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Cohort diagnostics

Introduction

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

Again, we’ll begin by creating our study cohorts.

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")

Cohort diagnostics

We can run cohort diagnostics analyses for each of our overall cohorts like so:

cohort_diag <- cohortDiagnostics(cdm$injuries)

Our results will include a summary of the overlap between our cohorts. We could visualise this

plotCohortOverlap(cohort_diag, uniqueCombinations = TRUE)

Moreover, our results will also include a summary of the characteristics of each cohort, stratified by age group and sex.

tableCharacteristics(cohort_diag, groupColumn = c("age_group", "sex"))
CDM name
Eunomia Synpuf
Variable name Variable level Estimate name
Cohort name
ankle_fracture ankle_sprain forearm_fracture hip_fracture
overall; overall
Number records - N 0 28 0 0
Number subjects - N 0 27 0 0
Cohort start date - Median [Q25 - Q75] - 2009-04-23 [2008-10-30 - 2010-02-02] - -
Range - 2008-01-10 to 2010-09-13 - -
Cohort end date - Median [Q25 - Q75] - 2009-04-24 [2008-10-30 - 2010-02-02] - -
Range - 2008-01-10 to 2010-09-13 - -
Age - Median [Q25 - Q75] - 72 [66 - 77] - -
Mean (SD) - 71.14 (15.68) - -
Range - 27 to 98 - -
Sex Female N (%) - 11 (39.29%) - -
Male N (%) - 17 (60.71%) - -
Prior observation - Median [Q25 - Q75] - 478 [303 - 762] - -
Mean (SD) - 499.54 (296.82) - -
Range - 9 to 986 - -
Future observation - Median [Q25 - Q75] - 572 [280 - 768] - -
Mean (SD) - 575.89 (301.07) - -
Range - 109 to 1,086 - -
Days in cohort - Median [Q25 - Q75] - 1 [1 - 1] - -
Mean (SD) - 1.11 (0.42) - -
Range - 1 to 3 - -
Number visits prior year - Median [Q25 - Q75] - 31.00 [16.50 - 45.00] - -
Mean (SD) - 31.71 (20.36) - -
Range - 0.00 to 73.00 - -
18 to 64; overall
Number records - N - 5 - -
Number subjects - N - 5 - -
Cohort start date - Median [Q25 - Q75] - 2009-09-08 [2009-01-19 - 2010-05-24] - -
Range - 2008-02-03 to 2010-06-19 - -
Cohort end date - Median [Q25 - Q75] - 2009-09-08 [2009-01-19 - 2010-05-24] - -
Range - 2008-02-03 to 2010-06-19 - -
Age - Median [Q25 - Q75] - 44 [43 - 56] - -
Mean (SD) - 46.60 (13.79) - -
Range - 27 to 63 - -
Sex Female N (%) - 2 (40.00%) - -
Male N (%) - 3 (60.00%) - -
Prior observation - Median [Q25 - Q75] - 616 [384 - 874] - -
Mean (SD) - 561.40 (362.64) - -
Range - 33 to 900 - -
Future observation - Median [Q25 - Q75] - 479 [221 - 711] - -
Mean (SD) - 533.60 (362.64) - -
Range - 195 to 1,062 - -
Days in cohort - Median [Q25 - Q75] - 1 [1 - 1] - -
Mean (SD) - 1.00 (0.00) - -
Range - 1 to 1 - -
Number visits prior year - Median [Q25 - Q75] - 23.00 [5.00 - 26.00] - -
Mean (SD) - 20.20 (17.46) - -
Range - 2.00 to 45.00 - -
65 to 150; overall
Number records - N - 23 - -
Number subjects - N - 22 - -
Cohort start date - Median [Q25 - Q75] - 2009-04-04 [2008-10-28 - 2009-12-27] - -
Range - 2008-01-10 to 2010-09-13 - -
Cohort end date - Median [Q25 - Q75] - 2009-04-05 [2008-10-28 - 2009-12-27] - -
Range - 2008-01-10 to 2010-09-13 - -
Age - Median [Q25 - Q75] - 75 [68 - 81] - -
Mean (SD) - 76.48 (10.03) - -
Range - 66 to 98 - -
Sex Female N (%) - 9 (39.13%) - -
Male N (%) - 14 (60.87%) - -
Prior observation - Median [Q25 - Q75] - 459 [302 - 726] - -
Mean (SD) - 486.09 (288.36) - -
Range - 9 to 986 - -
Future observation - Median [Q25 - Q75] - 598 [316 - 775] - -
Mean (SD) - 585.09 (294.69) - -
Range - 109 to 1,086 - -
Days in cohort - Median [Q25 - Q75] - 1 [1 - 1] - -
Mean (SD) - 1.13 (0.46) - -
Range - 1 to 3 - -
Number visits prior year - Median [Q25 - Q75] - 40.00 [20.50 - 47.00] - -
Mean (SD) - 34.22 (20.41) - -
Range - 0.00 to 73.00 - -
overall; Female
Number records - N - 11 - -
Number subjects - N - 11 - -
Cohort start date - Median [Q25 - Q75] - 2008-12-02 [2008-03-30 - 2009-04-11] - -
Range - 2008-01-10 to 2010-04-02 - -
Cohort end date - Median [Q25 - Q75] - 2008-12-04 [2008-03-30 - 2009-04-11] - -
Range - 2008-01-10 to 2010-04-02 - -
Age - Median [Q25 - Q75] - 70 [66 - 74] - -
Mean (SD) - 70.09 (12.28) - -
Range - 43 to 92 - -
Sex Female N (%) - 11 (100.00%) - -
Prior observation - Median [Q25 - Q75] - 336 [88 - 466] - -
Mean (SD) - 342.91 (288.53) - -
Range - 9 to 822 - -
Future observation - Median [Q25 - Q75] - 742 [415 - 1,006] - -
Mean (SD) - 702.27 (325.00) - -
Range - 249 to 1,086 - -
Days in cohort - Median [Q25 - Q75] - 1 [1 - 1] - -
Mean (SD) - 1.18 (0.60) - -
Range - 1 to 3 - -
Number visits prior year - Median [Q25 - Q75] - 28.00 [6.50 - 45.00] - -
Mean (SD) - 26.82 (20.58) - -
Range - 0.00 to 51.00 - -
overall; Male
Number records - N - 17 - -
Number subjects - N - 16 - -
Cohort start date - Median [Q25 - Q75] - 2009-10-08 [2009-01-03 - 2010-04-17] - -
Range - 2008-03-21 to 2010-09-13 - -
Cohort end date - Median [Q25 - Q75] - 2009-10-08 [2009-01-03 - 2010-04-17] - -
Range - 2008-03-21 to 2010-09-13 - -
Age - Median [Q25 - Q75] - 75 [66 - 79] - -
Mean (SD) - 71.82 (17.88) - -
Range - 27 to 98 - -
Sex Male N (%) - 17 (100.00%) - -
Prior observation - Median [Q25 - Q75] - 646 [368 - 837] - -
Mean (SD) - 600.88 (262.41) - -
Range - 80 to 986 - -
Future observation - Median [Q25 - Q75] - 449 [258 - 727] - -
Mean (SD) - 494.12 (262.41) - -
Range - 109 to 1,015 - -
Days in cohort - Median [Q25 - Q75] - 1 [1 - 1] - -
Mean (SD) - 1.06 (0.24) - -
Range - 1 to 2 - -
Number visits prior year - Median [Q25 - Q75] - 34.00 [23.00 - 45.00] - -
Mean (SD) - 34.88 (20.18) - -
Range - 5.00 to 73.00 - -

You can also visualise the age distribution:

tableCharacteristics(cohort_diag, groupColumn = c("age_group", "sex"))
CDM name
Eunomia Synpuf
Variable name Variable level Estimate name
Cohort name
ankle_fracture ankle_sprain forearm_fracture hip_fracture
overall; overall
Number records - N 0 28 0 0
Number subjects - N 0 27 0 0
Cohort start date - Median [Q25 - Q75] - 2009-04-23 [2008-10-30 - 2010-02-02] - -
Range - 2008-01-10 to 2010-09-13 - -
Cohort end date - Median [Q25 - Q75] - 2009-04-24 [2008-10-30 - 2010-02-02] - -
Range - 2008-01-10 to 2010-09-13 - -
Age - Median [Q25 - Q75] - 72 [66 - 77] - -
Mean (SD) - 71.14 (15.68) - -
Range - 27 to 98 - -
Sex Female N (%) - 11 (39.29%) - -
Male N (%) - 17 (60.71%) - -
Prior observation - Median [Q25 - Q75] - 478 [303 - 762] - -
Mean (SD) - 499.54 (296.82) - -
Range - 9 to 986 - -
Future observation - Median [Q25 - Q75] - 572 [280 - 768] - -
Mean (SD) - 575.89 (301.07) - -
Range - 109 to 1,086 - -
Days in cohort - Median [Q25 - Q75] - 1 [1 - 1] - -
Mean (SD) - 1.11 (0.42) - -
Range - 1 to 3 - -
Number visits prior year - Median [Q25 - Q75] - 31.00 [16.50 - 45.00] - -
Mean (SD) - 31.71 (20.36) - -
Range - 0.00 to 73.00 - -
18 to 64; overall
Number records - N - 5 - -
Number subjects - N - 5 - -
Cohort start date - Median [Q25 - Q75] - 2009-09-08 [2009-01-19 - 2010-05-24] - -
Range - 2008-02-03 to 2010-06-19 - -
Cohort end date - Median [Q25 - Q75] - 2009-09-08 [2009-01-19 - 2010-05-24] - -
Range - 2008-02-03 to 2010-06-19 - -
Age - Median [Q25 - Q75] - 44 [43 - 56] - -
Mean (SD) - 46.60 (13.79) - -
Range - 27 to 63 - -
Sex Female N (%) - 2 (40.00%) - -
Male N (%) - 3 (60.00%) - -
Prior observation - Median [Q25 - Q75] - 616 [384 - 874] - -
Mean (SD) - 561.40 (362.64) - -
Range - 33 to 900 - -
Future observation - Median [Q25 - Q75] - 479 [221 - 711] - -
Mean (SD) - 533.60 (362.64) - -
Range - 195 to 1,062 - -
Days in cohort - Median [Q25 - Q75] - 1 [1 - 1] - -
Mean (SD) - 1.00 (0.00) - -
Range - 1 to 1 - -
Number visits prior year - Median [Q25 - Q75] - 23.00 [5.00 - 26.00] - -
Mean (SD) - 20.20 (17.46) - -
Range - 2.00 to 45.00 - -
65 to 150; overall
Number records - N - 23 - -
Number subjects - N - 22 - -
Cohort start date - Median [Q25 - Q75] - 2009-04-04 [2008-10-28 - 2009-12-27] - -
Range - 2008-01-10 to 2010-09-13 - -
Cohort end date - Median [Q25 - Q75] - 2009-04-05 [2008-10-28 - 2009-12-27] - -
Range - 2008-01-10 to 2010-09-13 - -
Age - Median [Q25 - Q75] - 75 [68 - 81] - -
Mean (SD) - 76.48 (10.03) - -
Range - 66 to 98 - -
Sex Female N (%) - 9 (39.13%) - -
Male N (%) - 14 (60.87%) - -
Prior observation - Median [Q25 - Q75] - 459 [302 - 726] - -
Mean (SD) - 486.09 (288.36) - -
Range - 9 to 986 - -
Future observation - Median [Q25 - Q75] - 598 [316 - 775] - -
Mean (SD) - 585.09 (294.69) - -
Range - 109 to 1,086 - -
Days in cohort - Median [Q25 - Q75] - 1 [1 - 1] - -
Mean (SD) - 1.13 (0.46) - -
Range - 1 to 3 - -
Number visits prior year - Median [Q25 - Q75] - 40.00 [20.50 - 47.00] - -
Mean (SD) - 34.22 (20.41) - -
Range - 0.00 to 73.00 - -
overall; Female
Number records - N - 11 - -
Number subjects - N - 11 - -
Cohort start date - Median [Q25 - Q75] - 2008-12-02 [2008-03-30 - 2009-04-11] - -
Range - 2008-01-10 to 2010-04-02 - -
Cohort end date - Median [Q25 - Q75] - 2008-12-04 [2008-03-30 - 2009-04-11] - -
Range - 2008-01-10 to 2010-04-02 - -
Age - Median [Q25 - Q75] - 70 [66 - 74] - -
Mean (SD) - 70.09 (12.28) - -
Range - 43 to 92 - -
Sex Female N (%) - 11 (100.00%) - -
Prior observation - Median [Q25 - Q75] - 336 [88 - 466] - -
Mean (SD) - 342.91 (288.53) - -
Range - 9 to 822 - -
Future observation - Median [Q25 - Q75] - 742 [415 - 1,006] - -
Mean (SD) - 702.27 (325.00) - -
Range - 249 to 1,086 - -
Days in cohort - Median [Q25 - Q75] - 1 [1 - 1] - -
Mean (SD) - 1.18 (0.60) - -
Range - 1 to 3 - -
Number visits prior year - Median [Q25 - Q75] - 28.00 [6.50 - 45.00] - -
Mean (SD) - 26.82 (20.58) - -
Range - 0.00 to 51.00 - -
overall; Male
Number records - N - 17 - -
Number subjects - N - 16 - -
Cohort start date - Median [Q25 - Q75] - 2009-10-08 [2009-01-03 - 2010-04-17] - -
Range - 2008-03-21 to 2010-09-13 - -
Cohort end date - Median [Q25 - Q75] - 2009-10-08 [2009-01-03 - 2010-04-17] - -
Range - 2008-03-21 to 2010-09-13 - -
Age - Median [Q25 - Q75] - 75 [66 - 79] - -
Mean (SD) - 71.82 (17.88) - -
Range - 27 to 98 - -
Sex Male N (%) - 17 (100.00%) - -
Prior observation - Median [Q25 - Q75] - 646 [368 - 837] - -
Mean (SD) - 600.88 (262.41) - -
Range - 80 to 986 - -
Future observation - Median [Q25 - Q75] - 449 [258 - 727] - -
Mean (SD) - 494.12 (262.41) - -
Range - 109 to 1,015 - -
Days in cohort - Median [Q25 - Q75] - 1 [1 - 1] - -
Mean (SD) - 1.06 (0.24) - -
Range - 1 to 2 - -
Number visits prior year - Median [Q25 - Q75] - 34.00 [23.00 - 45.00] - -
Mean (SD) - 34.88 (20.18) - -
Range - 5.00 to 73.00 - -

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They may not be fully stable and should be used with caution. We make no claims about them.
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