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",