Package index

Run all diagnostics

phenotypeDiagnostics()

Phenotype a cohort

Run individual diagnostics

databaseDiagnostics()

Database diagnostics

codelistDiagnostics()

Run codelist-level diagnostics

cohortDiagnostics()

Run cohort-level diagnostics

populationDiagnostics()

Population-level diagnostics

Visualise results

shinyDiagnostics()

Create a shiny app summarising your phenotyping results

Clinical and database descriptions

getClinicalDescription()

Get clinical descriptions using an LLM

importClinicalDescription()

Import clinical descriptions

importDatabaseDescription()

Import database descriptions

shinyDescriptions()

Shiny app to create descriptions for contextualising diagnostic results

Expectations for phenotyping results

getCohortExpectations()

Get cohort expectations using an LLM

tableCohortExpectations()

Create a table summarising cohort expectations

Download templates

downloadDatabaseDescriptionTemplate()

Download a Clinical Description Template

downloadClinicalDescriptionTemplate()

Download a Clinical Description Template

Codelist diagnostics helper

addCodelistAttribute()

Adds the cohort_codelist attribute to a cohort