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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_sprain
overall; overall
Number records - N 28
Number subjects - N 27
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_sprain
overall; overall
Number records - N 28
Number subjects - N 27
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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.