inst/doc/a04_MatchedDiagnostics.R

In PhenotypeR: Assess Study Cohorts Using a Common Data Model

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>", message = FALSE, warning = FALSE,
  fig.width = 7
)

library(CDMConnector)
if (Sys.getenv("EUNOMIA_DATA_FOLDER") == "") Sys.setenv("EUNOMIA_DATA_FOLDER" = tempdir())
if (!dir.exists(Sys.getenv("EUNOMIA_DATA_FOLDER"))) dir.create(Sys.getenv("EUNOMIA_DATA_FOLDER"))
if (!eunomiaIsAvailable()) downloadEunomiaData(datasetName = "synpuf-1k")

## ----eval=FALSE---------------------------------------------------------------
# library(CDMConnector)
# library(CohortConstructor)
# library(CodelistGenerator)
# library(PatientProfiles)
# library(CohortCharacteristics)
# library(PhenotypeR)
# library(dplyr)
# library(ggplot2)
# 
# con <- DBI::dbConnect(duckdb::duckdb(),
#                       CDMConnector::eunomiaDir("synpuf-1k", "5.3"))
# cdm <- CDMConnector::cdmFromCon(con = con,
#                                 cdmName = "Eunomia Synpuf",
#                                 cdmSchema   = "main",
#                                 writeSchema = "main",
#                                 achillesSchema = "main")
# 
# cdm$injuries <- conceptCohort(cdm = cdm,
#   conceptSet = list(
#     "ankle_sprain" = 81151,
#     "ankle_fracture" = 4059173,
#     "forearm_fracture" = 4278672,
#     "hip_fracture" = 4230399
#   ),
#   name = "injuries")

## ----eval=FALSE---------------------------------------------------------------
# matched_diag <- matchedDiagnostics(cdm$injuries)