first_case: First Case selection

In jomuller/ITCARES: an Interactive Tool for Case-crossover Analyses of electronic medical REcords for patient Safety

Description

Selects the first case stays of electronic medical records (EMRs) dataset and exclude patients with stays containing exclusion criteria within two years.

Usage

first_case(data, diagnoses_case, diagnoses_exclusion, exclude_in_case_stay,
  n_of_stays_max)

Arguments

data	A data.table of electronic medical records (EMRs).
diagnoses_case	A character vector containing codes to identify primary outcome diagnoses in stays.
diagnoses_exclusion	A character vector containing codes to identify exclusion diagnoses in stays.
exclude_in_case_stay	A Boolean. If TRUE, a case stay containing an exclusion criteria is discarded. If FALSE, case stays are not sought for exclusion criteria.
n_of_stays_max	A scalar giving the maximum number of stays allowed in the whole database for a unique patient.

Details

A case is defined as a patient who has experienced the primary outcome for the first time. Patients are excluded if they had a medical history defined by a list of one or more exclusion criteria. Stays containing one or more exclusion criteria are sought within a two year period before case. Any patient exceeding maximum number of stays is discarded.

Value

A data.table with selected first case stays.

Examples

data(ep)
obj0 <- ep

obj1 <- first_case(
  data = obj0,
  diagnoses_case =  'PE',
  diagnoses_exclusion = 'EXCLUSION',
  exclude_in_case_stay = FALSE,
  n_of_stays_max = 20
)

obj1 

obj2 <- age_study_period_restrictions(
  data = obj0,
  cases = obj1,
  starting_year = 2007,
  final_year = 2013,
  age_min = 0,
  age_max = 120
)

obj2

obj3 <- case_crossover(
  case_stay = obj2,
  data = obj0,
  exposure_diagnoses = '',
  exposure_procedures = 'THR',
  screening_index_stay = FALSE,
  unique_exposure = TRUE,
  interval_length = 42,
  number_of_interval = 8,
  wash_out = 365,
  los_max = 42
)
obj3 
obj3$graph

jomuller/ITCARES documentation built on May 19, 2019, 7:26 p.m.