Cohort diagnostics

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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
Variable name	Variable level	Estimate 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
Variable name	Variable level	Estimate 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

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