├── .Rbuildignore ├── .github ├── .gitignore ├── pull_request_template.md └── workflows │ ├── R_CMD_check_Hades.yml │ └── R_CMD_check_main_weekly.yaml ├── .gitignore ├── DESCRIPTION ├── DataQualityDashboard.Rproj ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R ├── calculateNotApplicableStatus.R ├── constants.R ├── convertResultsCase.R ├── evaluateThresholds.R ├── executeDqChecks.R ├── getCheckId.R ├── listChecks.R ├── processCheck.R ├── reEvaluateThresholds.R ├── readThresholdFile.R ├── recordResult.R ├── runCheck.R ├── sqlOnly.R ├── summarizeResults.R ├── view.R ├── writeDBResultsTo.R ├── writeJsonResultsTo.R └── writeResultsTo.R ├── README.md ├── _pkgdown.yml ├── compare_versions ├── deploy.sh ├── docs ├── 404.html ├── LICENSE-text.html ├── articles │ ├── AddNewCheck.html │ ├── CheckStatusDefinitions.html │ ├── CheckTypeDescriptions.html │ ├── CheckTypeDescriptions_files │ │ ├── header-attrs-2.11 │ │ │ └── header-attrs.js │ │ └── header-attrs-2.6 │ │ │ └── header-attrs.js │ ├── DataQualityDashboard.html │ ├── DataQualityDashboard_files │ │ ├── header-attrs-2.11 │ │ │ └── header-attrs.js │ │ └── header-attrs-2.6 │ │ │ └── header-attrs.js │ ├── DqdForCohorts.html │ ├── DqdForCohorts_files │ │ ├── header-attrs-2.11 │ │ │ └── header-attrs.js │ │ └── header-attrs-2.6 │ │ │ └── header-attrs.js │ ├── SqlOnly.html │ ├── Thresholds.html │ ├── Thresholds_files │ │ ├── header-attrs-2.11 │ │ │ └── header-attrs.js │ │ └── header-attrs-2.6 │ │ │ └── header-attrs.js │ ├── checkIndex.html │ ├── checks │ │ ├── cdmDatatype.html │ │ ├── cdmField.html │ │ ├── cdmTable.html │ │ ├── fkClass.html │ │ ├── fkDomain.html │ │ ├── isForeignKey.html │ │ ├── isPrimaryKey.html │ │ ├── isRequired.html │ │ ├── isStandardValidConcept.html │ │ ├── measureConditionEraCompleteness.html │ │ ├── measureObservationPeriodOverlap.html │ │ ├── measurePersonCompleteness.html │ │ ├── measureValueCompleteness.html │ │ ├── plausibleAfterBirth.html │ │ ├── plausibleBeforeDeath.html │ │ ├── plausibleGenderUseDescendants.html │ │ ├── plausibleStartBeforeEnd.html │ │ ├── plausibleTemporalAfter.html │ │ ├── plausibleUnitConceptIds.html │ │ ├── plausibleValueHigh.html │ │ ├── plausibleValueLow.html │ │ ├── sourceConceptRecordCompleteness.html │ │ ├── sourceValueCompleteness.html │ │ ├── standardConceptRecordCompleteness.html │ │ └── withinVisitDates.html │ ├── images │ │ ├── SQLRenderDeveloper.png │ │ ├── fieldLevelFile.png │ │ └── library_SQLRender.png │ └── index.html ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── pull_request_template.html ├── reference │ ├── convertJsonResultsFileCase.html │ ├── dot-applyNotApplicable.html │ ├── dot-calculateNotApplicableStatus.html │ ├── dot-containsNAchecks.html │ ├── dot-evaluateThresholds.html │ ├── dot-getCheckId.html │ ├── dot-hasNAchecks.html │ ├── dot-processCheck.html │ ├── dot-recordResult.html │ ├── dot-runCheck.html │ ├── dot-summarizeResults.html │ ├── dot-writeResultsToCsv.html │ ├── dot-writeResultsToJson.html │ ├── dot-writeResultsToTable.html │ ├── executeDqChecks.html │ ├── figures │ │ └── dqDashboardScreenshot.png │ ├── index.html │ ├── listDqChecks.html │ ├── reEvaluateThresholds.html │ ├── viewDqDashboard.html │ ├── writeDBResultsToJson.html │ ├── writeJsonResultsToCsv.html │ └── writeJsonResultsToTable.html └── sitemap.xml ├── extras ├── DataQualityDashboard.pdf ├── DevelopersREADME.md ├── PackageMaintenance.R ├── checkDescriptionTemplate.Rmd ├── codeToRun.R ├── codeToRun_sqlOnly.R ├── createCheckDoc.R ├── indexMultipleJsons.R ├── newFieldLevelFile.R ├── removeZeroDenoms.R ├── updateThresholds.R └── viewResults.R ├── inst ├── CITATION ├── csv │ ├── OMOP_CDMv5.2_Check_Descriptions.csv │ ├── OMOP_CDMv5.2_Concept_Level.csv │ ├── OMOP_CDMv5.2_Field_Level.csv │ ├── OMOP_CDMv5.2_Table_Level.csv │ ├── OMOP_CDMv5.3_Check_Descriptions.csv │ ├── OMOP_CDMv5.3_Concept_Level.csv │ ├── OMOP_CDMv5.3_Field_Level.csv │ ├── OMOP_CDMv5.3_Table_Level.csv │ ├── OMOP_CDMv5.4_Check_Descriptions.csv │ ├── OMOP_CDMv5.4_Concept_Level.csv │ ├── OMOP_CDMv5.4_Field_Level.csv │ ├── OMOP_CDMv5.4_Table_Level.csv │ └── unittest_OMOP_CDMv5.3_Concept_Level.csv ├── doc │ ├── AddNewCheck.pdf │ ├── CheckStatusDefinitions.pdf │ ├── CheckTypeDescriptions.pdf │ ├── DataQualityDashboard.pdf │ ├── DqdForCohorts.pdf │ ├── SqlOnly.pdf │ └── Thresholds.pdf ├── shinyApps │ ├── app.R │ └── www │ │ ├── css │ │ └── resume.css │ │ ├── favicon.ico │ │ ├── htmlwidgets │ │ ├── dqDashPOC.js │ │ ├── dqDashPOC.yaml │ │ └── lib │ │ │ ├── dqCheckRenderer.js │ │ │ ├── dqDashboardComponent.js │ │ │ ├── dqDashboardTemplate.hbs │ │ │ ├── dqDashboardTemplate.hbs.json │ │ │ ├── dqMetadataComponent.js │ │ │ ├── dqMetadataHeading.js │ │ │ └── handlebars-latest.js │ │ ├── img │ │ ├── close.png │ │ ├── details_close.png │ │ ├── details_open.png │ │ ├── ohdsi.png │ │ └── open.png │ │ ├── index.html │ │ ├── js │ │ ├── loadResults.js │ │ └── resume.js │ │ └── vendor │ │ ├── bootstrap │ │ ├── css │ │ │ ├── bootstrap-grid.css │ │ │ ├── bootstrap-grid.css.map │ │ │ ├── bootstrap-grid.min.css │ │ │ ├── bootstrap-grid.min.css.map │ │ │ ├── bootstrap-reboot.css │ │ │ ├── bootstrap-reboot.css.map │ │ │ ├── bootstrap-reboot.min.css │ │ │ ├── bootstrap-reboot.min.css.map │ │ │ ├── bootstrap.css │ │ │ ├── bootstrap.css.map │ │ │ ├── bootstrap.min.css │ │ │ └── bootstrap.min.css.map │ │ └── js │ │ │ ├── bootstrap.bundle.js │ │ │ ├── bootstrap.bundle.js.map │ │ │ ├── bootstrap.bundle.min.js │ │ │ ├── bootstrap.bundle.min.js.map │ │ │ ├── bootstrap.js │ │ │ ├── bootstrap.js.map │ │ │ ├── bootstrap.min.js │ │ │ └── bootstrap.min.js.map │ │ ├── dt │ │ ├── buttons │ │ │ └── 1.5.6 │ │ │ │ ├── css │ │ │ │ └── buttons.dataTables.min.css │ │ │ │ └── js │ │ │ │ ├── buttons.colVis.min.js │ │ │ │ ├── buttons.html5.min.js │ │ │ │ └── dataTables.buttons.min.js │ │ └── v │ │ │ └── dt │ │ │ └── dt-1.10.18 │ │ │ ├── datatables.min.css │ │ │ ├── datatables.min.js │ │ │ └── images │ │ │ ├── sort_asc.png │ │ │ ├── sort_asc_disabled.png │ │ │ ├── sort_both.png │ │ │ ├── sort_desc.png │ │ │ └── sort_desc_disabled.png │ │ ├── fontawesome-free │ │ ├── css │ │ │ ├── all.css │ │ │ ├── all.min.css │ │ │ ├── brands.css │ │ │ ├── brands.min.css │ │ │ ├── fontawesome.css │ │ │ ├── fontawesome.min.css │ │ │ ├── regular.css │ │ │ ├── regular.min.css │ │ │ ├── solid.css │ │ │ ├── solid.min.css │ │ │ ├── svg-with-js.css │ │ │ ├── svg-with-js.min.css │ │ │ ├── v4-shims.css │ │ │ └── v4-shims.min.css │ │ └── webfonts │ │ │ ├── fa-brands-400.eot │ │ │ ├── fa-brands-400.svg │ │ │ ├── fa-brands-400.ttf │ │ │ ├── fa-brands-400.woff │ │ │ ├── fa-brands-400.woff2 │ │ │ ├── fa-regular-400.eot │ │ │ ├── fa-regular-400.svg │ │ │ ├── fa-regular-400.ttf │ │ │ ├── fa-regular-400.woff │ │ │ ├── fa-regular-400.woff2 │ │ │ ├── fa-solid-900.eot │ │ │ ├── fa-solid-900.svg │ │ │ ├── fa-solid-900.ttf │ │ │ ├── fa-solid-900.woff │ │ │ └── fa-solid-900.woff2 │ │ ├── googlefonts │ │ ├── Muli-400,400i,800,800i.css │ │ ├── Saira_Extra_Condensed-500,700.css │ │ ├── muli_v27_TRUNC_5Fz4eqVxg.ttf │ │ ├── muli_v27_TRUNC_lOl0k30e0.ttf │ │ ├── muli_v27_TRUNC_nOkEk30e0.ttf │ │ ├── muli_v27_TRUNC_xF04eqVxg.ttf │ │ ├── sairaec_v11_TRUNC_G2vh2wpk.ttf │ │ └── sairaec_v11_TRUNC_U23h2wpk.ttf │ │ ├── jquery-easing │ │ ├── jquery.easing.compatibility.js │ │ ├── jquery.easing.js │ │ └── jquery.easing.min.js │ │ └── jquery │ │ ├── jquery.js │ │ ├── jquery.min.js │ │ ├── jquery.min.map │ │ ├── jquery.slim.js │ │ ├── jquery.slim.min.js │ │ └── jquery.slim.min.map └── sql │ └── sql_server │ ├── concept_plausible_gender.sql │ ├── concept_plausible_gender_use_descendants.sql │ ├── concept_plausible_unit_concept_ids.sql │ ├── concept_plausible_value_high.sql │ ├── concept_plausible_value_low.sql │ ├── field_cdm_datatype.sql │ ├── field_cdm_field.sql │ ├── field_concept_record_completeness.sql │ ├── field_fk_class.sql │ ├── field_fk_domain.sql │ ├── field_is_not_nullable.sql │ ├── field_is_primary_key.sql │ ├── field_is_standard_valid_concept.sql │ ├── field_measure_value_completeness.sql │ ├── field_plausible_after_birth.sql │ ├── field_plausible_before_death.sql │ ├── field_plausible_during_life.sql │ ├── field_plausible_start_before_end.sql │ ├── field_plausible_temporal_after.sql │ ├── field_plausible_value_high.sql │ ├── field_plausible_value_low.sql │ ├── field_source_value_completeness.sql │ ├── field_within_visit_dates.sql │ ├── is_foreign_key.sql │ ├── result_dataframe_ddl.sql │ ├── sqlOnly │ ├── cte_sql_for_results_table.sql │ └── insert_ctes_into_result_table.sql │ ├── table_cdm_table.sql │ ├── table_concept_completeness.sql │ ├── table_condition_era_completeness.sql │ ├── table_observation_period_overlap.sql │ └── table_person_completeness.sql ├── man ├── convertJsonResultsFileCase.Rd ├── dot-applyNotApplicable.Rd ├── dot-calculateNotApplicableStatus.Rd ├── dot-containsNAchecks.Rd ├── dot-evaluateThresholds.Rd ├── dot-getCheckId.Rd ├── dot-hasNAchecks.Rd ├── dot-processCheck.Rd ├── dot-recordResult.Rd ├── dot-runCheck.Rd ├── dot-summarizeResults.Rd ├── dot-writeResultsToCsv.Rd ├── dot-writeResultsToJson.Rd ├── dot-writeResultsToTable.Rd ├── executeDqChecks.Rd ├── figures │ └── dqDashboardScreenshot.png ├── listDqChecks.Rd ├── reEvaluateThresholds.Rd ├── viewDqDashboard.Rd ├── writeDBResultsToJson.Rd ├── writeJsonResultsToCsv.Rd └── writeJsonResultsToTable.Rd ├── tests ├── testthat.R └── testthat │ ├── _snaps │ └── executeDqChecks.md │ ├── setup.R │ ├── test-calculateNotApplicableStatus.R │ ├── test-convertResultsCase.R │ ├── test-evaluateThresholds.R │ ├── test-executeDqChecks.R │ ├── test-helpers.R │ ├── test-listChecks.R │ ├── test-plausibleAfterBirth.R │ ├── test-reEvaluateThresholds.R │ ├── test-writeDBResultsTo.R │ └── test-writeJsonResultsTo.R └── vignettes ├── AddNewCheck.rmd ├── CheckStatusDefinitions.rmd ├── DataQualityDashboard.rmd ├── DqdForCohorts.rmd ├── SqlOnly.rmd ├── Thresholds.rmd ├── checkIndex.Rmd ├── checks ├── cdmDatatype.Rmd ├── cdmField.Rmd ├── cdmTable.Rmd ├── fkClass.Rmd ├── fkDomain.Rmd ├── isForeignKey.Rmd ├── isPrimaryKey.Rmd ├── isRequired.Rmd ├── isStandardValidConcept.Rmd ├── measureConditionEraCompleteness.Rmd ├── measureObservationPeriodOverlap.Rmd ├── measurePersonCompleteness.Rmd ├── measureValueCompleteness.Rmd ├── plausibleAfterBirth.Rmd ├── plausibleBeforeDeath.Rmd ├── plausibleGenderUseDescendants.Rmd ├── plausibleStartBeforeEnd.Rmd ├── plausibleTemporalAfter.Rmd ├── plausibleUnitConceptIds.Rmd ├── plausibleValueHigh.Rmd ├── plausibleValueLow.Rmd ├── sourceConceptRecordCompleteness.Rmd ├── sourceValueCompleteness.Rmd ├── standardConceptRecordCompleteness.Rmd └── withinVisitDates.Rmd └── images ├── SQLRenderDeveloper.png ├── fieldLevelFile.png ├── hadesMini.png └── library_SQLRender.png /.Rbuildignore: -------------------------------------------------------------------------------- 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