apportion: Apportion CDI and MSSA records

In PublicHealthEngland/hcaidcs: R functions for the mandatory surveillance of bacteraemia and C. difficile infection

Apportion CDI and MSSA records

Description

Apportions records to apportioning algorithm. Includes a clause whereby records created prior to 26th October 2015 are not trust apportioned if patient location is Unknown. This is to ensure consistency with previous reports. See p 47 of Mandatory Surveillance protocol. Prior to the launch of the new DCS, users could create records where the patient location was Null and these cases would not have been apportioned automatically.

Usage

apportion(
  collection,
  patient_location,
  patient_category,
  date_admitted,
  specimen_date,
  date_entered
)

Arguments

collection	The collection (MRSA, MSSA, CDI, E. coli) to which the record belongs.
patient_location	The patient's location at time of sample
patient_category	The patient's category at time of sample
date_admitted	The date the patient was admitted for records from inpatients
specimen_date	The date of the specimen (POSIXct, POSIXt or Date format)
date_entered	Date record created normally 'data collection date' (POSIXct, POSIXt or Date format)

Value

A binary vector giving 1 for Trust-apportioned records and 0 for non-Trust apportioned records

Examples

apportion("mssa", "NHS Acute Trust", "In-patient",
date_admitted = lubridate::dmy("01-01-2015"), specimen_date =
lubridate::dmy("05-01-2015"), date_entered = lubridate::dmy("26-10-2015"))
## Not run: 
apportion("mssa", "NHS Acute Trust", "In-patient",
date_admitted = as.Date(NA_real_, origin = "01-01-1970"),
specimen_date = lubridate::dmy("01-01-2015"), date_entered =
lubridate::dmy("26-10-2015"))
apportion("mssa", "NHS Acute Trust", "In-patient", date_admitted =
lubridate::dmy(""), specimen_date = lubridate::dmy("01-01-2015"),
date_entered = lubridate::dmy("26-10-2015"))

## End(Not run)
apportion("mssa", "NHS Acute Trust", "In-patient", date_admitted =
lubridate::dmy("01-01-2015"),  specimen_date = lubridate::dmy("01-01-2015"),
date_entered = lubridate::dmy("26-10-2015"))
apportion("mssa", "NHS Acute Trust", "Outpatient", date_admitted =
lubridate::dmy("01-01-2015"),  specimen_date = lubridate::dmy("05-01-2015"),
date_entered = lubridate::dmy("26-10-2015"))
apportion("cdi", "NHS Acute Trust", "In-patient", date_admitted =
lubridate::dmy("01-01-2015"),  specimen_date = lubridate::dmy("05-01-2015"),
date_entered = lubridate::dmy("26-10-2015"))

PublicHealthEngland/hcaidcs documentation built on Jan. 19, 2024, 8:38 a.m.