@@ -7682,6 +7690,10 @@
           "comments": {
             "name": "comments",
             "spec": "col_character"
+          },
+          "order_provider_id": {
+            "name": "order_provider_id",
+            "spec": "col_character"
           }
         },
         "partitioning": {
@@ -7797,6 +7809,10 @@
           "comments": {
             "name": "comments",
             "spec": "col_character"
+          },
+          "order_provider_id": {
+            "name": "order_provider_id",
+            "spec": "col_character"
           }
         }
       },
@@ -8007,6 +8023,10 @@
           "order_status": {
             "name": "order_status",
             "spec": "col_character"
+          },
+          "order_provider_id": {
+            "name": "order_provider_id",
+            "spec": "col_character"
           }
         },
         "partitioning": {
@@ -8093,6 +8113,14 @@
           "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"
           }
         }
       },
@@ -8215,6 +8243,10 @@
           "warning": {
             "name": "warning",
             "spec": "col_integer"
+          },
+          "caregiver_id": {
+            "name": "caregiver_id",
+            "spec": "col_integer"
           }
         },
         "partitioning": {
@@ -8269,6 +8301,10 @@
           "warning": {
             "name": "warning",
             "spec": "col_integer"
+          },
+          "caregiver_id": {
+            "name": "caregiver_id",
+            "spec": "col_integer"
           }
         }
       },
@@ -8385,6 +8421,10 @@
             "name": "stay_id",
             "spec": "col_integer"
           },
+          "caregiver_id": {
+            "name": "caregiver_id",
+            "spec": "col_integer"
+          },
           "starttime": {
             "name": "starttime",
             "spec": "col_datetime",
@@ -8525,6 +8565,10 @@
           "valueuom": {
             "name": "valueuom",
             "spec": "col_character"
+          },
+          "caregiver_id": {
+            "name": "caregiver_id",
+            "spec": "col_integer"
           }
         }
       },
@@ -8645,6 +8689,10 @@
           "originalrate": {
             "name": "originalrate",
             "spec": "col_double"
+          },
+          "caregiver_id": {
+            "name": "caregiver_id",
+            "spec": "col_integer"
           }
         }
       },
@@ -8681,7 +8729,7 @@
         }
       },
       "caregiver": {
-        "files": "hosp/caregiver.csv.gz",
+        "files": "icu/caregiver.csv.gz",
         "defaults": [],
         "num_rows": 15468,
         "cols": {
@@ -8724,6 +8772,10 @@
             "name": "stay_id",
             "spec": "col_integer"
           },
+          "caregiver_id": {
+            "name": "caregiver_id",
+            "spec": "col_integer"
+          },
           "starttime": {
             "name": "starttime",
             "spec": "col_datetime",