Summarise the indications of individuals in a drug cohort

Summarise the observed indications of patients in a drug cohort based on their presence in an indication cohort in a specified time window. If an individual is not in one of the indication cohorts, they will be considered to have an unknown indication if they are present in one of the specified OMOP CDM clinical tables. Otherwise, if they are neither in an indication cohort or a clinical table they will be considered as having no observed indication.

Usage

summariseIndication(
  cohort,
  strata = list(),
  indicationCohortName,
  cohortId = NULL,
  indicationCohortId = NULL,
  indicationWindow = list(c(0, 0)),
  unknownIndicationTable = NULL,
  indexDate = "cohort_start_date",
  mutuallyExclusive = TRUE,
  censorDate = NULL,
  inObservation = TRUE,
  restrictIncident = FALSE
)

Arguments

cohort

A cohort_table object.

strata

A list of variables to stratify results. These variables must have been added as additional columns in the cohort table.

indicationCohortName

Name of the cohort table containing potential indications.

cohortId

A cohort definition id to restrict by. If NULL, all cohorts will be included.

indicationCohortId

Cohort definition IDs of the indications of interest. If NULL, all cohorts in indicationCohortName are included.

indicationWindow

Time windows over which to identify indications.

unknownIndicationTable

Tables in the OMOP CDM to search for unknown indications.

indexDate

Name of a column that indicates the date to start the analysis.

mutuallyExclusive

Whether intersections should be mutually exclusive. If TRUE, cohort combinations are reported as mutually exclusive categories; if FALSE, each cohort is reported independently.

censorDate

Name of a column that indicates the date to stop the analysis, if NULL end of individuals observation is used.

inObservation

Whether to restrict the analysis to individuals in observation. If TRUE, individuals not in observation are excluded. If FALSE, they are included as a separate category.

restrictIncident

Whether to include only target cohort records that start during the analysis period. If FALSE, all target cohort records that overlap with the study period will be included.

Value

A summarised result

Examples

# \donttest{
library(DrugUtilisation)
library(dplyr, warn.conflicts = FALSE)
library(CDMConnector)

cdm <- mockDrugUtilisation(source = "duckdb")
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/Rtmp8PRavt/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.

indications <- list(headache = 378253, asthma = 317009)
cdm <- generateConceptCohortSet(cdm = cdm,
                                conceptSet = indications,
                                name = "indication_cohorts")

cdm <- generateIngredientCohortSet(cdm = cdm,
                                   name = "drug_cohort",
                                   ingredient = "acetaminophen")
#> ℹ Subsetting drug_exposure table
#> ℹ Checking whether any record needs to be dropped.
#> ℹ Collapsing overlaping records.
#> ℹ Collapsing records with gapEra = 1 days.

cdm$drug_cohort |>
  summariseIndication(
    indicationCohortName = "indication_cohorts",
    unknownIndicationTable = "condition_occurrence",
    indicationWindow = list(c(-Inf, 0))
  ) |>
  glimpse()
#> ℹ Intersect with indications table (indication_cohorts)
#> ℹ Summarising indications.
#> Rows: 10
#> Columns: 13
#> $ result_id        <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
#> $ cdm_name         <chr> "DUS MOCK", "DUS MOCK", "DUS MOCK", "DUS MOCK", "DUS …
#> $ group_name       <chr> "cohort_name", "cohort_name", "cohort_name", "cohort_…
#> $ group_level      <chr> "acetaminophen", "acetaminophen", "acetaminophen", "a…
#> $ strata_name      <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ strata_level     <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ variable_name    <chr> "Indication any time before or on index date", "Indic…
#> $ variable_level   <chr> "asthma", "asthma", "headache", "headache", "asthma a…
#> $ estimate_name    <chr> "count", "percentage", "count", "percentage", "count"…
#> $ estimate_type    <chr> "integer", "percentage", "integer", "percentage", "in…
#> $ estimate_value   <chr> "1", "16.66667", "1", "16.66667", "0", "0", "0", "0",…
#> $ additional_name  <chr> "window_name", "window_name", "window_name", "window_…
#> $ additional_level <chr> "-inf to 0", "-inf to 0", "-inf to 0", "-inf to 0", "…
# }