Concatenating cohort records"

In CohortConstructor: Build and Manipulate Study Cohorts Using a Common Data Model

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(CohortConstructor)
library(CohortCharacteristics)
library(ggplot2)

knitr::opts_chunk$set(
  collapse = TRUE,
  eval = TRUE, message = FALSE, warning = FALSE,
  comment = "#>"
)

library(CDMConnector)
library(dplyr, warn.conflicts = FALSE)

if (Sys.getenv("EUNOMIA_DATA_FOLDER") == ""){
  Sys.setenv("EUNOMIA_DATA_FOLDER" = file.path(tempdir(), "eunomia"))}
if (!dir.exists(Sys.getenv("EUNOMIA_DATA_FOLDER"))){ dir.create(Sys.getenv("EUNOMIA_DATA_FOLDER"))
  downloadEunomiaData()  
}

For this example we'll use the Eunomia synthetic data from the CDMConnector package.

con <- DBI::dbConnect(duckdb::duckdb(), dbdir = eunomiaDir())
cdm <- CDMConnector::cdmFromCon(con, cdmSchema = "main", 
                    writeSchema = "main", writePrefix = "my_study_")

Let's start by creating a cohort of users of acetaminophen

cdm$medications <- conceptCohort(cdm = cdm, 
                                 conceptSet = list("acetaminophen" = 1127433), 
                                 name = "medications")
cohortCount(cdm$medications)

We can merge cohort records using the collapseCohorts() function in the CohortConstructor package. The function allows us to specifying the number of days between two cohort entries, which will then be merged into a single record.

Let's first define a new cohort where records within 1095 days (~ 3 years) of each other will be merged.

cdm$medications_collapsed <- cdm$medications |> 
  collapseCohorts(
  gap = 1095,
  name = "medications_collapsed"
)

Let's compare how this function would change the records of a single individual.

cdm$medications |>
  filter(subject_id == 1)
cdm$medications_collapsed |>
  filter(subject_id == 1)

Subject 1 initially had 4 records between 1971 and 1982. After specifying that records within three years of each other are to be merged, the number of records decreases to three. The record from 1980-03-15 to 1980-03-29 and the record from 1982-09-11 to 1982-10-02 are merged to create a new record from 1980-03-15 to 1982-10-02.

Now let's look at how the cohorts have been changed.

summary_attrition <- summariseCohortAttrition(cdm$medications_collapsed)
tableCohortAttrition(summary_attrition)

CohortConstructor documentation built on June 8, 2025, 12:49 p.m.