Codelist diagnostics

Introduction

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

We’ll begin by creating our study cohorts.

library(CDMConnector)
library(CohortConstructor)
library(CodelistGenerator)
library(PhenotypeR)
library(MeasurementDiagnostics)
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$injuries <- conceptCohort(cdm = cdm,
  conceptSet = list(
    "ankle_sprain" = 81151,
    "ankle_fracture" = 4059173,
    "forearm_fracture" = 4278672,
    "hip_fracture" = 4230399,
    "measurements_cohort" = c(40660437L, 2617206L, 4034850L,  2617239L, 4098179L)
  ),
  name = "injuries")
cdm$injuries |> 
  glimpse()
#> Rows: ??
#> Columns: 4
#> Database: DuckDB v1.3.1 [root@Darwin 24.5.0:R 4.5.1//private/var/folders/sw/rd8zn92n2nz45cfcc5dcs_080000gr/T/Rtmp3Yhuv6/file135ce691a8ade.duckdb]
#> $ cohort_definition_id <int> 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5…
#> $ subject_id           <int> 29, 426, 559, 811, 820, 1076, 735, 172, 251, 527,…
#> $ cohort_start_date    <date> 2008-04-22, 2008-10-01, 2009-06-12, 2008-06-25, …
#> $ cohort_end_date      <date> 2008-04-22, 2008-10-01, 2009-06-12, 2008-06-25, …

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)

Codelist diagnostics builds on CodelistGenerator and MeasurementDiagnostics R packages to perform the following analyses:

The output of a function is a summarised result table.

Add codelist attribute

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)

Visualise the results

We will now use different functions to visualise the results generated by CohortDiagnostics. Notice that these functions are from CodelistGenerator and MeasurementDiagnostics R packages packages.

Achilles code use

tableAchillesCodeUse(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_sprain condition Sprain of ankle 81151 standard SNOMED 31 27
measurements_cohort measurement Prostate cancer screening; prostate specific antigen test (psa) 2617206 standard HCPCS 146 124
Screening cytopathology, cervical or vaginal (any reporting system), collected in preservative fluid, automated thin layer preparation, with screening by automated system and manual rescreening under physician supervision 2617239 standard HCPCS 52 47
Laboratory test 4034850 standard SNOMED 101 95
Drug screen, qualitative; multiple drug classes by high complexity test method (e.g., immunoassay, enzyme assay), per patient encounter 40660437 standard HCPCS 45 26
Immunology laboratory test 4098179 standard SNOMED 20 20

Orphan code use

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
measurements_cohort procedure Antibody screen, RBC, each serum technique 2212937 standard CPT4 55 53
Antibody identification, RBC antibodies, each panel for each serum technique 2212939 standard CPT4 1 1
Pathology consultation during surgery; cytologic examination (eg, touch prep, squash prep), initial site 2213298 standard CPT4 3 3
measurement Screening cytopathology, cervical or vaginal (any reporting system), collected in preservative fluid, automated thin layer preparation, requiring interpretation by physician 2617226 standard HCPCS 1 1
Screening cytopathology smears, cervical or vaginal, performed by automated system with manual rescreening 2617241 standard HCPCS 1 1
Wet mounts, including preparations of vaginal, cervical or skin specimens 2720582 standard HCPCS 1 1
Detection of parasite 4047338 standard SNOMED 3 3
Antenatal RhD antibody screening 4060266 standard SNOMED 8 8
Type 1 hypersensitivity skin test 4091110 standard SNOMED 3 3
Hematology screening test 4198132 standard SNOMED 20 20
Sickle cell disease screening test 4199173 standard SNOMED 9 9
Microscopic examination of cervical Papanicolaou smear 4208622 standard SNOMED 10 10
Genetic test 4237017 standard SNOMED 23 23
Blood group typing 4258677 standard SNOMED 14 14
Microscopic examination of vaginal Papanicolaou smear 4258831 standard SNOMED 22 22

Cohort code use

tableCohortCodeUse(code_diag)
Database name
Eunomia Synpuf
Cohort name Codelist name Standard concept name Standard concept ID Source concept name Source concept ID Source concept value Domain ID Diagnostic Phenotyper version
Estimate name
Person count Record count
ankle_sprain ankle_sprain Sprain of ankle 81151 Other sprains and strains of ankle 44829371 84509 condition codelistDiagnostics 0.2.0 6 6
Sprain of ankle, unspecified site 44820150 84500 condition codelistDiagnostics 0.2.0 23 25
overall - NA NA NA NA codelistDiagnostics 0.2.0 27 31
measurements_cohort measurements_cohort Drug screen, qualitative; multiple drug classes by high complexity test method (e.g., immunoassay, enzyme assay), per patient encounter 40660437 Drug screen, qualitative; multiple drug classes by high complexity test method (e.g., immunoassay, enzyme assay), per patient encounter 40660437 G0431 measurement codelistDiagnostics 0.2.0 26 45
Immunology laboratory test 4098179 Antibody response examination 44830850 V7261 measurement codelistDiagnostics 0.2.0 11 11
Other and unspecified nonspecific immunological findings 44830461 79579 measurement codelistDiagnostics 0.2.0 9 9
Laboratory test 4034850 Laboratory examination 44836706 V726 measurement codelistDiagnostics 0.2.0 45 48
Laboratory examination ordered as part of a routine general medical examination 44823881 V7262 measurement codelistDiagnostics 0.2.0 14 14
Laboratory examination, unspecified 44835527 V7260 measurement codelistDiagnostics 0.2.0 16 16
Other laboratory examination 44835528 V7269 measurement codelistDiagnostics 0.2.0 13 13
Pre-procedural laboratory examination 44827407 V7263 measurement codelistDiagnostics 0.2.0 10 10
Prostate cancer screening; prostate specific antigen test (psa) 2617206 Prostate cancer screening; prostate specific antigen test (psa) 2617206 G0103 measurement codelistDiagnostics 0.2.0 124 146
Screening cytopathology, cervical or vaginal (any reporting system), collected in preservative fluid, automated thin layer preparation, with screening by automated system and manual rescreening under physician supervision 2617239 Screening cytopathology, cervical or vaginal (any reporting system), collected in preservative fluid, automated thin layer preparation, with screening by automated system and manual rescreening under physician supervision 2617239 G0145 measurement codelistDiagnostics 0.2.0 47 52
overall - NA NA NA NA codelistDiagnostics 0.2.0 255 364

Measurement timings

tableMeasurementTimings(code_diag)
CDM name Cohort name Variable name Estimate name Estimate value
measurements_cohort
Eunomia Synpuf measurements_cohort Number records N 364
Number subjects N 255
Time (days) Median [Q25 - Q75] 150.00 [19.00 - 356.00]
Range 0.00 to 930.00
Measurements per subject Median [Q25 - Q75] 2.00 [1.00 - 2.00]
Range 1.00 to 10.00
 
plotMeasurementTimings(code_diag)

Measurement value as concept

tableMeasurementValueAsConcept(code_diag)
CDM name Cohort name Concept name Concept ID Domain ID Variable name Value as concept name Value as concept ID Estimate name Estimate value
measurements_cohort
Eunomia Synpuf measurements_cohort overall overall overall Value as concept name No matching concept 0 N (%) 364 (100.00%)
Laboratory test 4034850 Measurement Value as concept name No matching concept 0 N (%) 101 (100.00%)
Prostate cancer screening; prostate specific antigen test (psa) 2617206 Measurement Value as concept name No matching concept 0 N (%) 146 (100.00%)
Drug screen, qualitative; multiple drug classes by high complexity test method (e.g., immunoassay, enzyme assay), per patient encounter 40660437 Measurement Value as concept name No matching concept 0 N (%) 45 (100.00%)
Immunology laboratory test 4098179 Measurement Value as concept name No matching concept 0 N (%) 20 (100.00%)
Screening cytopathology, cervical or vaginal (any reporting system), collected in preservative fluid, automated thin layer preparation, with screening by automated system and manual rescreening under physician supervision 2617239 Measurement Value as concept name No matching concept 0 N (%) 52 (100.00%)
 
plotMeasurementValueAsConcept(code_diag)

Measurement value as numeric

tableMeasurementValueAsNumeric(code_diag)
CDM name Cohort name Concept name Concept ID Domain ID Unit concept name Unit concept ID Estimate name Estimate value
measurements_cohort
Eunomia Synpuf measurements_cohort overall overall overall No matching concept 0 N 364
Median [Q25 - Q75] -
Q05 - Q95 -
Q01 - Q99 -
Range -
Missing value, N (%) 364 (100.00%)
Prostate cancer screening; prostate specific antigen test (psa) 2617206 Measurement No matching concept 0 N 146
Median [Q25 - Q75] -
Q05 - Q95 -
Q01 - Q99 -
Range -
Missing value, N (%) 146 (100.00%)
Laboratory test 4034850 Measurement No matching concept 0 N 101
Median [Q25 - Q75] -
Q05 - Q95 -
Q01 - Q99 -
Range -
Missing value, N (%) 101 (100.00%)
Screening cytopathology, cervical or vaginal (any reporting system), collected in preservative fluid, automated thin layer preparation, with screening by automated system and manual rescreening under physician supervision 2617239 Measurement No matching concept 0 N 52
Median [Q25 - Q75] -
Q05 - Q95 -
Q01 - Q99 -
Range -
Missing value, N (%) 52 (100.00%)
Drug screen, qualitative; multiple drug classes by high complexity test method (e.g., immunoassay, enzyme assay), per patient encounter 40660437 Measurement No matching concept 0 N 45
Median [Q25 - Q75] -
Q05 - Q95 -
Q01 - Q99 -
Range -
Missing value, N (%) 45 (100.00%)
Immunology laboratory test 4098179 Measurement No matching concept 0 N 20
Median [Q25 - Q75] -
Q05 - Q95 -
Q01 - Q99 -
Range -
Missing value, N (%) 20 (100.00%)
 
plotMeasurementValueAsNumeric(code_diag)