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'. * 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
)

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.

Value

A summarised result

Examples

library(PhenotypeR)

cdm <- mockPhenotypeR()

result <- phenotypeDiagnostics(cdm$my_cohort)

CDMConnector::cdmDisconnect(cdm = cdm)

PhenotypeR documentation built on April 3, 2025, 10:46 p.m.