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COVID Flag

covid_flag.Rd

covid_flag returns COVID-19 diagnosis status for each genc_id based on ICD-10-CA diagnosis codes.

Returns a table with two separate flags identifying encounters with confirmed and suspected COVID-19 diagnoses using ICD-10-CA U07.1 and U07.2 respectively.

A confirmed COVID-19 diagnosis (U07.1) is coded when there is a positive COVID-19 test. Effective April 1 2023, U07.1 is coded when COVID-19 was confirmed by any COVID-19 test, including polymerase chain reaction (PCR) tests, point-of-care molecular tests (POCT), or rapid antigen tests (RAT). For data prior to April 1, 2023, U07.1 was only coded when COVID-19 was confirmed by a PCR lab test (for details, see CIHI diagnosis type definitions).

A suspected COVID-19 diagnosis (U07.2) is coded when an encounter is clinically or epidemiological diagnosed but the associated COVID-19 tests are inconclusive, not available, or not performed.

Usage

covid_flag(cohort, ipdiag, erdiag)

Arguments

cohort

(data.frame or data.table) Cohort table with all relevant encounters of interest, where each row corresponds to a single encounter. Must contain GEMINI Encounter ID (genc_id).

ipdiag

(data.table) ipdiagnosis table as defined in the GEMINI Data Repository Dictionary. This table must contain genc_id and diagnosis_code (as ICD-10-CA alphanumeric code) in long format.

erdiag

(data.table) erdiagnosis table as defined in the GEMINI Data Repository Dictionary. This table must contain genc_id and er_diagnosis_code (as ICD-10-CA alphanumeric code) in long format. Typically, ER diagnoses should be included when deriving the COVID flags in order to increase sensitivity. However, in certain scenarios, users may choose to only include IP diagnoses by specifying erdiag = NULL. This may be useful when comparing cohorts with different rates of ER admissions.

Value

data.table with the same number of rows as input cohort with additional derived boolean fields labelled as "covid_icd_confirmed_flag" and "covid_icd_suspected_flag". Possible values are TRUE, FALSE or NA. NA indicates that an encounter does not have a diagnosis code in the diagnosis table input.

When one tries to left-join the output of this function with another table (another list of admissions in the left), make sure list of admissions (or patient) aligns in both tables.

Details

Below is the current ICD-10-CA diagnosis codes related to COVID-19. For more details, please refer to the references in this page.

  • U07.1 : For confirmed cases of COVID-19, assign U07.1 Emergency use of U07.1 (COVID-19, virus identified)

  • U07.2 : For suspected cases of COVID-19, assign U07.2 Emergency use of U07.2 (COVID-19, virus not identified)

  • U07.3 : Multisystem inflammatory syndrome associated with COVID-19

  • U07.4 : post COVID-19 condition

  • U07.5 : personal history of COVID-19

  • U07.6 : Need for immunization against COVID-19. This code is for use when a person encounters health services for the sole purpose of receiving the COVID-19 vaccine.

  • U07.7 : COVID-19 vaccines causing adverse effect in therapeutic use. This emergency use code is an external cause code. This code would normally be located at the ICD-10-CA block Y40-Y59 Drugs, medicaments and biological substances causing adverse effects in therapeutic use.

Note

This function does not differentiate between diagnosis types. That is, the COVID flags are derived based on all diagnosis codes that are provided as input to this function. By default, users should include all diagnosis types to identify COVID. However, if users wish to include only certain diagnosis types (e.g., type-M for most responsible discharge diagnosis), the ipdiag and erdiag input tables should be filtered accordingly based on diagnosis_type prior to running this function (for more details, see CIHI diagnosis type definitions.

References

CIHI COVID-19 data collection and coding direction

Examples

if (FALSE) { # \dontrun{
drv <- dbDriver("PostgreSQL")
dbcon <- DBI::dbConnect(drv,
  dbname = "db",
  host = "domain_name.ca",
  port = 1234,
  user = getPass("Enter user:"),
  password = getPass("password")
)

ipadm <- dbGetQuery(dbcon, "select * from admdad") %>% data.table()
ipdiagnosis <- dbGetQuery(dbcon, "select * from ipdiagnosis") %>% data.table()
erdiagnosis <- dbGetQuery(dbcon, "select * from erdiagnosis") %>% data.table()

covid <- covid_flag(cohort = ipadm, ipdiag = ipdiagnosis, erdiag = )
} # }