phenotypeDiagnostics: Phenotype a cohort

In PhenotypeR: Assess Study Cohorts Using a Common Data Model

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'.

Usage

phenotypeDiagnostics(
  cohort,
  diagnostics = c("databaseDiagnostics", "codelistDiagnostics", "cohortDiagnostics",
    "populationDiagnostics"),
  survival = FALSE,
  matchedSample = 1000,
  populationSample = 1e+06,
  populationDateRange = as.Date(c(NA, NA))
)

Arguments

cohort	Cohort table in a cdm reference
diagnostics	Vector indicating which diagnostics to perform. Options include: 'databaseDiagnostics', 'codelistDiagnostics', 'cohortDiagnostics', and 'populationDiagnostics'.
survival	Boolean variable. Whether to conduct survival analysis (TRUE) or not (FALSE).
matchedSample	The number of people to take a random sample for matching. If 'matchedSample = NULL', no sampling will be performed. If 'matchedSample = 0', no matched cohorts will be created.
populationSample	Number of people from the cdm to sample. If NULL no sampling will be performed. Sample will be within populationDateRange if specified.
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.

Value

A summarised result

Examples

library(PhenotypeR)

cdm <- mockPhenotypeR()

result <- phenotypeDiagnostics(cdm$my_cohort)

CDMConnector::cdmDisconnect(cdm = cdm)

PhenotypeR documentation built on Aug. 8, 2025, 6:30 p.m.