checkBase function

General check function

Function that performs various checks to ensure the database is correctly formatted, and adjusts overlapping patient records.

checkBase(
  base,
  convertDates = FALSE,
  dateFormat = NULL,
  deleteMissing = NULL,
  deleteErrors = NULL,
  subjectID = "sID",
  facilityID = "fID",
  disDate = "Ddate",
  admDate = "Adate",
  maxIteration = 25,
  retainAuxData = TRUE,
  verbose = TRUE,
  ...
)

Arguments

• base: (data.table). A patient discharge database, in the form of a data.table. The data.table should have at least the following columns: sID: patientID (character) fID: facilityID (character) Adate: admission date (POSIXct, but character can be converted to POSIXct) Ddate: discharge date (POSIXct, but character can be converted to POSIXct)
• convertDates: (boolean) indicating if dates need to be converted to POSIXct if they are not
• dateFormat: (character) giving the input format of the date character string (e.g. "ymd" for dates like "2019-10-30") See parse_date_time for more information on the format.
• deleteMissing: (character) How to handle records that contain a missing value in at least one of the four mandatory variables: NULL (default): do not delete. Stops the function with an error message. "record": deletes just the incorrect record. "patient": deletes all records of each patient with one or more incorrect records.
• deleteErrors: (character) How incorrect records should be deleted: "record" deletes just the incorrect record "patient" deletes all records of each patient with one or more incorrect records.
• subjectID: (character) the columns name containing the subject ID. Default is "sID"
• facilityID: (character) the columns name containing the facility ID. Default is "fID"
• disDate: (character) the columns name containing the discharge date. Default is "Ddate"
• admDate: (character) the columns name containing the admission date. Default is "Adate"
• maxIteration: (integer) the maximum number of times the function will try and remove overlapping admissions
• retainAuxData: (boolean) allow retaining additional data provided in the database. Default is TRUE.
• verbose: (boolean) print diagnostic messages. Default is TRUE.
• ...: other parameters passed on to internal functions

Returns

The adjusted database as a data.table with a new class attribute "hospinet.base" and an attribute "report" containing information related to the quality of the database.

Examples

## create a "fake and custom" data base
mydb = create_fake_subjectDB(n_subjects = 100, n_facilities = 100)
setnames(mydb, 1:4, c("myPatientId", "myHealthCareCenterID", "DateOfAdmission", "DateOfDischarge"))
mydb[,DateOfAdmission:= as.character(DateOfAdmission)]
mydb[,DateOfDischarge:= as.character(DateOfDischarge)]

head(mydb)
#   myPatientId myHealthCareCenterID DateOfAdmission DateOfDischarge
#1:        s001                 f078      2019-01-26      2019-02-01
#2:        s002                 f053      2019-01-18      2019-01-21
#3:        s002                 f049      2019-02-25      2019-03-05
#4:        s002                 f033      2019-04-17      2019-04-21
#5:        s003                 f045      2019-02-02      2019-02-04
#6:        s003                 f087      2019-03-12      2019-03-19

str(mydb)
#Classes ‘data.table’ and 'data.frame': 262 obs. of  4 variables:
# $ myPatientId         : chr  "s001" "s002" "s002" "s002" ...
# $ myHealthCareCenterID: chr  "f078" "f053" "f049" "f033" ...
# $ DateOfAdmission     : chr  "2019-01-26" "2019-01-18" "2019-02-25" "2019-04-17" ...
# $ DateOfDischarge     : chr  "2019-02-01" "2019-01-21" "2019-03-05" "2019-04-21" ...
#- attr(*, ".internal.selfref")=<externalptr> 

my_checked_db = checkBase(mydb, 
     subjectID = "myPatientId", 
     facilityID = "myHealthCareCenterID", 
     disDate = "DateOfDischarge",
     admDate = "DateOfAdmission", 
     convertDates = TRUE, 
     dateFormat = "ymd")

#Converting Adate, Ddate to Date format
#Checking for missing values...
#Checking for duplicated records...
#Removed 0 duplicates
#Done.

head(my_checked_db)
#    sID  fID      Adate      Ddate
#1: s001 f078 2019-01-26 2019-02-01
#2: s002 f053 2019-01-18 2019-01-21
#3: s002 f049 2019-02-25 2019-03-05
#4: s002 f033 2019-04-17 2019-04-21
#5: s003 f045 2019-02-02 2019-02-04
#6: s003 f087 2019-03-12 2019-03-19
str(my_checked_db)
#Classes ‘hospinet.base’, ‘data.table’ and 'data.frame':        262 obs. of  4 variables:
#$ sID  : chr  "s001" "s002" "s002" "s002" ...
#$ fID  : chr  "f078" "f053" "f049" "f033" ...
#$ Adate: POSIXct, format: "2019-01-26" "2019-01-18" "2019-02-25" "2019-04-17" ...
#$ Ddate: POSIXct, format: "2019-02-01" "2019-01-21" "2019-03-05" "2019-04-21" ...
# ...

## Show the quality report
attr(my_checked_db, "report")

See Also

parse_date_time