Files in OHDSI/PheValuator
Rapid Phenotype Evaluation
.Rbuildignore
.github/pull_request_template.md
.github/workflows/R_CMD_check_Hades.yaml
.github/workflows/R_CMD_check_main_weekly.yaml
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
PheValuator.Rproj
R/Analyses.R
R/CreateArgFunctions.R
R/CreateEvalCohort.R
R/CreateEvaluationCohort.R
R/CreatePhenoModel.R
R/DefaultCovariateSettings.R
R/PheValuator.R
R/RunAnalyses.R
R/TestPhenotype.R
README.md
_pkgdown.yml
compare_versions
deploy.sh
docs/404.html
docs/articles/EvaluatingPhenotypeAlgorithms.html
docs/articles/EvaluatingPhenotypeAlgorithms_files/accessible-code-block-0.0.1/empty-anchor.js
docs/articles/EvaluatingPhenotypeAlgorithms_files/header-attrs-2.7/header-attrs.js
docs/articles/index.html
docs/articles/pheValuatorT2DMResults.png
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/pull_request_template.html
docs/reference/PheValuator-package.html
docs/reference/PheValuator.html
docs/reference/computePerformanceMetricsFromCounts.html
docs/reference/createAcutePhenotypeModel.html
docs/reference/createChronicPhenotypeModel.html
docs/reference/createCreateEvaluationCohortArgs.html
docs/reference/createDefaultAcuteCovariateSettings.html
docs/reference/createDefaultChronicCovariateSettings.html
docs/reference/createDefaultCovariateSettings.html
docs/reference/createEvaluationCohort.html
docs/reference/createPheValuatorAnalysis.html
docs/reference/createPhenotypeModel.html
docs/reference/createTestPhenotypeAlgorithmArgs.html
docs/reference/exportPheValuatorResults.html
docs/reference/index.html
docs/reference/launchPheValuatorExplorer.html
docs/reference/loadPheValuatorAnalysisList.html
docs/reference/prepareForShiny.html
docs/reference/prettyPhenotypeOutput.html
docs/reference/recalibrateModel.html
docs/reference/runPheValuatorAnalyses.html
docs/reference/savePheValuatorAnalysisList.html
docs/reference/summarizePheValuatorAnalyses.html
docs/reference/testPhenotypeAlgorithm.html
docs/sitemap.xml
examplePackage/.Rbuildignore
examplePackage/.Rprofile
examplePackage/.gitignore
examplePackage/DESCRIPTION
examplePackage/NAMESPACE
examplePackage/R/CreateCohorts.R
examplePackage/R/PheValuator.R
examplePackage/README.md
examplePackage/examplePackage.Rproj
examplePackage/extras/CodeToRun.R
examplePackage/extras/CreateAnalysisSettings.R
examplePackage/extras/PackageMaintenance.R
examplePackage/inst/cohorts/Pneumonia_All_Occurrences.json
examplePackage/inst/cohorts/Pneumonia_Level_1_xSpec.json
examplePackage/inst/cohorts/Pneumonia_Level_2_xSpec.json
examplePackage/inst/cohorts/Pneumonia_Level_3_xSpec.json
examplePackage/inst/cohorts/Pneumonia_xSens.json
examplePackage/inst/settings/CohortsToCreate.csv
examplePackage/inst/settings/pheValuatorAnalysisList.json
examplePackage/inst/sql/sql_server/CreateCohortTable.sql
examplePackage/inst/sql/sql_server/GetCounts.sql
examplePackage/inst/sql/sql_server/Pneumonia_All_Occurrences.sql
examplePackage/inst/sql/sql_server/Pneumonia_Level_1_xSpec.sql
examplePackage/inst/sql/sql_server/Pneumonia_Level_2_xSpec.sql
examplePackage/inst/sql/sql_server/Pneumonia_Level_3_xSpec.sql
examplePackage/inst/sql/sql_server/Pneumonia_xSens.sql
examplePackage/man/execute.Rd
extras/CopyOfEvaluatingPhenotypeAlgorithms.rmd
extras/CreateAcutePhenotypeModel.R
extras/CreateChronicPhenotypeModel.R
extras/CreateCohorts.sql
extras/CreateCohortsAcuteEvaluationOrig.sql
extras/CreateCohortsV6.sql
extras/CreateConceptSet.R
extras/DefaultCovariateSettings.R
extras/ErrorCheck.R
extras/Export.R
extras/GetPerformanceCharacteristics.R
extras/ImmortalTimeBias/Death event.json
extras/ImmortalTimeBias/[OKR4] Multiple Sclerosis with 2nd diagnosis 1-60D after index.json
extras/ImmortalTimeBias/[PheValuator] Atrial fibrillation with 2nd code 1-30D.json
extras/ImmortalTimeBias/[PheValuator] Atrial fibrillation with 2nd code 1-365D.json
extras/ImmortalTimeBias/[PheValuator] Atrial fibrillation with 2nd code 1-90D.json
extras/ImmortalTimeBias/[PheValuator] Atrial fibrillation with 2nd code 1-AllD.json
extras/ImmortalTimeBias/[PheValuator] Chronic Heart Failure with 2nd code 1-30D.json
extras/ImmortalTimeBias/[PheValuator] Chronic Heart Failure with 2nd code 1-365D.json
extras/ImmortalTimeBias/[PheValuator] Chronic Heart Failure with 2nd code 1-90D.json
extras/ImmortalTimeBias/[PheValuator] Chronic Heart Failure with 2nd code 1-AllD.json
extras/ImmortalTimeBias/[PheValuator] Chronic kidney disease with 2nd code 1-30D.json
extras/ImmortalTimeBias/[PheValuator] Chronic kidney disease with 2nd code 1-365D.json
extras/ImmortalTimeBias/[PheValuator] Chronic kidney disease with 2nd code 1-90D.json
extras/ImmortalTimeBias/[PheValuator] Chronic kidney disease with 2nd code 1-AllD.json
extras/ImmortalTimeBias/[PheValuator] Coronary artery disease with 2nd code 1-30D.json
extras/ImmortalTimeBias/[PheValuator] Coronary artery disease with 2nd code 1-365D.json
extras/ImmortalTimeBias/[PheValuator] Coronary artery disease with 2nd code 1-90D.json
extras/ImmortalTimeBias/[PheValuator] Coronary artery disease with 2nd code 1-AllD.json
extras/ImmortalTimeBias/[PheValuator] Ingrown nail.json
extras/ImmortalTimeBias/[PheValuator] Migraine with 2nd code 1-30D.json
extras/ImmortalTimeBias/[PheValuator] Migraine with 2nd code 1-365D.json
extras/ImmortalTimeBias/[PheValuator] Migraine with 2nd code 1-90D.json
extras/ImmortalTimeBias/[PheValuator] Migraine with 2nd code 1-AllD.json
extras/ImmortalTimeBias/[PheValuator] Multiple Sclerosis with 2nd code 1-30D.json
extras/ImmortalTimeBias/[PheValuator] Multiple Sclerosis with 2nd code 1-365D.json
extras/ImmortalTimeBias/[PheValuator] Multiple Sclerosis with 2nd code 1-90D.json
extras/ImmortalTimeBias/[PheValuator] Multiple myeloma with 2nd code 1-30D.json
extras/ImmortalTimeBias/[PheValuator] Multiple myeloma with 2nd code 1-365D.json
extras/ImmortalTimeBias/[PheValuator] Multiple myeloma with 2nd code 1-90D.json
extras/ImmortalTimeBias/[PheValuator] Multiple myeloma with 2nd code 1-AllD.json
extras/ImmortalTimeBias/[PheValuator] Overactive Bladder with 2nd code 1-30D.json
extras/ImmortalTimeBias/[PheValuator] Overactive Bladder with 2nd code 1-365D.json
extras/ImmortalTimeBias/[PheValuator] Overactive Bladder with 2nd code 1-90D.json
extras/ImmortalTimeBias/[PheValuator] Overactive Bladder with 2nd code 1-AllD.json
extras/ImmortalTimeBias/[PheValuator] Plaque psoriasis with 2nd code 1-30D.json
extras/ImmortalTimeBias/[PheValuator] Plaque psoriasis with 2nd code 1-365D.json
extras/ImmortalTimeBias/[PheValuator] Plaque psoriasis with 2nd code 1-90D.json
extras/ImmortalTimeBias/[PheValuator] Plaque psoriasis with 2nd code 1-AllD.json
extras/ImmortalTimeBias/[PheValuator] Psoriatic arthritis with 2nd code 1-30D.json
extras/ImmortalTimeBias/[PheValuator] Psoriatic arthritis with 2nd code 1-365D.json
extras/ImmortalTimeBias/[PheValuator] Psoriatic arthritis with 2nd code 1-90D.json
extras/ImmortalTimeBias/[PheValuator] Psoriatic arthritis with 2nd code 1-AllD.json
extras/ImmortalTimeBias/[PheValuator] Ulcerative colitis with 2nd code 1-30D.json
extras/ImmortalTimeBias/[PheValuator] Ulcerative colitis with 2nd code 1-365D.json
extras/ImmortalTimeBias/[PheValuator] Ulcerative colitis with 2nd code 1-90D.json
extras/ImmortalTimeBias/[PheValuator] Ulcerative colitis with 2nd code 1-AllD.json
extras/MultiAnalysesVignetteDataFetch.R
extras/OutputFunctions.R
extras/PackageMaintenance.R
extras/PheValuator.pdf
extras/PheValuatorAcuteDiseaseScript.R
extras/PhenotypeBenchmark/Ankylosing spondylitis_Curtis 1.json
extras/PhenotypeBenchmark/Ankylosing spondylitis_Curtis 2.json
extras/PhenotypeBenchmark/Ankylosing spondylitis_Curtis 3.json
extras/PhenotypeBenchmark/Ankylosing spondylitis_Curtis 4.json
extras/PhenotypeBenchmark/Ankylosing spondylitis_Dubreuil 1.json
extras/PhenotypeBenchmark/Ankylosing spondylitis_Dubreuil 2.json
extras/PhenotypeBenchmark/Ankylosing spondylitis_Dubreuil 3.json
extras/PhenotypeBenchmark/Ankylosing spondylitis_Dubreuil 4.json
extras/PhenotypeBenchmark/Ankylosing spondylitis_Dubreuil 5.json
extras/PhenotypeBenchmark/Ankylosing spondylitis_Dubreuil 6.json
extras/PhenotypeBenchmark/Atopic dermatitis_Hsu 1.json
extras/PhenotypeBenchmark/Atopic dermatitis_Hsu 2.json
extras/PhenotypeBenchmark/Atopic dermatitis_Hsu 3.json
extras/PhenotypeBenchmark/Atopic dermatitis_Hsu 4.json
extras/PhenotypeBenchmark/Atopic dermatitis_Hsu 5.json
extras/PhenotypeBenchmark/Atopic dermatitis_Hsu 6.json
extras/PhenotypeBenchmark/Atopic dermatitis_Hsu 7.json
extras/PhenotypeBenchmark/Atopic dermatitis_Hsu 8.json
extras/PhenotypeBenchmark/Atrial Fibrillation_Navar-Boggan 1.json
extras/PhenotypeBenchmark/Autism_Burke 1.json
extras/PhenotypeBenchmark/Autism_Burke 2.json
extras/PhenotypeBenchmark/BenchmarkDataOHDSI.csv
extras/PhenotypeBenchmark/Bipolar_Castro 1.json
extras/PhenotypeBenchmark/Bipolar_Castro 2.json
extras/PhenotypeBenchmark/Crohns Disease_Ananthakrishnan 1.json
extras/PhenotypeBenchmark/Crohns Disease_Ananthakrishnan 2.json
extras/PhenotypeBenchmark/Crohns Disease_Ananthakrishnan 3.json
extras/PhenotypeBenchmark/Crohns Disease_Ananthakrishnan 4.json
extras/PhenotypeBenchmark/Crohns Disease_Stepaniuk 1.json
extras/PhenotypeBenchmark/Crohns Disease_Thirumurthi 1.json
extras/PhenotypeBenchmark/Epilepsy_Christensen 1.json
extras/PhenotypeBenchmark/Epilepsy_Jette 1.json
extras/PhenotypeBenchmark/Epilepsy_Moura 1.json
extras/PhenotypeBenchmark/Epilepsy_Pugh 1.json
extras/PhenotypeBenchmark/Epilepsy_Tan 1.json
extras/PhenotypeBenchmark/Multiple Myeloma_Brandenburg 1.json
extras/PhenotypeBenchmark/Multiple Myeloma_Brandenburg 2.json
extras/PhenotypeBenchmark/Multiple Myeloma_Brandenburg 3.json
extras/PhenotypeBenchmark/Multiple Myeloma_Brandenburg 4.json
extras/PhenotypeBenchmark/Prostate Cancer_Parlett 1.json
extras/PhenotypeBenchmark/Prostate Cancer_Parlett 2.json
extras/PhenotypeBenchmark/Prostate Cancer_Parlett 3.json
extras/PhenotypeBenchmark/Prostate Cancer_Parlett 4.json
extras/PhenotypeBenchmark/Psoriasis_Elder 1.json
extras/PhenotypeBenchmark/Psoriasis_Elder 2.json
extras/PhenotypeBenchmark/Psoriasis_Elder 3.json
extras/PhenotypeBenchmark/Psoriasis_Icen 1.json
extras/PhenotypeBenchmark/Psoriasis_Seminara 1.json
extras/PhenotypeBenchmark/Psoriasis_Seminara 2.json
extras/PhenotypeBenchmark/Psoriasis_Seminara 3.json
extras/PhenotypeBenchmark/Pulmonary Embolism_Alotaibi 1.json
extras/PhenotypeBenchmark/Pulmonary Embolism_Alotaibi 2.json
extras/PhenotypeBenchmark/Pulmonary Embolism_White 1.json
extras/PhenotypeBenchmark/Pulmonary Embolism_White 2.json
extras/PhenotypeBenchmark/Rheumatoid Arthritis_Hanly 1.json
extras/PhenotypeBenchmark/Rheumatoid Arthritis_Hanly 2.json
extras/PhenotypeBenchmark/Rheumatoid Arthritis_Hanly 3.json
extras/PhenotypeBenchmark/Rheumatoid Arthritis_Ng 1.json
extras/PhenotypeBenchmark/Rheumatoid Arthritis_Ng 2.json
extras/PhenotypeBenchmark/Rheumatoid Arthritis_Ng 3.json
extras/PhenotypeBenchmark/Rheumatoid Arthritis_Ng 4.json
extras/PhenotypeBenchmark/Rheumatoid Arthritis_Ng 5.json
extras/PhenotypeBenchmark/Rheumatoid Arthritis_Ng 6.json
extras/PhenotypeBenchmark/Rheumatoid Arthritis_Widdifield 1.json
extras/PhenotypeBenchmark/Rheumatoid Arthritis_Widdifield 2.json
extras/PhenotypeBenchmark/Rheumatoid Arthritis_Widdifield 3.json
extras/PhenotypeBenchmark/Rheumatoid Arthritis_Widdifield 4.json
extras/PhenotypeBenchmark/Systemic Lupus Erythematosus_Hanly 1.json
extras/PhenotypeBenchmark/Systemic Lupus Erythematosus_Hanly 2.json
extras/PhenotypeBenchmark/Systemic Lupus Erythematosus_Hanly 3.json
extras/PhenotypeBenchmark/Ulcerative Colitis_Ananthakrishnan 1.json
extras/PhenotypeBenchmark/Ulcerative Colitis_Ananthakrishnan 2.json
extras/PhenotypeBenchmark/Ulcerative Colitis_Ananthakrishnan 3.json
extras/PhenotypeBenchmark/Ulcerative Colitis_Ananthakrishnan 4.json
extras/PhenotypeBenchmark/Ulcerative Colitis_Stepaniuk 1.json
extras/PhenotypeBenchmark/Ulcerative Colitis_Thirumurthi 1.json
extras/PhenotypeBenchmark/Venous Thromboembolism_Alotaibi 1.json
extras/PhenotypeBenchmark/Venous Thromboembolism_Alotaibi 2.json
extras/PhenotypeBenchmark/Venous Thromboembolism_McPeek Hinz 1.json
extras/PhenotypeBenchmark/Venous Thromboembolism_White 1.json
extras/PhenotypeBenchmark/Venous Thromboembolism_White 2.json
extras/PhenotypeBenchmark/Viral Hepatitis B_Niu 1.json
extras/PhenotypeBenchmark/Viral Hepatitis B_Niu 2.json
extras/PhenotypeBenchmark/Viral Hepatitis B_Niu 3.json
extras/PhenotypeBenchmark/Viral Hepatitis C_Nui 1.json
extras/PhenotypeBenchmark/Viral Hepatitis C_Nui 2.json
extras/PhenotypeBenchmark/Viral Hepatitis C_Nui 3.json
extras/PhenotypeBenchmark/Viral Hepatitis C_Re 1.json
extras/RecalibrateModel.R
extras/Shiny.R
extras/TestCode.R
extras/TestConcepts.R
extras/TestPhenosFromFile.R
extras/eunomiaTestCohortBuildInternal.R
extras/eunomiaTestScriptInternal.R
extras/roxygenize.R
inst/doc/EvaluatingPhenotypeAlgorithms.pdf
inst/shiny/PheValuatorExplorer/PheValuatorExplorer.Rproj
inst/shiny/PheValuatorExplorer/global.R
inst/shiny/PheValuatorExplorer/html/phevaluatorResults.html
inst/shiny/PheValuatorExplorer/server.R
inst/shiny/PheValuatorExplorer/ui.R
inst/sql/sql_server/CreateCohortsAcuteEvaluation.sql
inst/sql/sql_server/CreateCohortsAcuteModel.sql
inst/sql/sql_server/DropTempTable.sql
inst/sql/sql_server/GetComparisonCohort.sql
inst/sql/sql_server/GetNumberOfEligibleVisits.sql
inst/sql/sql_server/GetxSpecCount.sql
inst/sql/sql_server/getPopnPrev.sql
man/PheValuator-package.Rd
man/computePerformanceMetricsFromCounts.Rd
man/createCreateEvaluationCohortArgs.Rd
man/createDefaultCovariateSettings.Rd
man/createEvaluationCohort.Rd
man/createPhevaluatorAnalysis.Rd
man/createTestPhenotypeAlgorithmArgs.Rd
man/loadPhevaluatorAnalysisList.Rd
man/runPheValuatorAnalyses.Rd
man/savePhevaluatorAnalysisList.Rd
man/summarizePheValuatorAnalyses.Rd
man/testPhenotypeAlgorithm.Rd
tests/testthat.R
tests/testthat/.gitignore
tests/testthat/cohorts/1001.json
tests/testthat/cohorts/1001.sql
tests/testthat/cohorts/2.json
tests/testthat/cohorts/2.sql
tests/testthat/cohorts/5.json
tests/testthat/cohorts/5.sql
tests/testthat/cohorts/6.json
tests/testthat/cohorts/6.sql
tests/testthat/cohorts/CohortsToCreate.csv
tests/testthat/cohorts/CreateCohortTable.sql
tests/testthat/cohorts/resultsDataModelSpecification.csv
tests/testthat/setup.R
tests/testthat/test_EndToEnd.R
vignettes/EvaluatingPhenotypeAlgorithms.rmd
vignettes/Figure1.png
vignettes/Figure2.png
vignettes/Figure3.png
vignettes/pheValuatorT2DMResults.png
