This comprises all the diagnostics that are being offered in this package, this includes:
A diagnostic on the OMOP CDM dataset as a whole via
databaseDiagnostics.A diagnostic on the codelists associated with cohorts via
codelistDiagnostics.A diagnostic on the cohort itself via
cohortDiagnostics.A diagnostic on the frequency of the cohort in the dataset population via
populationDiagnostics.
Arguments
- cohort
Cohort table in a cdm reference
- databaseDiagnostics
A list of arguments that uses
databaseDiagnostics. If the list is empty, the default values will be used. Example: In the following example, all diagnostics will be run except person table summary from databaseDiagnostics: *databaseDiagnostics = list( "personTableSummary" = FALSE )- codelistDiagnostics
A list of arguments that uses
codelistDiagnostics. If the list is empty, the default values will be used. Example: In the below example, all diagnostics will be run, and a subsample of 1,000 participants will be used to run measurement diagnostics and another independent subsample of 500 participants will be used to run drug diagnostics: *codelistDiagnostics = list( "measurementDiagnosticsSample" = 1000, "drugDiagnosticsSample" = 500 )- cohortDiagnostics
A list of arguments that uses
cohortDiagnostics. If the list is empty, the default values will be used. Example: *cohortDiagnostics = list( "cohortSurvival" = TRUE )- populationDiagnostics
A list of arguments that uses
populationDiagnostics. If the list is empty, the default values will be used. Example: In the below example, all diagnostics will be run and a subsample of 100,000 participants will be used to run populationDiagnostics. *populationDiagnostics = list( "populationSample" = 100000 )- stagingDirectory
Path to folder to save incremental results and log file
Examples
# \donttest{
library(omock)
library(CohortConstructor)
library(PhenotypeR)
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$warfarin <- conceptCohort(cdm,
conceptSet = list(warfarin = c(1310149L,
40163554L)),
name = "warfarin")
#> ℹ Subsetting table drug_exposure using 2 concepts with domain: drug.
#> ℹ Combining tables.
#> ℹ Creating cohort attributes.
#> ℹ Applying cohort requirements.
#> ℹ Merging overlapping records.
#> ✔ Cohort warfarin created.
result <- phenotypeDiagnostics(cdm$warfarin)
#> Logging PhenotypeR progress in
#> /tmp/RtmprdhPUv/phenotypeDiagnostics_log_{date}_{time}1c827db1f311.txt
#> ℹ Creating log file:
#> /tmp/RtmprdhPUv/phenotypeDiagnostics_log_2026_08_02_16_34_401c827db1f311.txt.
#> [2026-08-02 16:34:40] - Log file created
#> [2026-08-02 16:34:40] - Database diagnostics - getting CDM Snapshot
#> [2026-08-02 16:34:40] - Database diagnostics - summarising person table
#> ℹ The following estimates will be calculated:
#> • date_of_birth: 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 16:34:44.447456
#> ✔ Summary finished, at 2026-08-02 16:34:44.507474
#> [2026-08-02 16:34:44] - Database diagnostics - summarising observation period
#> ℹ retrieving cdm object from cdm_table.
#> Warning: ! There are 2649 individuals not included in the person table.
#> ℹ The following estimates will be calculated:
#> • observation_period_start_date: density
#> • observation_period_end_date: 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 16:34:47.628176
#> ✔ Summary finished, at 2026-08-02 16:34:47.706044
#> [2026-08-02 16:34:48] - Codelist diagnostics - index event breakdown
#> Getting counts of warfarin codes for cohort warfarin
#> Warning: The CDM reference containing the cohort must also contain achilles tables.
#> Returning only index event breakdown.
#> [2026-08-02 16:34:50] - Cohort diagnostics - cohort attrition
#> [2026-08-02 16:34:50] - Cohort diagnostics - cohort count
#> ℹ summarising data
#> ℹ summarising cohort warfarin
#> ✔ summariseCharacteristics finished!
#> → Skipping cohort sampling as all cohorts have less than 20000 individuals.
#> [2026-08-02 16:34:51] - Cohort diagnostics - matched cohorts
#> → Sampling cohort `tmp_022_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
#> [2026-08-02 16:35:01] - Cohort diagnostics - cohort characteristics
#> 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!
#> [2026-08-02 16:35:06] - Cohort diagnostics - age density
#> 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 16:35:07.617219
#> ✔ Summary finished, at 2026-08-02 16:35:07.739151
#> 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`
#> [2026-08-02 16:35:08] - Cohort diagnostics - 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
#> 237 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
#> 237 estimates dropped as frequency less than 1%
#> ✔ Summarising large scale characteristics
#> `cohort_sample` and `matched_sample` cast to character.
#> [2026-08-02 16:35:45] - Population diagnosics - denominator cohort
#> [2026-08-02 16:35:45] - Population diagnosics - sampling person table to 1e+05
#> people
#> ℹ Creating denominator cohorts
#> ✔ Cohorts created in 0 min and 3 sec
#> [2026-08-02 16:35:49] - Population diagnosics - incidence
#> ℹ Getting incidence for analysis 1 of 7
#> ℹ Getting incidence for analysis 2 of 7
#> ℹ Getting incidence for analysis 3 of 7
#> ℹ Getting incidence for analysis 4 of 7
#> ℹ Getting incidence for analysis 5 of 7
#> ℹ Getting incidence for analysis 6 of 7
#> ℹ Getting incidence for analysis 7 of 7
#> ✔ Overall time taken: 0 mins and 9 secs
#> [2026-08-02 16:35:59] - Population diagnosics - prevalence
#> ℹ Getting prevalence for analysis 1 of 7
#> ℹ Getting prevalence for analysis 2 of 7
#> ℹ Getting prevalence for analysis 3 of 7
#> ℹ Getting prevalence for analysis 4 of 7
#> ℹ Getting prevalence for analysis 5 of 7
#> ℹ Getting prevalence for analysis 6 of 7
#> ℹ Getting prevalence for analysis 7 of 7
#> ✔ Time taken: 0 mins and 6 secs
#> `populationDateStart`, `populationDateEnd`, and `populationSample` cast to
#> character.
#> `populationDateStart` and `populationDateEnd` eliminated from settings as all
#> elements are NA.
#> [2026-08-02 16:36:06] - Exporting log file
# }