epidm (version 1.0.6)

cip_spells: Continuous Inpatient (CIP) Spells

Description

Creates Continuous Inpatient (CIP) spells by combining one or more provider spells into a single uninterrupted period of inpatient care. CIP definitions follow the NHS Digital methodology: transfers between providers can be part of the same CIP spell where specific admission, discharge, and timing criteria are met. A CIP spell begins when a patient is admitted under consultant care and ends when they are discharged or die. http://content.digital.nhs.uk/media/11859/Provider-Spells-Methodology/pdf/Spells_Methodology.pdf

Where spells meet the CIP criteria, they are merged into a continuous spell. The output includes a CIP index and the derived start and end dates for the full CIP period.

Usage

cip_spells(
  x,
  group_vars,
  spell_start_date,
  admission_method,
  admission_source,
  spell_end_date,
  discharge_destination,
  patient_classification,
  .forceCopy = FALSE
)

Value

A data.table containing the original data and three new variables:

cip_indx

Unique identifier for the derived CIP spell.

cip_spell_start

Start date for the continuous inpatient spell.

cip_spell_end

End date for the continuous inpatient spell.

Arguments

x

A data.frame or data.table; will be converted to a data.table (usually HES/SUS data)

group_vars

Character vector of variables used to group records (minimum: a patient identifier).

spell_start_date

Quoted column name containing the provider spell admission date.

admission_method

CDS admission method code.

admission_source

CDS admission source code.

spell_end_date

Quoted column name containing the provider spell discharge date.

discharge_destination

CDS discharge destination code.

patient_classification

CDS patient classification code.

.forceCopy

Logical (default FALSE). If FALSE, the input is converted to a data.table and modified by reference. If TRUE, the input must already be a data.table, and the function will create an explicit copy to avoid modifying the original object.

Examples

cip_test <- data.frame(
  id = c('465','465','465','465','8418','8418','8418',
         '8418','8418','8418','8418','8418','26443',
         '26443','26443','33299','33299','33299','33299',
         '33299','33299','33299','33299','33299','33299',
         '52635','52635','52635','52635','52635','52635',
         '52635','52635','52635','52635','52635','52635',
         '52635','52635','52635','52635','52635','52635',
         '52635','52635','52635','52635','52635','52635',
         '52635','52635','52635','78915','78915','78915'),
  provider = c('X1T','X1T','X1T','X1T','KHA','KHA','KHA',
               'KHA','KHA','KHA','KHA','KHA','BX2','BX2',
               'BX2','PXH','PXH','PXH','PXH','PXH','PXH',
               'PXH','PXH','PXH','PXH','9HA','9HA','9HA',
               '9HA','9HA','9HA','9HA','9HA','9HA','9HA',
               '9HA','9HA','9HA','9HA','9HA','9HA','YYT',
               'YYT','YYT','YYT','YYT','YYT','YYT','YYT',
               'YYT','YYT','YYT','ABX','ABX','ABX'),
  spell_start = as.Date(c(
    '2020-03-07','2020-03-07','2020-03-25','2020-04-03','2020-01-25',
    '2020-01-26','2020-07-14','2020-08-02','2020-08-12','2020-08-19',
    '2020-08-19','2020-11-19','2019-11-12','2020-04-17','2020-04-23',
    '2020-07-03','2020-01-17','2020-02-07','2020-03-20','2020-04-27',
    '2020-06-21','2020-07-02','2020-10-17','2020-11-27','2021-01-02',
    '2019-12-31','2020-01-02','2020-01-14','2020-01-16','2020-02-07',
    '2020-02-11','2020-02-14','2020-02-18','2020-02-21','2020-02-25',
    '2020-02-28','2020-03-09','2020-03-11','2020-03-12','2020-03-13',
    '2020-03-14','2020-02-04','2020-02-07','2020-02-11','2020-02-14',
    '2020-02-18','2020-02-21','2020-02-25','2020-02-28','2020-03-09',
    '2020-03-11','2020-03-12','2020-04-16','2020-04-24','2020-05-13')),
  spell_end = as.Date(c(
    '2020-03-07','2020-03-25','2020-04-02','2020-04-27','2020-01-25',
    '2020-01-27','2020-07-17','2020-08-07','2020-08-14','2020-08-19',
    '2020-08-22','2020-12-16','2020-04-17','2020-04-23','2020-05-20',
    '2020-07-24','2020-01-28','2020-02-07','2020-03-23','2020-04-29',
    '2020-06-21','2020-07-03','2020-11-27','2021-01-02','2021-01-10',
    '2019-12-31','2020-01-11','2020-01-14','2020-02-04','2020-02-07',
    '2020-02-11','2020-02-14','2020-02-18','2020-02-21','2020-02-25',
    '2020-02-28','2020-03-09','2020-03-11','2020-03-12','2020-03-13',
    '2020-03-30','2020-02-07','2020-02-11','2020-02-14','2020-02-18',
    '2020-02-21','2020-02-25','2020-02-28','2020-03-09','2020-03-11',
    '2020-03-12','2020-03-13','2020-04-24','2020-05-13','2020-06-11')),
  adm_meth = c('21','81','21','81','21','21','11','21','21','21','21',
               '21','21','81','21','81','21','21','21','21','21','21',
               '21','13','13','12','22','12','2D','13','13','13','13',
               '13','13','13','13','13','13','13','21','81','81','81',
               '81','81','13','81','81','13','13','13','21','11','81'),
  adm_src = c('19','51','19','51','19','51','19','51','19','19','19',
              '51','19','51','19','51','19','19','19','19','19','19',
              '19','51','19','19','19','19','19','19','19','19','19',
              '19','19','19','51','51','51','51','19','51','51','51',
              '51','51','51','51','51','51','51','51','19','51','51'),
  dis_meth = c('1','1','1','1','1','1','1','1','1','1','1','4','1','1',
               '4','1','1','1','1','1','1','1','8','1','4','1','1','1',
               '1','1','1','1','1','1','1','1','1','1','1','1','1','1',
               '1','1','1','1','1','1','1','1','1','1','1','1','2'),
  dis_dest = c('51','51','51','54','51','19','19','19','19','51','19',
               '79','51','51','79','65','19','19','19','19','19','29',
               '98','51','79','19','19','19','51','19','19','19','51',
               '51','51','19','19','51','51','19','51','51','51','51',
               '51','51','51','51','51','51','51','51','29','54','19'),
  patclass = c('1','1','1','1','1','1','1','1','1','1','1','1','1','1',
               '1','1','1','1','1','1','1','1','1','1','1','2','1','2',
               '1','2','2','2','2','2','2','2','2','2','2','2','1','1',
               '1','1','1','1','1','1','1','1','1','1','1','1','1')
)

cip_spells(x=cip_test,
  group_vars = c('id','provider'),
  patient_classification = 'patclass',
  spell_start_date = 'spell_start',
  admission_method = 'adm_meth',
  admission_source = 'adm_src',
  spell_end_date = 'spell_end',
  discharge_destination = 'dis_dest'
)[]