Applying demographic requirements to a cohort

library(CodelistGenerator)
library(CohortConstructor)
library(CohortCharacteristics)
library(ggplot2)
library(omock)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union

In this vignette we’ll show how requirements related to patient demographics can be applied to a cohort. Again we’ll use the Eunomia synthetic data.

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")
#> ℹ Reading GiBleed tables.
#> ℹ Adding drug_strength table.

Let’s start by creating a cohort of people with a fracture. We’ll first look for codes that might represent a fracture and the build a cohort using these codes, setting cohort exit to 180 days after the fracture.

fracture_codes <- getCandidateCodes(cdm, "fracture")
#> Limiting to domains of interest
#> Getting concepts to include
#> Adding descendants
#> Search completed. Finishing up.
#> ✔ 9 candidate concepts identified
#> 
#> Time taken: 0 minutes and 0 seconds
fracture_codes <- list("fracture" = fracture_codes$concept_id)
cdm$fracture <- conceptCohort(cdm = cdm, 
                                 conceptSet = fracture_codes, 
                                 name = "fracture")
#> ℹ Subsetting table condition_occurrence using 9 concepts with domain:
#>   condition.
#> ℹ Combining tables.
#> ℹ Creating cohort attributes.
#> ℹ Applying cohort requirements.
#> ℹ Merging overlapping records.
#> ✔ Cohort fracture created.

summary_attrition <- summariseCohortAttrition(cdm$fracture)
plotCohortAttrition(summary_attrition)

Restrict cohort by age

We can choose a specific age range for individuals in our cohort using requireAge() from CohortConstructor.

cdm$fracture <- cdm$fracture |> 
  requireAge(indexDate = "cohort_start_date",
             ageRange = list(c(18, 100)))

summary_attrition <- summariseCohortAttrition(cdm$fracture)
plotCohortAttrition(summary_attrition)

Note that by default individuals are filtered based on the age they were when they entered the cohort.

Restrict cohort by sex

We can also specify a sex criteria for individuals in our cohort using requireSex() from CohortConstructor.

cdm$fracture <- cdm$fracture |> 
  requireSex(sex = "Female")

summary_attrition <- summariseCohortAttrition(cdm$fracture)
plotCohortAttrition(summary_attrition)

Restrict cohort by number of prior observations

We can also specify a minimum number of days of prior observations for each individual using requirePriorObservation() from CohortConstructor.

cdm$fracture <- cdm$fracture |> 
  requirePriorObservation(indexDate = "cohort_start_date",
                          minPriorObservation = 365)

summary_attrition <- summariseCohortAttrition(cdm$fracture)
#> `min_prior_observation` casted to character.
plotCohortAttrition(summary_attrition)

As well as specifying a minimum amount of prior observation, we can require some mimimum amount of follow-up by using requireFutureObservation() in a similar way.

Applying multiple demographic requirements to a cohort

We can implement multiple demographic requirements at the same time by using the more general requireDemographics() function.

cdm$fracture <- conceptCohort(cdm = cdm, 
                                 conceptSet = fracture_codes, 
                                 name = "fracture") |> 
  requireDemographics(indexDate = "cohort_start_date",
                      ageRange = c(18,100),
                      sex = "Female",
                      minPriorObservation = 365, 
                      minFutureObservation = 30)
#> ℹ Subsetting table condition_occurrence using 9 concepts with domain:
#>   condition.
#> ℹ Combining tables.
#> ℹ Creating cohort attributes.
#> ℹ Applying cohort requirements.
#> ℹ Merging overlapping records.
#> ✔ Cohort fracture created.

summary_attrition <- summariseCohortAttrition(cdm$fracture)
#> `min_prior_observation` and `min_future_observation` casted to
#> character.
plotCohortAttrition(summary_attrition)