inst/doc/a07_RunCodelistDiagnostics.R

In CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use

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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = NOT_CRAN)

## ----include = FALSE----------------------------------------------------------
#  CDMConnector::requireEunomia("synpuf-1k", "5.3")

## ----message=FALSE, warning=FALSE---------------------------------------------
#  library(DBI)
#  library(duckdb)
#  library(dplyr)
#  library(CDMConnector)
#  library(CodelistGenerator)
#  library(CohortConstructor)
#  
#  # Connect to the database and create the cdm object
#  con <- dbConnect(duckdb(),
#                        eunomiaDir("synpuf-1k", "5.3"))
#  cdm <- cdmFromCon(con = con,
#                    cdmName = "Eunomia Synpuf",
#                    cdmSchema   = "main",
#                    writeSchema = "main",
#                    achillesSchema = "main")
#  
#  # Create a codelist for depression
#  depression <- getCandidateCodes(cdm,
#                                  keywords = "depression")
#  depression <- list("depression" = depression$concept_id)

## ----message=FALSE, warning=FALSE---------------------------------------------
#  achilles_code_use <- summariseAchillesCodeUse(depression,
#                                                cdm,
#                                                countBy = c("record", "person"))

## ----message=FALSE, warning=FALSE---------------------------------------------
#  tableAchillesCodeUse(achilles_code_use,
#                       type = "gt")

## ----message=FALSE, warning=FALSE---------------------------------------------
#  code_use <- summariseCodeUse(depression,
#                               cdm,
#                               countBy = c("record", "person"),
#                               byYear  = FALSE,
#                               bySex   = FALSE,
#                               ageGroup =  list("<=50" = c(0,50), ">50" = c(51,Inf)),
#                               dateRange = as.Date(c("2010-01-01", "2020-01-01")))
#  
#  tableCodeUse(code_use, type = "gt")

## ----message=FALSE, warning=FALSE---------------------------------------------
#  orphan <- summariseOrphanCodes(depression, cdm)
#  tableOrphanCodes(orphan, type = "gt")

## ----message=FALSE, warning=FALSE---------------------------------------------
#  unmapped <- summariseUnmappedCodes(depression, cdm)
#  tableUnmappedCodes(unmapped, type = "gt")

## ----message=FALSE, warning=FALSE---------------------------------------------
#  cdm[["depression"]] <- conceptCohort(cdm,
#                                       conceptSet = depression,
#                                       name = "depression")

## ----message=FALSE, warning=FALSE---------------------------------------------
#  cohort_code_use <- summariseCohortCodeUse(depression,
#                                            cdm,
#                                            cohortTable = "depression",
#                                            countBy = c("record", "person"))
#  tableCohortCodeUse(cohort_code_use)

## ----message=FALSE, warning=FALSE---------------------------------------------
#  cohort_code_use <- summariseCohortCodeUse(depression,
#                                            cdm,
#                                            cohortTable = "depression",
#                                            countBy = c("record", "person"),
#                                            timing = "entry")
#  tableCohortCodeUse(cohort_code_use)

## ----message=FALSE, warning=FALSE---------------------------------------------
#  cohort_code_use <- summariseCohortCodeUse(depression,
#                                            cdm,
#                                            cohortTable = "depression",
#                                            countBy = c("record", "person"),
#                                            byYear = FALSE,
#                                            bySex = TRUE,
#                                            ageGroup = NULL)
#  tableCohortCodeUse(cohort_code_use)