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,
  survival = FALSE,
  match = TRUE,
  matchedSample = 1000,
  populationDiagnostics = TRUE,
  populationSample = 1e+06,
  populationDateRange = as.Date(c(NA, NA))
)

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.
survival: Boolean variable. Whether to conduct survival analysis (TRUE) or not (FALSE).
match: Boolean variable. Whether to conduct the analysis for the matched cohorts (TRUE) or not (FALSE).
matchedSample: Only if match = TRUE. The number of people to take a random sample for matching. If NULL, no sampling will be performed.
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.

Examples

Run this code

# \donttest{
library(PhenotypeR)

cdm <- mockPhenotypeR()

result <- phenotypeDiagnostics(cdm$my_cohort)

CDMConnector::cdmDisconnect(cdm = cdm)
# }

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