populationDiagnostics: Population-level diagnostics

In PhenotypeR: Assess Study Cohorts Using a Common Data Model

Population-level diagnostics

Description

phenotypeR diagnostics on the cohort of input with relation to a denomination population. Diagnostics include:

* Incidence * Prevalence

Usage

populationDiagnostics(
  cohort,
  populationSample = 1e+06,
  populationDateRange = as.Date(c(NA, NA))
)

Arguments

cohort	Cohort table in a cdm reference
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.

Value

A summarised result

Examples

library(PhenotypeR)
library(dplyr)

cdm <- mockPhenotypeR()

dateStart <- cdm$my_cohort |>
  summarise(start = min(cohort_start_date, na.rm = TRUE)) |>
  pull("start")
dateEnd   <- cdm$my_cohort |>
  summarise(start = max(cohort_start_date, na.rm = TRUE)) |>
  pull("start")

result <- cdm$my_cohort |>
  populationDiagnostics(populationDateRange = c(dateStart, dateEnd))

CDMConnector::cdmDisconnect(cdm = cdm)

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