PhenotypeR (version 0.3.2)

shinyDiagnostics: Create a shiny app summarising your phenotyping results

Description

A shiny app that is designed for any diagnostics results from phenotypeR, 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

shinyDiagnostics(
  result,
  directory,
  minCellCount = 5,
  open = rlang::is_interactive(),
  expectations = NULL
)

Value

A shiny app

Arguments

result

A summarised result

directory

Directory where to save report

minCellCount

Minimum cell count for suppression when exporting results.

open

If TRUE, the shiny app will be launched in a new session. If FALSE, the shiny app will be created but not launched.

expectations

Data frame or tibble with cohort expectations. It must contain the following columns: cohort_name, estimate, value, and source.

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)

expectations <- dplyr::tibble("cohort_name" = "warfarin",
                       "value" = c("Mean age",
                                   "Male percentage",
                                   "Survival probability after 5y"),
                       "estimate" = c("32", "74%",  "4%"),
                       "source" = c("AlbertAI"))

shinyDiagnostics(result, tempdir(), expectations = expectations)

CDMConnector::cdmDisconnect(cdm = cdm)
# }