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Codelist diagnostics

a02_CodelistDiagnostics.Rmd

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(), 
                      CDMConnector::eunomiaDir("synpuf-1k", "5.3"))
cdm <- CDMConnector::cdmFromCon(con = con, 
                                cdmName = "Eunomia Synpuf",
                                cdmSchema   = "main",
                                writeSchema = "main", 
                                achillesSchema = "main")

cdm$injuries <- conceptCohort(cdm = cdm,
  conceptSet = list(
    "ankle_sprain" = 81151,
    "ankle_fracture" = 4059173,
    "forearm_fracture" = 4278672,
    "hip_fracture" = 4230399
  ),
  name = "injuries")
cdm$injuries |> 
  glimpse()
#> Rows: ??
#> Columns: 4
#> Database: DuckDB v1.1.3 [unknown@Linux 6.8.0-1021-azure:R 4.4.2//tmp/RtmpSNREcu/file21d77eb16cd.duckdb]
#> $ cohort_definition_id <int> 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2…
#> $ subject_id           <int> 435, 743, 1212, 519, 347, 328, 466, 480, 429, 461…
#> $ cohort_start_date    <date> 2008-12-19, 2010-04-02, 2010-04-17, 2008-03-21, …
#> $ cohort_end_date      <date> 2008-12-19, 2010-04-02, 2010-04-17, 2008-03-21, …

Summarising code use

To get a good understanding of the codes we’ve used to define our cohorts we can use the codelistDiagnostics() function.

code_diag <- codelistDiagnostics(cdm$injuries)

From our results we can see a table of counts of our codes in our database based on the achilles results.

Database name
Eunomia Synpuf
Codelist name Domain ID Standard concept name Standard concept ID Standard concept Vocabulary ID
Estimate name
Record count Person count
ankle_sprain condition Sprain of ankle 81151 standard SNOMED 31 27

And we can also see orphan codes, which are codes that we did not include in our cohort definition but maybe could have. These are codes being used in the database that are associated with codes we included in our definition. So although many can be false positives, we may identify some codes that we may want to our cohort definitions.

tableOrphanCodes(code_diag)
Database name
Eunomia Synpuf
Codelist name Domain ID Standard concept name Standard concept ID Standard concept Vocabulary ID
Estimate name
Record count Person count
ankle_fracture condition Open fracture of medial malleolus 432749 standard SNOMED 3 3
Open fracture of lateral malleolus 437998 standard SNOMED 3 3
Closed bimalleolar fracture 438879 standard SNOMED 9 7
Closed fracture of medial malleolus 439162 standard SNOMED 4 3
Open bimalleolar fracture 441154 standard SNOMED 1 1
Closed trimalleolar fracture 441155 standard SNOMED 5 4
Closed fracture of lateral malleolus 441428 standard SNOMED 21 12
Closed fracture of talus 74777 standard SNOMED 2 2
Closed fracture of ankle 75095 standard SNOMED 19 16
Open fracture of talus 77131 standard SNOMED 2 2
Open fracture of ankle 78888 standard SNOMED 5 4
ankle_sprain condition Sprain of distal tibiofibular ligament 73889 standard SNOMED 4 4
Sprain of calcaneofibular ligament 75667 standard SNOMED 1 1
Sprain of deltoid ligament of ankle 77707 standard SNOMED 4 4
forearm_fracture condition Closed fracture of shaft of bone of forearm 4101989 standard SNOMED 1 1
Open fracture of shaft of bone of forearm 4195752 standard SNOMED 2 2
Open fracture of neck of radius 432744 standard SNOMED 1 1
Open fracture of lower end of radius AND ulna 432747 standard SNOMED 1 1
Open fracture of proximal end of ulna 433047 standard SNOMED 2 2
Open fracture of shaft of ulna 433333 standard SNOMED 1 1
Open Colles' fracture 434767 standard SNOMED 2 2
Open fracture of upper end of forearm 434771 standard SNOMED 1 1
Closed fracture of distal end of ulna 435374 standard SNOMED 4 3
Closed fracture of radius AND ulna 435380 standard SNOMED 6 6
Closed Colles' fracture 435950 standard SNOMED 20 13
Closed fracture of proximal end of ulna 436251 standard SNOMED 1 1
Closed fracture of ulna 436541 standard SNOMED 1 1
Closed fracture of shaft of radius 436826 standard SNOMED 2 2
Closed fracture of neck of radius 436837 standard SNOMED 3 2
Closed fracture of distal end of radius 437116 standard SNOMED 48 33
Open fracture of lower end of forearm 437122 standard SNOMED 1 1
Open fracture of upper end of radius AND ulna 437393 standard SNOMED 1 1
Closed fracture of lower end of forearm 437394 standard SNOMED 4 3
Closed fracture of shaft of ulna 437400 standard SNOMED 1 1
Open fracture of ulna 438576 standard SNOMED 1 1
Closed fracture of radius 439166 standard SNOMED 11 7
Closed fracture of upper end of forearm 439940 standard SNOMED 4 3
Pathological fracture - forearm 440511 standard SNOMED 1 1
Closed fracture of lower end of radius AND ulna 440538 standard SNOMED 6 5
Closed fracture of upper end of radius AND ulna 440544 standard SNOMED 6 2
Open fracture of distal end of radius 440546 standard SNOMED 3 3
Open fracture of forearm 440851 standard SNOMED 1 1
Closed fracture of proximal end of radius 441973 standard SNOMED 3 3
Closed fracture of forearm 441974 standard SNOMED 1 1
Fracture of radius AND ulna 442598 standard SNOMED 1 1
Torus fracture of radius 443428 standard SNOMED 1 1
Closed fracture of olecranon process of ulna 73036 standard SNOMED 7 5
Closed fracture of head of radius 73341 standard SNOMED 6 4
Open fracture of coronoid process of ulna 74192 standard SNOMED 1 1
Open fracture of olecranon process of ulna 74763 standard SNOMED 4 4
Closed Monteggia's fracture 79165 standard SNOMED 1 1
Closed fracture of coronoid process of ulna 79172 standard SNOMED 2 2
Open Monteggia's fracture 81148 standard SNOMED 1 1
hip_fracture condition Closed intertrochanteric fracture 136834 standard SNOMED 56 38
Closed fracture proximal femur, subtrochanteric 4009610 standard SNOMED 12 9
Closed fracture of neck of femur 434500 standard SNOMED 144 77
Closed fracture of base of neck of femur 435956 standard SNOMED 15 10
Closed fracture of midcervical section of femur 436247 standard SNOMED 16 14
Closed fracture of intracapsular section of femur 437703 standard SNOMED 8 7
Closed transcervical fracture of femur 440556 standard SNOMED 20 17
Closed fracture of acetabulum 81696 standard SNOMED 10 6

addCodelistAttribute

Some cohorts that may be created manually may not have the codelists recorded in the cohort_codelist attribute. The package has a utility function to record a codelist in a cohort_table object:

cohortCodelist(cdm$injuries, cohortId = 1)
#> 
#> - ankle_fracture (1 codes)
cdm$injuries <- cdm$injuries |>
  addCodelistAttribute(codelist = list(new_codelist = c(1L, 2L)), cohortName = "ankle_fracture")
cohortCodelist(cdm$injuries, cohortId = 1)
#> 
#> - new_codelist (2 codes)