The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
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[@]dogado.de.

1.1 Introduction

In this example we’re going to summarise the characteristics of individuals with an ankle sprain, ankle fracture, forearm fracture, or a hip fracture using the Eunomia synthetic data.

We’ll begin by creating our study cohorts.

library(CDMConnector)
library(CohortCharacteristics)
library(dplyr)
library(ggplot2)

con <- DBI::dbConnect(duckdb::duckdb(),
  dbdir = CDMConnector::eunomia_dir()
)
cdm <- CDMConnector::cdm_from_con(con,
  cdm_schem = "main",
  write_schema = "main",
  cdm_name = "Eunomia"
)

cdm <- generateConceptCohortSet(
  cdm = cdm,
  name = "injuries",
  conceptSet = list(
    "ankle_sprain" = 81151,
    "ankle_fracture" = 4059173,
    "forearm_fracture" = 4278672,
    "hip_fracture" = 4230399
  ),
  end = "event_end_date",
  limit = "all"
)

1.2 Summarising cohort counts

We can first quickly summarise and present the overall counts of our cohorts.

cohort_counts <- summariseCohortCount(cdm[["injuries"]])
tableCohortCount(cohort_counts)
CDM name Variable name Estimate name Cohort name
Ankle sprain Ankle fracture Hip fracture Forearm fracture
Eunomia Number records N 1,915 464 138 569
Number subjects N 1,357 427 132 510

Moreover, we can also easily stratify these counts. For example, here we add age groups and then stratify our counts by t We can summarise the overall counts of our cohorts.

cdm[["injuries"]] <- cdm[["injuries"]] |>
  PatientProfiles::addAge(ageGroup = list(
    c(0, 3),
    c(4, 17),
    c(18, Inf)
  )) |>
  compute(temporary = FALSE, name = "injuries")

cohort_counts <- summariseCohortCount(cdm[["injuries"]], strata = "age_group")
tableCohortCount(cohort_counts)
CDM name Age group Variable name Estimate name Cohort name
Ankle sprain Ankle fracture Forearm fracture Hip fracture
Eunomia Overall Number records N 1,915 464 569 138
0 to 3 Number records N 202 49 51 7
18 or above Number records N 1,047 213 268 88
4 to 17 Number records N 666 202 250 43
Overall Number subjects N 1,357 427 510 132
0 to 3 Number subjects N 196 49 51 7
18 or above Number subjects N 847 204 249 83
4 to 17 Number subjects N 597 195 239 43

We can also apply minimum cell count suppression to our cohort counts. In this case we will obscure any counts below 10.

cohort_counts <- suppress(cohort_counts, minCellCount = 10)
tableCohortCount(cohort_counts)
CDM name Age group Variable name Estimate name Cohort name
Ankle sprain Ankle fracture Forearm fracture Hip fracture
Eunomia Overall Number records N 1,915 464 569 138
0 to 3 Number records N 202 49 51 <10
18 or above Number records N 1,047 213 268 88
4 to 17 Number records N 666 202 250 43
Overall Number subjects N 1,357 427 510 132
0 to 3 Number subjects N 196 49 51 <10
18 or above Number subjects N 847 204 249 83
4 to 17 Number subjects N 597 195 239 43

1.3 Summarising cohort attrition

Say we specify two inclusion criteria. First, we keep only cohort entries after the year 2000. Second, we keep only cohort entries for those aged 18 or older. We can easily create plots summarising our cohort attrition.

cdm <- generateConceptCohortSet(
  cdm = cdm,
  name = "ankle_sprain",
  conceptSet = list("ankle_sprain" = 81151),
  end = "event_end_date",
  limit = "all"
)

cdm[["ankle_sprain"]] <- cdm[["ankle_sprain"]] |>
  filter(year(cohort_start_date) >= 2000) |>
  recordCohortAttrition("Restrict to cohort_start_date >= 2000") |>
  compute(temporary = FALSE, name = "ankle_sprain")

attrition_summary <- summariseCohortAttrition(cdm[["ankle_sprain"]])

plotCohortAttrition(attrition_summary)
cdm[["ankle_sprain"]] <- cdm[["ankle_sprain"]] |>
  PatientProfiles::addAge() |>
  filter(age >= 18) |>
  compute(temporary = FALSE, name = "ankle_sprain") |>
  recordCohortAttrition("Restrict to age >= 18")

attrition_summary <- summariseCohortAttrition(cdm[["ankle_sprain"]])

plotCohortAttrition(attrition_summary, cohortId = 1)

We could, of course, have applied these requirements the other way around.

cdm <- generateConceptCohortSet(
  cdm = cdm,
  name = "ankle_sprain",
  conceptSet = list("ankle_sprain" = 81151),
  end = "event_end_date",
  limit = "all"
)

cdm[["ankle_sprain"]] <- cdm[["ankle_sprain"]] |>
  PatientProfiles::addAge() |>
  filter(age >= 18) |>
  compute(temporary = FALSE, name = "ankle_sprain") |>
  recordCohortAttrition("Restrict to age >= 18")

cdm[["ankle_sprain"]] <- cdm[["ankle_sprain"]] |>
  filter(year(cohort_start_date) >= 2000) |>
  recordCohortAttrition("Restrict to cohort_start_date >= 2000") |>
  compute(temporary = FALSE, name = "ankle_sprain")


attrition_summary <- summariseCohortAttrition(cdm[["ankle_sprain"]])

plotCohortAttrition(attrition_summary, cohortId = 1)

As well as plotting cohort attrition, we can also create a table of our results.

tableCohortAttrition(attrition_summary)
CDM name
Eunomia
Reason Variable
Number records Number subjects Excluded records Excluded subjects
ankle_sprain
Initial qualifying events 1915 1357 0 0
Restrict to age >= 18 1047 847 868 510
Restrict to cohort_start_date >= 2000 454 420 593 427

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.
Health stats visible at Monitor.