The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

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> "overlap", "reference", "comparator", "overlap", "ref…
#> $ variable_level   <chr> "number_subjects", "number_subjects", "number_subject…
#> $ estimate_name    <chr> "count", "count", "count", "percentage", "percentage"…
#> $ estimate_type    <chr> "integer", "integer", "integer", "percentage", "perce…
#> $ estimate_value   <chr> "136", "1", "2543", "5.07462686567164", "0.0373134328…
#> $ 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
In both cohorts Only in reference cohort Only in comparator cohort
Eunomia
11289_warfarin 161_acetaminophen N (%) 136 (5.07%) 1 (0.04%) 2,543 (94.89%)
7052_morphine N (%) 6 (3.61%) 131 (78.92%) 29 (17.47%)
161_acetaminophen 11289_warfarin N (%) 136 (5.07%) 2,543 (94.89%) 1 (0.04%)
7052_morphine N (%) 35 (1.31%) 2,644 (98.69%) 0 (0.00%)
7052_morphine 11289_warfarin N (%) 6 (3.61%) 29 (17.47%) 131 (78.92%)
161_acetaminophen N (%) 35 (1.31%) 0 (0.00%) 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
In both cohorts Only in reference cohort Only in comparator cohort
Eunomia
11289_warfarin 161_acetaminophen overall N (%) 136 (5.07%) 1 (0.04%) 2,543 (94.89%)
7052_morphine overall N (%) 6 (3.61%) 131 (78.92%) 29 (17.47%)
161_acetaminophen 11289_warfarin overall N (%) 136 (5.07%) 2,543 (94.89%) 1 (0.04%)
7052_morphine overall N (%) 35 (1.31%) 2,644 (98.69%) 0 (0.00%)
7052_morphine 11289_warfarin overall N (%) 6 (3.61%) 29 (17.47%) 131 (78.92%)
161_acetaminophen overall N (%) 35 (1.31%) 0 (0.00%) 2,644 (98.69%)
11289_warfarin 161_acetaminophen 0 to 49 N (%) 8 (0.30%) 1 (0.04%) 2,653 (99.66%)
7052_morphine 0 to 49 N (%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
161_acetaminophen 11289_warfarin 0 to 49 N (%) 8 (0.30%) 2,653 (99.66%) 1 (0.04%)
7052_morphine 0 to 49 N (%) 25 (0.94%) 2,636 (99.06%) 0 (0.00%)
7052_morphine 11289_warfarin 0 to 49 N (%) 0 (0.00%) 0 (0.00%) 0 (0.00%)
161_acetaminophen 0 to 49 N (%) 25 (0.94%) 0 (0.00%) 2,636 (99.06%)
11289_warfarin 161_acetaminophen 50 to 150 N (%) 102 (8.85%) 26 (2.25%) 1,025 (88.90%)
7052_morphine 50 to 150 N (%) 6 (4.55%) 122 (92.42%) 4 (3.03%)
161_acetaminophen 11289_warfarin 50 to 150 N (%) 102 (8.85%) 1,025 (88.90%) 26 (2.25%)
7052_morphine 50 to 150 N (%) 10 (0.89%) 1,117 (99.11%) 0 (0.00%)
7052_morphine 11289_warfarin 50 to 150 N (%) 6 (4.55%) 4 (3.03%) 122 (92.42%)
161_acetaminophen 50 to 150 N (%) 10 (0.89%) 0 (0.00%) 1,117 (99.11%)
 
plotCohortOverlap(
  medsOverlap,
  y = c("cohort_name_reference", "cohort_name_comparator"),
  facet = c("age_group"),
  uniqueCombinations = TRUE
)

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.