PhenotypeR (version 0.3.3)

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`.

Usage

phenotypeDiagnostics(
  cohort,
  diagnostics = c("databaseDiagnostics", "codelistDiagnostics", "cohortDiagnostics",
    "populationDiagnostics"),
  measurementSample = 20000,
  drugExposureSample = 20000,
  survival = FALSE,
  cohortSample = 20000,
  matchedSample = 1000,
  populationSample = 1e+06,
  populationDateRange = as.Date(c(NA, NA))
)

Value

A summarised result

Arguments

cohort

Cohort table in a cdm reference

diagnostics

Vector indicating which diagnostics to perform. Options include: `databaseDiagnostics`, `codelistDiagnostics`, `cohortDiagnostics`, and `populationDiagnostics`.

measurementSample

The number of people to take a random sample for measurement diagnostics. If `measurementSample = NULL`, no sampling will be performed. If `measurementSample = 0` measurement diagnostics will not be run.

drugExposureSample

The number of people to take a random sample for drug diagnostics. If `drugExposureSample = NULL`, no sampling will be performed. If `drugExposureSample = 0` drug diagnostics will not be run.

survival

TRUE or FALSE. Whether to conduct survival analysis (TRUE) or not (FALSE).

cohortSample

The number of people to take a random sample for cohortDiagnostics. If `cohortSample = NULL`, no sampling will be performed.

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.

Examples

# \donttest{
library(omock)
library(CohortConstructor)
library(PhenotypeR)

cdm <- mockCdmFromDataset(source = "duckdb")
cdm$warfarin <- conceptCohort(cdm,
                              conceptSet =  list(warfarin = c(1310149L,
                                                              40163554L)),
                              name = "warfarin")

result <- phenotypeDiagnostics(cdm$warfarin)
# }