Summarise cohort overlap

When creating multiple cohorts we might be interested in the overlap between them. That is, how many individuals appear in multiple cohorts. CohortCharacteristics provides functions to generate such estimates and then summarise these estimates in tables and plots.

To see how this works let’s create a few medication cohorts with the Eunomia synthetic dataset.

library(duckdb)
library(CDMConnector)
library(dplyr, warn.conflicts = FALSE)
library(CodelistGenerator)
library(PatientProfiles)
library(CohortCharacteristics)

con <- dbConnect(duckdb(), dbdir = eunomiaDir())
cdm <- cdmFromCon(
  con = con, cdmSchem = "main", writeSchema = "main", cdmName = "Eunomia"
)

medsCs <- getDrugIngredientCodes(
  cdm = cdm,
  name = c(
    "acetaminophen",
    "morphine",
    "warfarin"
  )
)

cdm <- generateConceptCohortSet(
  cdm = cdm,
  name = "meds",
  conceptSet = medsCs,
  end = "event_end_date",
  limit = "all",
  overwrite = TRUE
)

settings(cdm$meds)
#> # A tibble: 3 × 6
#>   cohort_definition_id cohort_name    limit prior_observation future_observation
#>                  <int> <chr>          <chr>             <dbl>              <dbl>
#> 1                    1 11289_warfarin all                   0                  0
#> 2                    2 161_acetamino… all                   0                  0
#> 3                    3 7052_morphine  all                   0                  0
#> # ℹ 1 more variable: end <chr>
cohortCount(cdm$meds)
#> # A tibble: 3 × 3
#>   cohort_definition_id number_records number_subjects
#>                  <int>          <int>           <int>
#> 1                    1            137             137
#> 2                    2          13908            2679
#> 3                    3             35              35

Now we have our cohorts we can summarise the overlap between them.

medsOverlap <- cdm$meds |>
  summariseCohortOverlap()
medsOverlap |>
  glimpse()
#> Rows: 36
#> Columns: 13
#> $ result_id        <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,…
#> $ cdm_name         <chr> "Eunomia", "Eunomia", "Eunomia", "Eunomia", "Eunomia"…
#> $ group_name       <chr> "cohort_name_reference &&& cohort_name_comparator", "…
#> $ group_level      <chr> "11289_warfarin &&& 161_acetaminophen", "11289_warfar…
#> $ strata_name      <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ strata_level     <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ variable_name    <chr> "Only in reference cohort", "In both cohorts", "Only …
#> $ variable_level   <chr> "Subjects", "Subjects", "Subjects", "Subjects", "Subj…
#> $ estimate_name    <chr> "count", "count", "count", "count", "count", "count",…
#> $ estimate_type    <chr> "integer", "integer", "integer", "integer", "integer"…
#> $ estimate_value   <chr> "1", "136", "2543", "131", "6", "29", "2543", "136", …
#> $ additional_name  <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ additional_level <chr> "overall", "overall", "overall", "overall", "overall"…

We have table and plotting functions to help view our results.

tableCohortOverlap(medsOverlap, uniqueCombinations = FALSE)

Cohort name reference	Cohort name comparator	Estimate name	Variable name
			Only in reference cohort	In both cohorts	Only in comparator cohort
Eunomia
11289_warfarin	161_acetaminophen	N (%)	1 (0.04%)	136 (5.07%)	2,543 (94.89%)
	7052_morphine	N (%)	131 (78.92%)	6 (3.61%)	29 (17.47%)
161_acetaminophen	11289_warfarin	N (%)	2,543 (94.89%)	136 (5.07%)	1 (0.04%)
	7052_morphine	N (%)	2,644 (98.69%)	35 (1.31%)	0 (0.00%)
7052_morphine	11289_warfarin	N (%)	29 (17.47%)	6 (3.61%)	131 (78.92%)
	161_acetaminophen	N (%)	0 (0.00%)	35 (1.31%)	2,644 (98.69%)

plotCohortOverlap(medsOverlap, uniqueCombinations = FALSE)

As well as generating these estimates for cohorts overall, we can also obtain stratified estimates. In this example we’ll add age groups to our cohort table, and then obtain estimates stratified by these groups.

cdm$meds <- cdm$meds |>
  addAge(ageGroup = list(c(0, 49), c(50, 150))) |>
  compute(temporary = FALSE, name = "meds") |>
  newCohortTable()
medsOverlap <- cdm$meds |>
  summariseCohortOverlap(strata = list("age_group"))

As with our overall results, we can quickly create tables and figures to view our stratified results.

tableCohortOverlap(medsOverlap, uniqueCombinations = FALSE)

Cohort name reference	Cohort name comparator	Age group	Estimate name	Variable name
				Only in reference cohort	In both cohorts	Only in comparator cohort
Eunomia
11289_warfarin	161_acetaminophen	overall	N (%)	1 (0.04%)	136 (5.07%)	2,543 (94.89%)
	7052_morphine	overall	N (%)	131 (78.92%)	6 (3.61%)	29 (17.47%)
161_acetaminophen	11289_warfarin	overall	N (%)	2,543 (94.89%)	136 (5.07%)	1 (0.04%)
	7052_morphine	overall	N (%)	2,644 (98.69%)	35 (1.31%)	0 (0.00%)
7052_morphine	11289_warfarin	overall	N (%)	29 (17.47%)	6 (3.61%)	131 (78.92%)
	161_acetaminophen	overall	N (%)	0 (0.00%)	35 (1.31%)	2,644 (98.69%)
11289_warfarin	161_acetaminophen	0 to 49	N (%)	1 (0.04%)	8 (0.30%)	2,653 (99.66%)
		50 to 150	N (%)	26 (2.25%)	102 (8.85%)	1,025 (88.90%)
	7052_morphine	0 to 49	N (%)	9 (26.47%)	0 (0.00%)	25 (73.53%)
		50 to 150	N (%)	122 (92.42%)	6 (4.55%)	4 (3.03%)
161_acetaminophen	11289_warfarin	0 to 49	N (%)	2,653 (99.66%)	8 (0.30%)	1 (0.04%)
		50 to 150	N (%)	1,025 (88.90%)	102 (8.85%)	26 (2.25%)
	7052_morphine	0 to 49	N (%)	2,636 (99.06%)	25 (0.94%)	0 (0.00%)
		50 to 150	N (%)	1,117 (99.11%)	10 (0.89%)	0 (0.00%)
7052_morphine	11289_warfarin	0 to 49	N (%)	25 (73.53%)	0 (0.00%)	9 (26.47%)
		50 to 150	N (%)	4 (3.03%)	6 (4.55%)	122 (92.42%)
	161_acetaminophen	0 to 49	N (%)	0 (0.00%)	25 (0.94%)	2,636 (99.06%)
		50 to 150	N (%)	0 (0.00%)	10 (0.89%)	1,117 (99.11%)

plotCohortOverlap(
  medsOverlap,
  y = c("cohort_name_reference", "cohort_name_comparator"),
  facet = c("age_group"),
  uniqueCombinations = TRUE
)