OmopCheckout

The goal of OmopCheckout is to validate and explore summarised_result objects produced when working with the Observational Medical Outcomes Partnership (OMOP) Common Data Model. It helps ensure that results are correctly formatted and adequately suppressed before sharing. It also helps to explore what is the content of a summarised_result object.

Installation

OmopCheckout can be installed from cran with:

install.packages("OmopCheckout")

or you can install the development GitHub with:

# install.packages("pak")
pak::pkg_install("OHDSI/OmopCheckout")

What is a summarised_result?

A summarised_result is a standardised output format used across the OHDSI R package ecosystem (e.g. CohortCharacteristics, IncidencePrevalence, DrugUtilisation). To learn more, see the omopgenerics documentation.

Usage

library(OmopCheckout)
library(OmopViewer)

Full audit with checkout()

checkout() runs a complete audit of a summarised_result object covering suppression status, package metadata, and estimate types.

checkout(omopViewerResults)
#> ## <summarised_result>
#> 
#> ### Suppression
#> 
#> - Results suppressed with **minCellCount = 5** for result IDs: 1–122 (55,103 rows; 100.0%)
#> 
#> ### Packages
#> 
#> **CodelistGenerator (3.5.0)** for result IDs: 6–10 (183 rows ; 0.3%):
#> 
#> - *achilles_code_use* for result IDs: 9 (12 rows ; <0.1%)
#> - *code_use* for result IDs: 8 (24 rows ; <0.1%)
#> - *cohort_code_use* for result IDs: 7 (144 rows ; 0.3%)
#> - *orphan_code_use* for result IDs: 6 (2 rows ; <0.1%)
#> - *unmapped_codes* for result IDs: 10 (1 rows ; <0.1%)
#> 
#> **CohortCharacteristics (1.1.0)** for result IDs: 11–17 (31,413 rows ; 57.0%):
#> 
#> - *summarise_characteristics* for result IDs: 14 (63 rows ; 0.1%)
#> - *summarise_cohort_attrition* for result IDs: 13 (16 rows ; <0.1%)
#> - *summarise_cohort_count* for result IDs: 12 (2 rows ; <0.1%)
#> - *summarise_cohort_overlap* for result IDs: 11 (180 rows ; 0.3%)
#> - *summarise_cohort_timing* for result IDs: 15 (30,930 rows ; 56.1%)
#> - *summarise_large_scale_characteristics* for result IDs: 16–17 (222 rows ; 0.4%)
#> 
#> **CohortSurvival (1.1.0)** for result IDs: 96–115 (7,038 rows ; 12.8%):
#> 
#> - *survival_attrition* for result IDs: 108–111, 115 (84 rows ; 0.2%)
#> - *survival_estimates* for result IDs: 96–99, 112 (6,588 rows ; 12.0%)
#> - *survival_events* for result IDs: 100–103, 113 (252 rows ; 0.5%)
#> - *survival_summary* for result IDs: 104–107, 114 (114 rows ; 0.2%)
#> 
#> **DrugUtilisation (1.0.5)** for result IDs: 90–95 (339 rows ; 0.6%):
#> 
#> - *summarise_dose_coverage* for result IDs: 91 (32 rows ; 0.1%)
#> - *summarise_drug_restart* for result IDs: 94 (24 rows ; <0.1%)
#> - *summarise_drug_utilisation* for result IDs: 93 (72 rows ; 0.1%)
#> - *summarise_indication* for result IDs: 92 (36 rows ; 0.1%)
#> - *summarise_proportion_of_patients_covered* for result IDs: 90 (115 rows ; 0.2%)
#> - *summarise_treatment* for result IDs: 95 (60 rows ; 0.1%)
#> 
#> **IncidencePrevalence (1.2.1)** for result IDs: 18–89 (3,696 rows ; 6.7%):
#> 
#> - *incidence* for result IDs: 18–35 (1,176 rows ; 2.1%)
#> - *incidence_attrition* for result IDs: 36–53 (840 rows ; 1.5%)
#> - *prevalence* for result IDs: 54–71 (840 rows ; 1.5%)
#> - *prevalence_attrition* for result IDs: 72–89 (840 rows ; 1.5%)
#> 
#> **MeasurementDiagnostics (0.2.0)** for result IDs: 117–122 (8,312 rows ; 15.1%):
#> 
#> - *measurement_summary* for result IDs: 117, 120 (2,080 rows ; 3.8%)
#> - *measurement_value_as_concept* for result IDs: 119, 122 (16 rows ; <0.1%)
#> - *measurement_value_as_number* for result IDs: 118, 121 (6,216 rows ; 11.3%)
#> 
#> **OmopSketch (1.0.0)** for result IDs: 1–5 (4,049 rows ; 7.3%):
#> 
#> - *summarise_clinical_records* for result IDs: 3 (186 rows ; 0.3%)
#> - *summarise_missing_data* for result IDs: 4 (114 rows ; 0.2%)
#> - *summarise_observation_period* for result IDs: 2 (3,126 rows ; 5.7%)
#> - *summarise_omop_snapshot* for result IDs: 1 (15 rows ; <0.1%)
#> - *summarise_trend* for result IDs: 5 (608 rows ; 1.1%)
#> 
#> **omopgenerics (1.3.5)** for result IDs: 116 (73 rows ; 0.1%):
#> 
#> - *summarise_log_file* for result IDs: 116 (73 rows ; 0.1%)
#> 
#> 
#> ### Estimates
#> 
#> **achilles_code_use** for result IDs: 9 (12 rows ; <0.1%):
#> 
#> - *person_count* (6 rows; <0.1%)
#> - *record_count* (6 rows; <0.1%)
#> 
#> **code_use** for result IDs: 8 (24 rows ; <0.1%):
#> 
#> - *person_count* (12 rows; <0.1%)
#> - *record_count* (12 rows; <0.1%)
#> 
#> **cohort_code_use** for result IDs: 7 (144 rows ; 0.3%):
#> 
#> - *person_count* (72 rows; 0.1%)
#> - *record_count* (72 rows; 0.1%)
#> 
#> **incidence** for result IDs: 18–35 (1,176 rows ; 2.1%):
#> 
#> - *denominator_count* (168 rows; 0.3%)
#> - *incidence_100000_pys* (168 rows; 0.3%)
#> - *incidence_100000_pys_95CI_lower* (168 rows; 0.3%)
#> - *incidence_100000_pys_95CI_upper* (168 rows; 0.3%)
#> - *outcome_count* (168 rows; 0.3%)
#> - *person_days* (168 rows; 0.3%)
#> - *person_years* (168 rows; 0.3%)
#> 
#> **incidence_attrition** for result IDs: 36–53 (840 rows ; 1.5%):
#> 
#> - *count* (840 rows; 1.5%)
#> 
#> **measurement_summary** for result IDs: 117, 120 (2,080 rows ; 3.8%):
#> 
#> - *count* (6 rows; <0.1%)
#> - *density_x* (1027 rows; 1.9%)
#> - *density_y* (1027 rows; 1.9%)
#> - *max* (4 rows; <0.1%)
#> - *median* (4 rows; <0.1%)
#> - *min* (4 rows; <0.1%)
#> - *q25* (4 rows; <0.1%)
#> - *q75* (4 rows; <0.1%)
#> 
#> **measurement_value_as_concept** for result IDs: 119, 122 (16 rows ; <0.1%):
#> 
#> - *count* (8 rows; <0.1%)
#> - *percentage* (8 rows; <0.1%)
#> 
#> **measurement_value_as_number** for result IDs: 118, 121 (6,216 rows ; 11.3%):
#> 
#> - *count* (6 rows; <0.1%)
#> - *count_missing* (6 rows; <0.1%)
#> - *density_x* (3072 rows; 5.6%)
#> - *density_y* (3072 rows; 5.6%)
#> - *max* (6 rows; <0.1%)
#> - *median* (6 rows; <0.1%)
#> - *min* (6 rows; <0.1%)
#> - *percentage_missing* (6 rows; <0.1%)
#> - *q01* (6 rows; <0.1%)
#> - *q05* (6 rows; <0.1%)
#> - *q25* (6 rows; <0.1%)
#> - *q75* (6 rows; <0.1%)
#> - *q95* (6 rows; <0.1%)
#> - *q99* (6 rows; <0.1%)
#> 
#> **orphan_code_use** for result IDs: 6 (2 rows ; <0.1%):
#> 
#> - *person_count* (1 rows; <0.1%)
#> - *record_count* (1 rows; <0.1%)
#> 
#> **prevalence** for result IDs: 54–71 (840 rows ; 1.5%):
#> 
#> - *denominator_count* (168 rows; 0.3%)
#> - *outcome_count* (168 rows; 0.3%)
#> - *prevalence* (168 rows; 0.3%)
#> - *prevalence_95CI_lower* (168 rows; 0.3%)
#> - *prevalence_95CI_upper* (168 rows; 0.3%)
#> 
#> **prevalence_attrition** for result IDs: 72–89 (840 rows ; 1.5%):
#> 
#> - *count* (840 rows; 1.5%)
#> 
#> **summarise_characteristics** for result IDs: 14 (63 rows ; 0.1%):
#> 
#> - *count* (10 rows; <0.1%)
#> - *max* (7 rows; <0.1%)
#> - *mean* (5 rows; <0.1%)
#> - *median* (7 rows; <0.1%)
#> - *min* (7 rows; <0.1%)
#> - *percentage* (8 rows; <0.1%)
#> - *q25* (7 rows; <0.1%)
#> - *q75* (7 rows; <0.1%)
#> - *sd* (5 rows; <0.1%)
#> 
#> **summarise_clinical_records** for result IDs: 3 (186 rows ; 0.3%):
#> 
#> - *count* (30 rows; 0.1%)
#> - *max* (2 rows; <0.1%)
#> - *mean* (2 rows; <0.1%)
#> - *median* (2 rows; <0.1%)
#> - *min* (2 rows; <0.1%)
#> - *na_count* (39 rows; 0.1%)
#> - *na_percentage* (39 rows; 0.1%)
#> - *percentage* (28 rows; 0.1%)
#> - *q25* (2 rows; <0.1%)
#> - *q75* (2 rows; <0.1%)
#> - *sd* (2 rows; <0.1%)
#> - *zero_count* (18 rows; <0.1%)
#> - *zero_percentage* (18 rows; <0.1%)
#> 
#> **summarise_cohort_attrition** for result IDs: 13 (16 rows ; <0.1%):
#> 
#> - *count* (16 rows; <0.1%)
#> 
#> **summarise_cohort_count** for result IDs: 12 (2 rows ; <0.1%):
#> 
#> - *count* (2 rows; <0.1%)
#> 
#> **summarise_cohort_overlap** for result IDs: 11 (180 rows ; 0.3%):
#> 
#> - *count* (90 rows; 0.2%)
#> - *percentage* (90 rows; 0.2%)
#> 
#> **summarise_cohort_timing** for result IDs: 15 (30,930 rows ; 56.1%):
#> 
#> - *count* (60 rows; 0.1%)
#> - *density_x* (15360 rows; 27.9%)
#> - *density_y* (15360 rows; 27.9%)
#> - *max* (30 rows; 0.1%)
#> - *median* (30 rows; 0.1%)
#> - *min* (30 rows; 0.1%)
#> - *q25* (30 rows; 0.1%)
#> - *q75* (30 rows; 0.1%)
#> 
#> **summarise_dose_coverage** for result IDs: 91 (32 rows ; 0.1%):
#> 
#> - *count* (4 rows; <0.1%)
#> - *count_missing* (4 rows; <0.1%)
#> - *mean* (4 rows; <0.1%)
#> - *median* (4 rows; <0.1%)
#> - *percentage_missing* (4 rows; <0.1%)
#> - *q25* (4 rows; <0.1%)
#> - *q75* (4 rows; <0.1%)
#> - *sd* (4 rows; <0.1%)
#> 
#> **summarise_drug_restart** for result IDs: 94 (24 rows ; <0.1%):
#> 
#> - *count* (12 rows; <0.1%)
#> - *percentage* (12 rows; <0.1%)
#> 
#> **summarise_drug_utilisation** for result IDs: 93 (72 rows ; 0.1%):
#> 
#> - *count* (2 rows; <0.1%)
#> - *count_missing* (10 rows; <0.1%)
#> - *mean* (10 rows; <0.1%)
#> - *median* (10 rows; <0.1%)
#> - *percentage_missing* (10 rows; <0.1%)
#> - *q25* (10 rows; <0.1%)
#> - *q75* (10 rows; <0.1%)
#> - *sd* (10 rows; <0.1%)
#> 
#> **summarise_indication** for result IDs: 92 (36 rows ; 0.1%):
#> 
#> - *count* (18 rows; <0.1%)
#> - *percentage* (18 rows; <0.1%)
#> 
#> **summarise_large_scale_characteristics** for result IDs: 16–17 (222 rows ; 0.4%):
#> 
#> - *count* (111 rows; 0.2%)
#> - *percentage* (111 rows; 0.2%)
#> 
#> **summarise_log_file** for result IDs: 116 (73 rows ; 0.1%):
#> 
#> - *date_time* (37 rows; 0.1%)
#> - *elapsed_time* (36 rows; 0.1%)
#> 
#> **summarise_missing_data** for result IDs: 4 (114 rows ; 0.2%):
#> 
#> - *na_count* (39 rows; 0.1%)
#> - *na_percentage* (39 rows; 0.1%)
#> - *zero_count* (18 rows; <0.1%)
#> - *zero_percentage* (18 rows; <0.1%)
#> 
#> **summarise_observation_period** for result IDs: 2 (3,126 rows ; 5.7%):
#> 
#> - *count* (7 rows; <0.1%)
#> - *density_x* (1536 rows; 2.8%)
#> - *density_y* (1536 rows; 2.8%)
#> - *max* (3 rows; <0.1%)
#> - *mean* (3 rows; <0.1%)
#> - *median* (3 rows; <0.1%)
#> - *min* (3 rows; <0.1%)
#> - *na_count* (5 rows; <0.1%)
#> - *na_percentage* (5 rows; <0.1%)
#> - *percentage* (4 rows; <0.1%)
#> - *q05* (3 rows; <0.1%)
#> - *q25* (3 rows; <0.1%)
#> - *q75* (3 rows; <0.1%)
#> - *q95* (3 rows; <0.1%)
#> - *sd* (3 rows; <0.1%)
#> - *zero_count* (3 rows; <0.1%)
#> - *zero_percentage* (3 rows; <0.1%)
#> 
#> **summarise_omop_snapshot** for result IDs: 1 (15 rows ; <0.1%):
#> 
#> - *count* (1 rows; <0.1%)
#> - *description* (1 rows; <0.1%)
#> - *documentation_reference* (1 rows; <0.1%)
#> - *end_date* (1 rows; <0.1%)
#> - *holder_name* (1 rows; <0.1%)
#> - *package* (1 rows; <0.1%)
#> - *person_count* (1 rows; <0.1%)
#> - *release_date* (1 rows; <0.1%)
#> - *snapshot_date* (1 rows; <0.1%)
#> - *source_name* (1 rows; <0.1%)
#> - *start_date* (1 rows; <0.1%)
#> - *type* (1 rows; <0.1%)
#> - *version* (1 rows; <0.1%)
#> - *vocabulary_version* (1 rows; <0.1%)
#> - *write_schema* (1 rows; <0.1%)
#> 
#> **summarise_proportion_of_patients_covered** for result IDs: 90 (115 rows ; 0.2%):
#> 
#> - *denominator_count* (23 rows; <0.1%)
#> - *outcome_count* (23 rows; <0.1%)
#> - *ppc* (23 rows; <0.1%)
#> - *ppc_lower* (23 rows; <0.1%)
#> - *ppc_upper* (23 rows; <0.1%)
#> 
#> **summarise_treatment** for result IDs: 95 (60 rows ; 0.1%):
#> 
#> - *count* (30 rows; 0.1%)
#> - *percentage* (30 rows; 0.1%)
#> 
#> **summarise_trend** for result IDs: 5 (608 rows ; 1.1%):
#> 
#> - *count* (304 rows; 0.6%)
#> - *percentage* (304 rows; 0.6%)
#> 
#> **survival_attrition** for result IDs: 108–111, 115 (84 rows ; 0.2%):
#> 
#> - *count* (84 rows; 0.2%)
#> 
#> **survival_estimates** for result IDs: 96–99, 112 (6,588 rows ; 12.0%):
#> 
#> - *estimate* (2196 rows; 4.0%)
#> - *estimate_95CI_lower* (2196 rows; 4.0%)
#> - *estimate_95CI_upper* (2196 rows; 4.0%)
#> 
#> **survival_events** for result IDs: 100–103, 113 (252 rows ; 0.5%):
#> 
#> - *n_censor_count* (84 rows; 0.2%)
#> - *n_events_count* (84 rows; 0.2%)
#> - *n_risk_count* (84 rows; 0.2%)
#> 
#> **survival_summary** for result IDs: 104–107, 114 (114 rows ; 0.2%):
#> 
#> - *median_survival* (4 rows; <0.1%)
#> - *median_survival_95CI_higher* (4 rows; <0.1%)
#> - *median_survival_95CI_lower* (4 rows; <0.1%)
#> - *n_events_count* (6 rows; <0.1%)
#> - *number_records_count* (6 rows; <0.1%)
#> - *q05_survival* (4 rows; <0.1%)
#> - *q05_survival_95CI_higher* (4 rows; <0.1%)
#> - *q05_survival_95CI_lower* (4 rows; <0.1%)
#> - *q0_survival* (4 rows; <0.1%)
#> - *q0_survival_95CI_higher* (4 rows; <0.1%)
#> - *q0_survival_95CI_lower* (4 rows; <0.1%)
#> - *q100_survival* (4 rows; <0.1%)
#> - *q100_survival_95CI_higher* (4 rows; <0.1%)
#> - *q100_survival_95CI_lower* (4 rows; <0.1%)
#> - *q25_survival* (4 rows; <0.1%)
#> - *q25_survival_95CI_higher* (4 rows; <0.1%)
#> - *q25_survival_95CI_lower* (4 rows; <0.1%)
#> - *q75_survival* (4 rows; <0.1%)
#> - *q75_survival_95CI_higher* (4 rows; <0.1%)
#> - *q75_survival_95CI_lower* (4 rows; <0.1%)
#> - *q95_survival* (4 rows; <0.1%)
#> - *q95_survival_95CI_higher* (4 rows; <0.1%)
#> - *q95_survival_95CI_lower* (4 rows; <0.1%)
#> - *restricted_mean_survival* (6 rows; <0.1%)
#> - *restricted_mean_survival_95CI_lower* (6 rows; <0.1%)
#> - *restricted_mean_survival_95CI_upper* (6 rows; <0.1%)
#> 
#> **unmapped_codes** for result IDs: 10 (1 rows ; <0.1%):
#> 
#> - *record_count* (1 rows; <0.1%)

Check suppression with summarySuppress()

summarySuppress() reports the suppression status for each result_id — which results have been suppressed, with what minimum cell count, and how many rows are affected.

summarySuppress(omopViewerResults)
#> - Results suppressed with **minCellCount = 5** for result IDs: 1–122 (55,103 rows; 100.0%)

Summarise packages with summaryPackages()

summaryPackages() reports which package name and version produced each result, broken down by result type.

summaryPackages(omopViewerResults)
#> **CodelistGenerator (3.5.0)** for result IDs: 6–10 (183 rows ; 0.3%):
#> 
#> - *achilles_code_use* for result IDs: 9 (12 rows ; <0.1%)
#> - *code_use* for result IDs: 8 (24 rows ; <0.1%)
#> - *cohort_code_use* for result IDs: 7 (144 rows ; 0.3%)
#> - *orphan_code_use* for result IDs: 6 (2 rows ; <0.1%)
#> - *unmapped_codes* for result IDs: 10 (1 rows ; <0.1%)
#> 
#> **CohortCharacteristics (1.1.0)** for result IDs: 11–17 (31,413 rows ; 57.0%):
#> 
#> - *summarise_characteristics* for result IDs: 14 (63 rows ; 0.1%)
#> - *summarise_cohort_attrition* for result IDs: 13 (16 rows ; <0.1%)
#> - *summarise_cohort_count* for result IDs: 12 (2 rows ; <0.1%)
#> - *summarise_cohort_overlap* for result IDs: 11 (180 rows ; 0.3%)
#> - *summarise_cohort_timing* for result IDs: 15 (30,930 rows ; 56.1%)
#> - *summarise_large_scale_characteristics* for result IDs: 16–17 (222 rows ; 0.4%)
#> 
#> **CohortSurvival (1.1.0)** for result IDs: 96–115 (7,038 rows ; 12.8%):
#> 
#> - *survival_attrition* for result IDs: 108–111, 115 (84 rows ; 0.2%)
#> - *survival_estimates* for result IDs: 96–99, 112 (6,588 rows ; 12.0%)
#> - *survival_events* for result IDs: 100–103, 113 (252 rows ; 0.5%)
#> - *survival_summary* for result IDs: 104–107, 114 (114 rows ; 0.2%)
#> 
#> **DrugUtilisation (1.0.5)** for result IDs: 90–95 (339 rows ; 0.6%):
#> 
#> - *summarise_dose_coverage* for result IDs: 91 (32 rows ; 0.1%)
#> - *summarise_drug_restart* for result IDs: 94 (24 rows ; <0.1%)
#> - *summarise_drug_utilisation* for result IDs: 93 (72 rows ; 0.1%)
#> - *summarise_indication* for result IDs: 92 (36 rows ; 0.1%)
#> - *summarise_proportion_of_patients_covered* for result IDs: 90 (115 rows ; 0.2%)
#> - *summarise_treatment* for result IDs: 95 (60 rows ; 0.1%)
#> 
#> **IncidencePrevalence (1.2.1)** for result IDs: 18–89 (3,696 rows ; 6.7%):
#> 
#> - *incidence* for result IDs: 18–35 (1,176 rows ; 2.1%)
#> - *incidence_attrition* for result IDs: 36–53 (840 rows ; 1.5%)
#> - *prevalence* for result IDs: 54–71 (840 rows ; 1.5%)
#> - *prevalence_attrition* for result IDs: 72–89 (840 rows ; 1.5%)
#> 
#> **MeasurementDiagnostics (0.2.0)** for result IDs: 117–122 (8,312 rows ; 15.1%):
#> 
#> - *measurement_summary* for result IDs: 117, 120 (2,080 rows ; 3.8%)
#> - *measurement_value_as_concept* for result IDs: 119, 122 (16 rows ; <0.1%)
#> - *measurement_value_as_number* for result IDs: 118, 121 (6,216 rows ; 11.3%)
#> 
#> **OmopSketch (1.0.0)** for result IDs: 1–5 (4,049 rows ; 7.3%):
#> 
#> - *summarise_clinical_records* for result IDs: 3 (186 rows ; 0.3%)
#> - *summarise_missing_data* for result IDs: 4 (114 rows ; 0.2%)
#> - *summarise_observation_period* for result IDs: 2 (3,126 rows ; 5.7%)
#> - *summarise_omop_snapshot* for result IDs: 1 (15 rows ; <0.1%)
#> - *summarise_trend* for result IDs: 5 (608 rows ; 1.1%)
#> 
#> **omopgenerics (1.3.5)** for result IDs: 116 (73 rows ; 0.1%):
#> 
#> - *summarise_log_file* for result IDs: 116 (73 rows ; 0.1%)

Summarise estimates with summaryEstimates()

summaryEstimates() lists the estimate types (e.g. count, mean, sd) present in each result type, along with their row counts.

summaryEstimates(omopViewerResults)
#> **achilles_code_use** for result IDs: 9 (12 rows ; <0.1%):
#> 
#> - *person_count* (6 rows; <0.1%)
#> - *record_count* (6 rows; <0.1%)
#> 
#> **code_use** for result IDs: 8 (24 rows ; <0.1%):
#> 
#> - *person_count* (12 rows; <0.1%)
#> - *record_count* (12 rows; <0.1%)
#> 
#> **cohort_code_use** for result IDs: 7 (144 rows ; 0.3%):
#> 
#> - *person_count* (72 rows; 0.1%)
#> - *record_count* (72 rows; 0.1%)
#> 
#> **incidence** for result IDs: 18–35 (1,176 rows ; 2.1%):
#> 
#> - *denominator_count* (168 rows; 0.3%)
#> - *incidence_100000_pys* (168 rows; 0.3%)
#> - *incidence_100000_pys_95CI_lower* (168 rows; 0.3%)
#> - *incidence_100000_pys_95CI_upper* (168 rows; 0.3%)
#> - *outcome_count* (168 rows; 0.3%)
#> - *person_days* (168 rows; 0.3%)
#> - *person_years* (168 rows; 0.3%)
#> 
#> **incidence_attrition** for result IDs: 36–53 (840 rows ; 1.5%):
#> 
#> - *count* (840 rows; 1.5%)
#> 
#> **measurement_summary** for result IDs: 117, 120 (2,080 rows ; 3.8%):
#> 
#> - *count* (6 rows; <0.1%)
#> - *density_x* (1027 rows; 1.9%)
#> - *density_y* (1027 rows; 1.9%)
#> - *max* (4 rows; <0.1%)
#> - *median* (4 rows; <0.1%)
#> - *min* (4 rows; <0.1%)
#> - *q25* (4 rows; <0.1%)
#> - *q75* (4 rows; <0.1%)
#> 
#> **measurement_value_as_concept** for result IDs: 119, 122 (16 rows ; <0.1%):
#> 
#> - *count* (8 rows; <0.1%)
#> - *percentage* (8 rows; <0.1%)
#> 
#> **measurement_value_as_number** for result IDs: 118, 121 (6,216 rows ; 11.3%):
#> 
#> - *count* (6 rows; <0.1%)
#> - *count_missing* (6 rows; <0.1%)
#> - *density_x* (3072 rows; 5.6%)
#> - *density_y* (3072 rows; 5.6%)
#> - *max* (6 rows; <0.1%)
#> - *median* (6 rows; <0.1%)
#> - *min* (6 rows; <0.1%)
#> - *percentage_missing* (6 rows; <0.1%)
#> - *q01* (6 rows; <0.1%)
#> - *q05* (6 rows; <0.1%)
#> - *q25* (6 rows; <0.1%)
#> - *q75* (6 rows; <0.1%)
#> - *q95* (6 rows; <0.1%)
#> - *q99* (6 rows; <0.1%)
#> 
#> **orphan_code_use** for result IDs: 6 (2 rows ; <0.1%):
#> 
#> - *person_count* (1 rows; <0.1%)
#> - *record_count* (1 rows; <0.1%)
#> 
#> **prevalence** for result IDs: 54–71 (840 rows ; 1.5%):
#> 
#> - *denominator_count* (168 rows; 0.3%)
#> - *outcome_count* (168 rows; 0.3%)
#> - *prevalence* (168 rows; 0.3%)
#> - *prevalence_95CI_lower* (168 rows; 0.3%)
#> - *prevalence_95CI_upper* (168 rows; 0.3%)
#> 
#> **prevalence_attrition** for result IDs: 72–89 (840 rows ; 1.5%):
#> 
#> - *count* (840 rows; 1.5%)
#> 
#> **summarise_characteristics** for result IDs: 14 (63 rows ; 0.1%):
#> 
#> - *count* (10 rows; <0.1%)
#> - *max* (7 rows; <0.1%)
#> - *mean* (5 rows; <0.1%)
#> - *median* (7 rows; <0.1%)
#> - *min* (7 rows; <0.1%)
#> - *percentage* (8 rows; <0.1%)
#> - *q25* (7 rows; <0.1%)
#> - *q75* (7 rows; <0.1%)
#> - *sd* (5 rows; <0.1%)
#> 
#> **summarise_clinical_records** for result IDs: 3 (186 rows ; 0.3%):
#> 
#> - *count* (30 rows; 0.1%)
#> - *max* (2 rows; <0.1%)
#> - *mean* (2 rows; <0.1%)
#> - *median* (2 rows; <0.1%)
#> - *min* (2 rows; <0.1%)
#> - *na_count* (39 rows; 0.1%)
#> - *na_percentage* (39 rows; 0.1%)
#> - *percentage* (28 rows; 0.1%)
#> - *q25* (2 rows; <0.1%)
#> - *q75* (2 rows; <0.1%)
#> - *sd* (2 rows; <0.1%)
#> - *zero_count* (18 rows; <0.1%)
#> - *zero_percentage* (18 rows; <0.1%)
#> 
#> **summarise_cohort_attrition** for result IDs: 13 (16 rows ; <0.1%):
#> 
#> - *count* (16 rows; <0.1%)
#> 
#> **summarise_cohort_count** for result IDs: 12 (2 rows ; <0.1%):
#> 
#> - *count* (2 rows; <0.1%)
#> 
#> **summarise_cohort_overlap** for result IDs: 11 (180 rows ; 0.3%):
#> 
#> - *count* (90 rows; 0.2%)
#> - *percentage* (90 rows; 0.2%)
#> 
#> **summarise_cohort_timing** for result IDs: 15 (30,930 rows ; 56.1%):
#> 
#> - *count* (60 rows; 0.1%)
#> - *density_x* (15360 rows; 27.9%)
#> - *density_y* (15360 rows; 27.9%)
#> - *max* (30 rows; 0.1%)
#> - *median* (30 rows; 0.1%)
#> - *min* (30 rows; 0.1%)
#> - *q25* (30 rows; 0.1%)
#> - *q75* (30 rows; 0.1%)
#> 
#> **summarise_dose_coverage** for result IDs: 91 (32 rows ; 0.1%):
#> 
#> - *count* (4 rows; <0.1%)
#> - *count_missing* (4 rows; <0.1%)
#> - *mean* (4 rows; <0.1%)
#> - *median* (4 rows; <0.1%)
#> - *percentage_missing* (4 rows; <0.1%)
#> - *q25* (4 rows; <0.1%)
#> - *q75* (4 rows; <0.1%)
#> - *sd* (4 rows; <0.1%)
#> 
#> **summarise_drug_restart** for result IDs: 94 (24 rows ; <0.1%):
#> 
#> - *count* (12 rows; <0.1%)
#> - *percentage* (12 rows; <0.1%)
#> 
#> **summarise_drug_utilisation** for result IDs: 93 (72 rows ; 0.1%):
#> 
#> - *count* (2 rows; <0.1%)
#> - *count_missing* (10 rows; <0.1%)
#> - *mean* (10 rows; <0.1%)
#> - *median* (10 rows; <0.1%)
#> - *percentage_missing* (10 rows; <0.1%)
#> - *q25* (10 rows; <0.1%)
#> - *q75* (10 rows; <0.1%)
#> - *sd* (10 rows; <0.1%)
#> 
#> **summarise_indication** for result IDs: 92 (36 rows ; 0.1%):
#> 
#> - *count* (18 rows; <0.1%)
#> - *percentage* (18 rows; <0.1%)
#> 
#> **summarise_large_scale_characteristics** for result IDs: 16–17 (222 rows ; 0.4%):
#> 
#> - *count* (111 rows; 0.2%)
#> - *percentage* (111 rows; 0.2%)
#> 
#> **summarise_log_file** for result IDs: 116 (73 rows ; 0.1%):
#> 
#> - *date_time* (37 rows; 0.1%)
#> - *elapsed_time* (36 rows; 0.1%)
#> 
#> **summarise_missing_data** for result IDs: 4 (114 rows ; 0.2%):
#> 
#> - *na_count* (39 rows; 0.1%)
#> - *na_percentage* (39 rows; 0.1%)
#> - *zero_count* (18 rows; <0.1%)
#> - *zero_percentage* (18 rows; <0.1%)
#> 
#> **summarise_observation_period** for result IDs: 2 (3,126 rows ; 5.7%):
#> 
#> - *count* (7 rows; <0.1%)
#> - *density_x* (1536 rows; 2.8%)
#> - *density_y* (1536 rows; 2.8%)
#> - *max* (3 rows; <0.1%)
#> - *mean* (3 rows; <0.1%)
#> - *median* (3 rows; <0.1%)
#> - *min* (3 rows; <0.1%)
#> - *na_count* (5 rows; <0.1%)
#> - *na_percentage* (5 rows; <0.1%)
#> - *percentage* (4 rows; <0.1%)
#> - *q05* (3 rows; <0.1%)
#> - *q25* (3 rows; <0.1%)
#> - *q75* (3 rows; <0.1%)
#> - *q95* (3 rows; <0.1%)
#> - *sd* (3 rows; <0.1%)
#> - *zero_count* (3 rows; <0.1%)
#> - *zero_percentage* (3 rows; <0.1%)
#> 
#> **summarise_omop_snapshot** for result IDs: 1 (15 rows ; <0.1%):
#> 
#> - *count* (1 rows; <0.1%)
#> - *description* (1 rows; <0.1%)
#> - *documentation_reference* (1 rows; <0.1%)
#> - *end_date* (1 rows; <0.1%)
#> - *holder_name* (1 rows; <0.1%)
#> - *package* (1 rows; <0.1%)
#> - *person_count* (1 rows; <0.1%)
#> - *release_date* (1 rows; <0.1%)
#> - *snapshot_date* (1 rows; <0.1%)
#> - *source_name* (1 rows; <0.1%)
#> - *start_date* (1 rows; <0.1%)
#> - *type* (1 rows; <0.1%)
#> - *version* (1 rows; <0.1%)
#> - *vocabulary_version* (1 rows; <0.1%)
#> - *write_schema* (1 rows; <0.1%)
#> 
#> **summarise_proportion_of_patients_covered** for result IDs: 90 (115 rows ; 0.2%):
#> 
#> - *denominator_count* (23 rows; <0.1%)
#> - *outcome_count* (23 rows; <0.1%)
#> - *ppc* (23 rows; <0.1%)
#> - *ppc_lower* (23 rows; <0.1%)
#> - *ppc_upper* (23 rows; <0.1%)
#> 
#> **summarise_treatment** for result IDs: 95 (60 rows ; 0.1%):
#> 
#> - *count* (30 rows; 0.1%)
#> - *percentage* (30 rows; 0.1%)
#> 
#> **summarise_trend** for result IDs: 5 (608 rows ; 1.1%):
#> 
#> - *count* (304 rows; 0.6%)
#> - *percentage* (304 rows; 0.6%)
#> 
#> **survival_attrition** for result IDs: 108–111, 115 (84 rows ; 0.2%):
#> 
#> - *count* (84 rows; 0.2%)
#> 
#> **survival_estimates** for result IDs: 96–99, 112 (6,588 rows ; 12.0%):
#> 
#> - *estimate* (2196 rows; 4.0%)
#> - *estimate_95CI_lower* (2196 rows; 4.0%)
#> - *estimate_95CI_upper* (2196 rows; 4.0%)
#> 
#> **survival_events** for result IDs: 100–103, 113 (252 rows ; 0.5%):
#> 
#> - *n_censor_count* (84 rows; 0.2%)
#> - *n_events_count* (84 rows; 0.2%)
#> - *n_risk_count* (84 rows; 0.2%)
#> 
#> **survival_summary** for result IDs: 104–107, 114 (114 rows ; 0.2%):
#> 
#> - *median_survival* (4 rows; <0.1%)
#> - *median_survival_95CI_higher* (4 rows; <0.1%)
#> - *median_survival_95CI_lower* (4 rows; <0.1%)
#> - *n_events_count* (6 rows; <0.1%)
#> - *number_records_count* (6 rows; <0.1%)
#> - *q05_survival* (4 rows; <0.1%)
#> - *q05_survival_95CI_higher* (4 rows; <0.1%)
#> - *q05_survival_95CI_lower* (4 rows; <0.1%)
#> - *q0_survival* (4 rows; <0.1%)
#> - *q0_survival_95CI_higher* (4 rows; <0.1%)
#> - *q0_survival_95CI_lower* (4 rows; <0.1%)
#> - *q100_survival* (4 rows; <0.1%)
#> - *q100_survival_95CI_higher* (4 rows; <0.1%)
#> - *q100_survival_95CI_lower* (4 rows; <0.1%)
#> - *q25_survival* (4 rows; <0.1%)
#> - *q25_survival_95CI_higher* (4 rows; <0.1%)
#> - *q25_survival_95CI_lower* (4 rows; <0.1%)
#> - *q75_survival* (4 rows; <0.1%)
#> - *q75_survival_95CI_higher* (4 rows; <0.1%)
#> - *q75_survival_95CI_lower* (4 rows; <0.1%)
#> - *q95_survival* (4 rows; <0.1%)
#> - *q95_survival_95CI_higher* (4 rows; <0.1%)
#> - *q95_survival_95CI_lower* (4 rows; <0.1%)
#> - *restricted_mean_survival* (6 rows; <0.1%)
#> - *restricted_mean_survival_95CI_lower* (6 rows; <0.1%)
#> - *restricted_mean_survival_95CI_upper* (6 rows; <0.1%)
#> 
#> **unmapped_codes** for result IDs: 10 (1 rows ; <0.1%):
#> 
#> - *record_count* (1 rows; <0.1%)

Output options

All functions support the same output argument:

# Print to console (default)
checkout(omopViewerResults, output = "console")

# Return as a character string
report <- checkout(omopViewerResults, output = "text")

# Open as HTML in the RStudio viewer
checkout(omopViewerResults, output = "show")

# Save to a Markdown file
checkout(omopViewerResults, output = "my_report.md")

Interactive Shiny app

For a point-and-click interface, launch the built-in Shiny app with checkoutShiny(). It allows you to upload a summarised_result .csv file and interactively explore and validate its contents.

checkoutShiny()