inst/doc/a07_benchmark.R

In IncidencePrevalence: Estimate Incidence and Prevalence using the OMOP Common Data Model

## ----include = FALSE----------------------------------------------------------
NOT_CRAN <- identical(tolower(Sys.getenv("NOT_CRAN")), "true")

knitr::opts_chunk$set(
  collapse = TRUE,
  eval = TRUE, 
  warning = FALSE, 
  message = FALSE,
  comment = "#>",
  echo = FALSE,
  eval = NOT_CRAN,
  fig.width = 7,
  fig.height = 5
)

## ----message=FALSE, warning=FALSE---------------------------------------------
# library(IncidencePrevalence)
# library(visOmopResults)
# library(dplyr)
# library(ggplot2)
# library(stringr)
# 
# cdm <- mockIncidencePrevalence(
#   sampleSize = 100,
#   earliestObservationStartDate = as.Date("2010-01-01"),
#   latestObservationStartDate = as.Date("2010-01-01"),
#   minDaysToObservationEnd = 364,
#   maxDaysToObservationEnd = 364,
#   outPre = 0.1
# )
# 
# timings <- benchmarkIncidencePrevalence(cdm)
# timings |>
#   glimpse()

## -----------------------------------------------------------------------------
# visOmopTable(timings,
#   hide = c(
#     "variable_name", "variable_level",
#     "strata_name", "strata_level"
#   ),
#   groupColumn = "task"
# )

## -----------------------------------------------------------------------------
# test_db <- IncidencePrevalenceBenchmarkResults |>
#   filter(str_detect(cdm_name, "CPRD", negate = TRUE))
# test_db |>
#   glimpse()

## -----------------------------------------------------------------------------
# visOmopTable(bind(timings, test_db),
#   settingsColumn = "package_version",
#   hide = c(
#     "variable_name", "variable_level",
#     "strata_name", "strata_level"
#   ),
#   groupColumn = "task"
# )

## -----------------------------------------------------------------------------
# real_db <- IncidencePrevalenceBenchmarkResults |>
#   filter(str_detect(cdm_name, "CPRD"))
# visOmopTable(real_db,
#   settingsColumn = "package_version",
#   hide = c(
#     "variable_name", "variable_level",
#     "strata_name", "strata_level"
#   ),
#   groupColumn = "task"
# )

## ----eval = FALSE-------------------------------------------------------------
# library(CDMConnector)
# library(IncidencePrevalence)
# 
# cdm <- cdmFromCon("....")
# timings <- benchmarkIncidencePrevalence(cdm)
# exportSummarisedResult(
#   timings,
#   minCellCount = 5,
#   fileName = "results_{cdm_name}_{date}.csv",
#   path = getwd()
# )