PhenotypeR (version 0.1.4)

phenotypeDiagnostics: Phenotype a cohort

Description

This comprises all the diagnostics that are being offered in this package, this includes:

* A diagnostics on the database via `databaseDiagnostics`. * A diagnostics on the cohort_codelist attribute of the cohort via `codelistDiagnostics`. * A diagnostics on the cohort via `cohortDiagnostics`. * A diagnostics on the population via `populationDiagnostics`. * A diagnostics on the matched cohort via `matchedDiagnostics`.

Usage

phenotypeDiagnostics(
  cohort,
  databaseDiagnostics = TRUE,
  codelistDiagnostics = TRUE,
  cohortDiagnostics = TRUE,
  populationDiagnostics = TRUE,
  populationSample = 1e+06,
  populationDateRange = as.Date(c(NA, NA)),
  matchedDiagnostics = TRUE,
  matchedSample = 1000
)

Value

A summarised result

Arguments

cohort

Cohort table in a cdm reference

databaseDiagnostics

If TRUE, database diagnostics will be run.

codelistDiagnostics

If TRUE, codelist diagnostics will be run.

cohortDiagnostics

If TRUE, cohort diagnostics will be run.

populationDiagnostics

If TRUE, population diagnostics will be run.

populationSample

Number of people from the cdm to sample. If NULL no sampling will be performed

populationDateRange

Two dates. The first indicating the earliest cohort start date and the second indicating the latest possible cohort end date. If NULL or the first date is set as missing, the earliest observation_start_date in the observation_period table will be used for the former. If NULL or the second date is set as missing, the latest observation_end_date in the observation_period table will be used for the latter.

matchedDiagnostics

If TRUE, cohort to population diagnostics will be run.

matchedSample

The number of people to take a random sample for matching. If NULL, no sampling will be performed.

Examples

# \donttest{
library(PhenotypeR)

cdm <- mockPhenotypeR()

result <- phenotypeDiagnostics(cdm$my_cohort)

CDMConnector::cdmDisconnect(cdm = cdm)
# }