Codelist diagnostics

Introduction

In this example we’re going to summarise the characteristics of individuals with an ankle sprain, ankle fracture, forearm fracture, or a hip fracture using the Eunomia synthetic data.

We’ll begin by creating our study cohorts.

library(CDMConnector)
library(CohortConstructor)
library(CodelistGenerator)
library(phenotypeR)
library(dplyr)
library(ggplot2)

con <- DBI::dbConnect(duckdb::duckdb(),
  dbdir = CDMConnector::eunomia_dir()
)
cdm <- CDMConnector::cdm_from_con(con,
  cdm_schem = "main",
  write_schema = "main",
  cdm_name = "Eunomia"
)

cdm$injuries <- conceptCohort(cdm = cdm,
  conceptSet = list(
    "ankle_sprain" = 81151,
    "ankle_fracture" = 4059173,
    "forearm_fracture" = 4278672,
    "hip_fracture" = 4230399
  ),
  name = "injuries")
cdm$injuries |> 
  glimpse()
#> Rows: ??
#> Columns: 4
#> Database: DuckDB v1.1.0 [unknown@Linux 6.8.0-1014-azure:R 4.4.1//tmp/RtmpbpMFwy/file1940715e8f2f.duckdb]
#> $ cohort_definition_id <int> 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 1, 2, 2, 2…
#> $ subject_id           <int> 4748, 63, 452, 905, 1751, 2006, 2153, 3397, 3666,…
#> $ cohort_start_date    <date> 1984-10-25, 2000-10-15, 1964-10-26, 1979-02-26, …
#> $ cohort_end_date      <date> 1984-12-24, 2000-10-29, 1964-11-30, 1979-03-12, …

Summarising code use

code_diag <- codelistDiagnostics(cdm$injuries)
tableCohortCodeUse(code_diag)

							Database name
							Eunomia
Cohort name	Codelist name	Standard concept name	Standard concept ID	Source concept name	Source concept id	Domain id	Estimate name
							Record count	Person count
ankle_fracture	ankle_fracture	overall	-	overall	overall	overall	464	427
		Fracture of ankle	4059173	Fracture of ankle	4059173	condition	464	427
ankle_sprain	ankle_sprain	overall	-	overall	overall	overall	1,915	1,357
		Sprain of ankle	81151	Sprain of ankle	81151	condition	1,915	1,357
forearm_fracture	forearm_fracture	overall	-	overall	overall	overall	569	510
		Fracture of forearm	4278672	Fracture of forearm	4278672	condition	569	510
hip_fracture	hip_fracture	overall	-	overall	overall	overall	138	132
		Closed fracture of hip	4230399	Closed fracture of hip	4230399	condition	138	132