Runs phenotypeR diagnostics on the cohort. The diganostics include:
Age groups and sex summarised.
A summary of visits of everyone in the cohort using visit_occurrence table.
A summary of age and sex density of the cohort.
Attrition of the cohorts.
Overlap between cohorts (if more than one cohort is being used).
Usage
cohortDiagnostics(
cohort,
cohortId = NULL,
cohortCount = TRUE,
cohortCharacteristics = TRUE,
largeScaleCharacteristics = TRUE,
compareCohorts = FALSE,
cohortSurvival = FALSE,
cohortSample = 20000,
matchedSample = 1000
)Arguments
- cohort
Cohort table in a cdm reference
- cohortId
Specific cohort definition ID for which to run cohort diagnostics.
- cohortCount
Whether to run
CohortCharacteristics::summariseCohortCount()andCohortCharacteristics::summariseCohortAttrition()(TRUE) or not (FALSE).- cohortCharacteristics
Whether to run
CohortCharacteristics::summariseCharacteristics()and summarise age density (TRUE) or not (FALSE).- largeScaleCharacteristics
Whether to run
CohortCharacteristics::summariseLargeScaleCharacteristics()(TRUE) or not (FALSE).- compareCohorts
Whether to run
CohortCharacteristics::summariseCohortOverlap()andCohortCharacteristics::summariseCohortTiming()(TRUE) or not (FALSE). Notice that, if set to TRUE, the diagnostics will only be run when there are more than one cohort.- cohortSurvival
Whether to run
CohortSurvival::estimateSingleEventSurvival()(TRUE) or not (FALSE).- cohortSample
The number of people to take a random sample for cohortDiagnostics. If
cohortSample = NULL, no sampling will be performed.- matchedSample
The number of people to take a random sample for matching. If
matchedSample = NULL, no sampling will be performed. IfmatchedSample = 0, no matched cohorts will be created.
Examples
# \donttest{
library(omock)
library(CohortConstructor)
library(PhenotypeR)
library(omock)
library(CDMConnector)
cdm <- mockCdmFromDataset(source = "duckdb")
#> ℹ Loading bundled GiBleed tables from package data.
#> ℹ Adding drug_strength table.
#> ℹ Creating local <cdm_reference> object.
#> ℹ Inserting <cdm_reference> into duckdb.
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/RtmprdhPUv/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.
cdm$warfarin <- conceptCohort(cdm,
conceptSet = list(warfarin = c(1310149L,
40163554L)),
name = "warfarin")
#> ℹ Subsetting table drug_exposure using 2 concepts with domain: drug.
#> ℹ Combining tables.
#> ℹ Creating cohort attributes.
#> ℹ Applying cohort requirements.
#> ℹ Merging overlapping records.
#> ✔ Cohort warfarin created.
result <- cohortDiagnostics(cdm$warfarin)
#> ℹ summarising data
#> ℹ summarising cohort warfarin
#> ✔ summariseCharacteristics finished!
#> → Skipping cohort sampling as all cohorts have less than 20000 individuals.
#> → Sampling cohort `tmp_004_sampled_independent`
#> Returning entry cohort as the size of the cohorts to be sampled is equal or
#> smaller than `n`.
#> • Generating an age and sex matched cohort for warfarin
#> Starting matching
#> ℹ Creating copy of target cohort.
#> • 1 cohort to be matched.
#> ℹ Creating controls cohorts.
#> ℹ Excluding cases from controls
#> • Matching by gender_concept_id and year_of_birth
#> • Removing controls that were not in observation at index date
#> • Excluding target records whose pair is not in observation
#> • Adjusting ratio
#> Binding cohorts
#> ✔ Done
#> → Getting cohorts and indexes
#> ℹ adding demographics columns
#> ℹ adding tableIntersectCount 1/1
#> window names cast to snake_case:
#> • `-365 to -1` -> `365_to_1`
#> ℹ summarising data
#> ℹ summarising cohort warfarin
#> ℹ summarising cohort warfarin_sampled
#> ℹ summarising cohort warfarin_matched
#> ✔ summariseCharacteristics finished!
#> ℹ The following estimates will be calculated:
#> • age: density
#> ! Table is collected to memory as not all requested estimates are supported on
#> the database side.
#> → Start summary of data, at 2026-08-02 16:33:32.75927
#> ✔ Summary finished, at 2026-08-02 16:33:32.89767
#> Using defaults for windows for large scale characteristics: c(-365, -31),
#> c(-30, -1), c(0, 0), c(1, 30), and c(31, 365). These can be changed via passing
#> alternative windows as a global option
#> `PhenotypeR_summariseLargeScaleCharacteristics_window`
#> Using defaults for event tables for large scale characteristics:
#> condition_occurrence, measurement, procedure_occurrence, device_exposure, and
#> observation. These can be changed via passing alternative windows as a global
#> option `PhenotypeR_summariseLargeScaleCharacteristics_eventInWindow`
#> Using defaults for episode tables for large scale characteristics:
#> drug_exposure, drug_era, and visit_occurrence. These can be changed via passing
#> alternative windows as a global option
#> `PhenotypeR_summariseLargeScaleCharacteristics_episodeInWindow`
#> ℹ Summarising large scale characteristics
#> - getting characteristics from table condition_occurrence (1 of 7)
#> - getting characteristics from table condition_occurrence (1 of 7) for time wi…
#> - getting characteristics from table condition_occurrence (1 of 7) for time wi…
#> - getting characteristics from table condition_occurrence (1 of 7) for time wi…
#> - getting characteristics from table condition_occurrence (1 of 7) for time wi…
#> - getting characteristics from table condition_occurrence (1 of 7) for time wi…
#> - getting characteristics from table measurement (2 of 7)
#> - getting characteristics from table measurement (2 of 7) for time window -365…
#> - getting characteristics from table measurement (2 of 7) for time window -30 …
#> - getting characteristics from table measurement (2 of 7) for time window 0 an…
#> - getting characteristics from table measurement (2 of 7) for time window 1 an…
#> - getting characteristics from table measurement (2 of 7) for time window 31 a…
#> - getting characteristics from table procedure_occurrence (3 of 7)
#> - getting characteristics from table procedure_occurrence (3 of 7) for time wi…
#> - getting characteristics from table procedure_occurrence (3 of 7) for time wi…
#> - getting characteristics from table procedure_occurrence (3 of 7) for time wi…
#> - getting characteristics from table procedure_occurrence (3 of 7) for time wi…
#> - getting characteristics from table procedure_occurrence (3 of 7) for time wi…
#> - getting characteristics from table observation (4 of 7)
#> - getting characteristics from table observation (4 of 7) for time window -365…
#> - getting characteristics from table observation (4 of 7) for time window -30 …
#> - getting characteristics from table observation (4 of 7) for time window 0 an…
#> - getting characteristics from table observation (4 of 7) for time window 1 an…
#> - getting characteristics from table observation (4 of 7) for time window 31 a…
#> - getting characteristics from table drug_exposure (5 of 7)
#> - getting characteristics from table drug_exposure (5 of 7) for time window -3…
#> - getting characteristics from table drug_exposure (5 of 7) for time window -3…
#> - getting characteristics from table drug_exposure (5 of 7) for time window 0 …
#> - getting characteristics from table drug_exposure (5 of 7) for time window 1 …
#> - getting characteristics from table drug_exposure (5 of 7) for time window 31…
#> - getting characteristics from table drug_era (6 of 7)
#> - getting characteristics from table drug_era (6 of 7) for time window -365 an…
#> - getting characteristics from table drug_era (6 of 7) for time window -30 and…
#> - getting characteristics from table drug_era (6 of 7) for time window 0 and 0
#> - getting characteristics from table drug_era (6 of 7) for time window 1 and 30
#> - getting characteristics from table drug_era (6 of 7) for time window 31 and …
#> - getting characteristics from table visit_occurrence (7 of 7)
#> - getting characteristics from table visit_occurrence (7 of 7) for time window…
#> - getting characteristics from table visit_occurrence (7 of 7) for time window…
#> - getting characteristics from table visit_occurrence (7 of 7) for time window…
#> - getting characteristics from table visit_occurrence (7 of 7) for time window…
#> - getting characteristics from table visit_occurrence (7 of 7) for time window…
#> Formatting result
#> 247 estimates dropped as frequency less than 1%
#> ✔ Summarising large scale characteristics
#> ℹ Summarising large scale characteristics
#> - getting characteristics from table condition_occurrence (1 of 7)
#> - getting characteristics from table condition_occurrence (1 of 7) for time wi…
#> - getting characteristics from table condition_occurrence (1 of 7) for time wi…
#> - getting characteristics from table condition_occurrence (1 of 7) for time wi…
#> - getting characteristics from table condition_occurrence (1 of 7) for time wi…
#> - getting characteristics from table condition_occurrence (1 of 7) for time wi…
#> - getting characteristics from table measurement (2 of 7)
#> - getting characteristics from table measurement (2 of 7) for time window -365…
#> - getting characteristics from table measurement (2 of 7) for time window -30 …
#> - getting characteristics from table measurement (2 of 7) for time window 0 an…
#> - getting characteristics from table measurement (2 of 7) for time window 1 an…
#> - getting characteristics from table measurement (2 of 7) for time window 31 a…
#> - getting characteristics from table procedure_occurrence (3 of 7)
#> - getting characteristics from table procedure_occurrence (3 of 7) for time wi…
#> - getting characteristics from table procedure_occurrence (3 of 7) for time wi…
#> - getting characteristics from table procedure_occurrence (3 of 7) for time wi…
#> - getting characteristics from table procedure_occurrence (3 of 7) for time wi…
#> - getting characteristics from table procedure_occurrence (3 of 7) for time wi…
#> - getting characteristics from table observation (4 of 7)
#> - getting characteristics from table observation (4 of 7) for time window -365…
#> - getting characteristics from table observation (4 of 7) for time window -30 …
#> - getting characteristics from table observation (4 of 7) for time window 0 an…
#> - getting characteristics from table observation (4 of 7) for time window 1 an…
#> - getting characteristics from table observation (4 of 7) for time window 31 a…
#> - getting characteristics from table drug_exposure (5 of 7)
#> - getting characteristics from table drug_exposure (5 of 7) for time window -3…
#> - getting characteristics from table drug_exposure (5 of 7) for time window -3…
#> - getting characteristics from table drug_exposure (5 of 7) for time window 0 …
#> - getting characteristics from table drug_exposure (5 of 7) for time window 1 …
#> - getting characteristics from table drug_exposure (5 of 7) for time window 31…
#> - getting characteristics from table drug_era (6 of 7)
#> - getting characteristics from table drug_era (6 of 7) for time window -365 an…
#> - getting characteristics from table drug_era (6 of 7) for time window -30 and…
#> - getting characteristics from table drug_era (6 of 7) for time window 0 and 0
#> - getting characteristics from table drug_era (6 of 7) for time window 1 and 30
#> - getting characteristics from table drug_era (6 of 7) for time window 31 and …
#> - getting characteristics from table visit_occurrence (7 of 7)
#> - getting characteristics from table visit_occurrence (7 of 7) for time window…
#> - getting characteristics from table visit_occurrence (7 of 7) for time window…
#> - getting characteristics from table visit_occurrence (7 of 7) for time window…
#> - getting characteristics from table visit_occurrence (7 of 7) for time window…
#> - getting characteristics from table visit_occurrence (7 of 7) for time window…
#> Formatting result
#> 247 estimates dropped as frequency less than 1%
#> ✔ Summarising large scale characteristics
#> `cohort_sample` and `matched_sample` cast to character.
cdmDisconnect(cdm)
# }