Files in ohdsi-studies/EhdenRaPrediction
A Package Skeleton for Patient Level Prediction Studies
.Rbuildignore
.Rprofile
.gitignore
DESCRIPTION
EhdenRaPrediction.Rproj
HydraConfig.json
NAMESPACE
R/CreateAllCohorts.R
R/CreateCohorts.R
R/EHDENRAPrediction.R
R/Main.R
R/PackageResults.R
R/SubmitResults.R
R/createDocument.R
R/createPlpProtocol.R
R/createValidationPackage.R
R/populateShinyApp.R
R/readJson.R
README.md
documents/RA_PLP_protocol_09042021.docx
documents/RA_PLP_protocol_27012020.docx
extras/CodeToRun.R
extras/CreatePredictionAnalysisDetails.R
extras/PackageMaintenance.R
extras/packageDeps.R
inst/cohorts/EHDEN_RA_Acute_myocardial_infarction_events_in_any_visit.json
inst/cohorts/EHDEN_RA_Female_new_users_of_methoxtrexate_monotherapy_used_for_PLP_1.json
inst/cohorts/EHDEN_RA_Leukopenia_events_using_diagnoses_and_measurements.json
inst/cohorts/EHDEN_RA_New_users_of_methoxtrexate_monotherapy_used_for_PLP_1.json
inst/cohorts/EHDEN_RA_Opportunistic_Infections_3.json
inst/cohorts/EHDEN_RA_Pancytopenia_events_using_diagnoses_and_measurements.json
inst/cohorts/EHDEN_RA_Pancytopenia_or_leukopenia_events_using_diagnoses_and_measurements.json
inst/cohorts/EHDEN_RA_Persons_with_a_Malignant_neoplasm_of_breast_1_dx.json
inst/cohorts/EHDEN_RA_Persons_with_a_Malignant_neoplasm_of_colon_and_rectum_1_dx.json
inst/cohorts/EHDEN_RA_Persons_with_a_Malignant_neoplasm_of_uterus_1_dx.json
inst/cohorts/EHDEN_RA_Serious_Infection__events_3.json
inst/cohorts/EHDEN_RA_Serious_Infection_opportunistic_infections_and_other_infections_of_interest_event_2.json
inst/cohorts/EHDEN_RA_Stroke_ischemic_or_hemorrhagic_events_any_visit_2.json
inst/doc/UsingSkeletonPackage.pdf
inst/doc/UsingSkeletonPackage.tex
inst/settings/CohortsToCreate.csv
inst/settings/predictionAnalysisList.json
inst/shiny/PLPViewer/PLPViewer.Rproj
inst/shiny/PLPViewer/global.R
inst/shiny/PLPViewer/plots.R
inst/shiny/PLPViewer/server.R
inst/shiny/PLPViewer/ui.R
inst/shiny/PLPViewer/utils.R
inst/shiny/PLPViewer/www/about.png
inst/shiny/PLPViewer/www/custom.css
inst/shiny/PLPViewer/www/favicon.ico
inst/shiny/PLPViewer/www/logo.png
inst/sql/sql_server/CreateCohortTable.sql
inst/sql/sql_server/EHDEN_RA_Acute_myocardial_infarction_events_in_any_visit.sql
inst/sql/sql_server/EHDEN_RA_Female_new_users_of_methoxtrexate_monotherapy_used_for_PLP_1.sql
inst/sql/sql_server/EHDEN_RA_Leukopenia_events_using_diagnoses_and_measurements.sql
inst/sql/sql_server/EHDEN_RA_New_users_of_methoxtrexate_monotherapy_used_for_PLP_1.sql
inst/sql/sql_server/EHDEN_RA_Opportunistic_Infections_3.sql
inst/sql/sql_server/EHDEN_RA_Pancytopenia_events_using_diagnoses_and_measurements.sql
inst/sql/sql_server/EHDEN_RA_Pancytopenia_or_leukopenia_events_using_diagnoses_and_measurements.sql
inst/sql/sql_server/EHDEN_RA_Persons_with_a_Malignant_neoplasm_of_breast_1_dx.sql
inst/sql/sql_server/EHDEN_RA_Persons_with_a_Malignant_neoplasm_of_colon_and_rectum_1_dx.sql
inst/sql/sql_server/EHDEN_RA_Persons_with_a_Malignant_neoplasm_of_uterus_1_dx.sql
inst/sql/sql_server/EHDEN_RA_Serious_Infection__events_3.sql
inst/sql/sql_server/EHDEN_RA_Serious_Infection_opportunistic_infections_and_other_infections_of_interest_event_2.sql
inst/sql/sql_server/EHDEN_RA_Stroke_ischemic_or_hemorrhagic_events_any_visit_2.sql
inst/sql/sql_server/GetCounts.sql
man/EHDENRAPrediction.Rd
man/createCohorts.Rd
man/createJournalDocument.Rd
man/createMultiPlpReport.Rd
man/createPlpProtocol.Rd
man/execute.Rd
man/packageResults.Rd
man/submitResults.Rd
validationPackage/EhdenRaPredictionValidation/.Rbuildignore
validationPackage/EhdenRaPredictionValidation/.gitignore
validationPackage/EhdenRaPredictionValidation/DESCRIPTION
validationPackage/EhdenRaPredictionValidation/EhdenRaPredictionValidation.Rproj
validationPackage/EhdenRaPredictionValidation/HydraConfig.json
validationPackage/EhdenRaPredictionValidation/NAMESPACE
validationPackage/EhdenRaPredictionValidation/NEWS.md
validationPackage/EhdenRaPredictionValidation/R/CohortCovariateCode.R
validationPackage/EhdenRaPredictionValidation/R/EhdenRaPredictionValidation.R
validationPackage/EhdenRaPredictionValidation/R/PackageResults.R
validationPackage/EhdenRaPredictionValidation/R/helpers.R
validationPackage/EhdenRaPredictionValidation/R/main.R
validationPackage/EhdenRaPredictionValidation/_pkgdown.yml
validationPackage/EhdenRaPredictionValidation/docs/404.html
validationPackage/EhdenRaPredictionValidation/docs/articles/UsingSkeletonPredictionValidationPackage.html
validationPackage/EhdenRaPredictionValidation/docs/articles/index.html
validationPackage/EhdenRaPredictionValidation/docs/authors.html
validationPackage/EhdenRaPredictionValidation/docs/bootstrap-toc.css
validationPackage/EhdenRaPredictionValidation/docs/bootstrap-toc.js
validationPackage/EhdenRaPredictionValidation/docs/docsearch.css
validationPackage/EhdenRaPredictionValidation/docs/docsearch.js
validationPackage/EhdenRaPredictionValidation/docs/index.html
validationPackage/EhdenRaPredictionValidation/docs/link.svg
validationPackage/EhdenRaPredictionValidation/docs/news/index.html
validationPackage/EhdenRaPredictionValidation/docs/pkgdown.css
validationPackage/EhdenRaPredictionValidation/docs/pkgdown.js
validationPackage/EhdenRaPredictionValidation/docs/pkgdown.yml
validationPackage/EhdenRaPredictionValidation/docs/readme.html
validationPackage/EhdenRaPredictionValidation/docs/reference/EhdenRaPredictionValidation.html
validationPackage/EhdenRaPredictionValidation/docs/reference/checkInstall.html
validationPackage/EhdenRaPredictionValidation/docs/reference/createCohorts.html
validationPackage/EhdenRaPredictionValidation/docs/reference/execute.html
validationPackage/EhdenRaPredictionValidation/docs/reference/getCohortCovariateData.html
validationPackage/EhdenRaPredictionValidation/docs/reference/getTable1.html
validationPackage/EhdenRaPredictionValidation/docs/reference/index.html
validationPackage/EhdenRaPredictionValidation/docs/reference/packageResults.html
validationPackage/EhdenRaPredictionValidation/docs/reference/transportPlpModels.html
validationPackage/EhdenRaPredictionValidation/extras/PackageMaintenance.R
validationPackage/EhdenRaPredictionValidation/extras/codeToRun.R
validationPackage/EhdenRaPredictionValidation/inst/cohorts/EHDEN_RA_Acute_myocardial_infarction_events_in_any_visit.json
validationPackage/EhdenRaPredictionValidation/inst/cohorts/EHDEN_RA_Female_new_users_of_methoxtrexate_monotherapy_used_for_PLP_1.json
validationPackage/EhdenRaPredictionValidation/inst/cohorts/EHDEN_RA_Leukopenia_events_using_diagnoses_and_measurements.json
validationPackage/EhdenRaPredictionValidation/inst/cohorts/EHDEN_RA_New_users_of_methoxtrexate_monotherapy_used_for_PLP_1.json
validationPackage/EhdenRaPredictionValidation/inst/cohorts/EHDEN_RA_Opportunistic_Infections_3.json
validationPackage/EhdenRaPredictionValidation/inst/cohorts/EHDEN_RA_Pancytopenia_events_using_diagnoses_and_measurements.json
validationPackage/EhdenRaPredictionValidation/inst/cohorts/EHDEN_RA_Pancytopenia_or_leukopenia_events_using_diagnoses_and_measurements.json
validationPackage/EhdenRaPredictionValidation/inst/cohorts/EHDEN_RA_Persons_with_a_Malignant_neoplasm_of_breast_1_dx.json
validationPackage/EhdenRaPredictionValidation/inst/cohorts/EHDEN_RA_Persons_with_a_Malignant_neoplasm_of_colon_and_rectum_1_dx.json
validationPackage/EhdenRaPredictionValidation/inst/cohorts/EHDEN_RA_Persons_with_a_Malignant_neoplasm_of_uterus_1_dx.json
validationPackage/EhdenRaPredictionValidation/inst/cohorts/EHDEN_RA_Serious_Infection__events_3.json
validationPackage/EhdenRaPredictionValidation/inst/cohorts/EHDEN_RA_Serious_Infection_opportunistic_infections_and_other_infections_of_interest_event_2.json
validationPackage/EhdenRaPredictionValidation/inst/cohorts/EHDEN_RA_Stroke_ischemic_or_hemorrhagic_events_any_visit_2.json
validationPackage/EhdenRaPredictionValidation/inst/doc/UsingSkeletonPredictionValidationPackage.pdf
validationPackage/EhdenRaPredictionValidation/inst/doc/UsingSkeletonPredictionValidationPackage.tex
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/analysisRef.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/covariateSummary.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/executionSummary.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/inputSetting.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/model/analysisId.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/model/attributes.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/model/cohortId.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/model/covariateMap.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/model/dense.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/model/hyperParamSearch.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/model/index.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/model/metaData.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/model/model.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/model/modelSettings.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/model/outcomeId.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/model/populationSettings.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/model/trainCVAuc.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/model/trainingTime.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/model/transform.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/model/varImp.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/performanceEvaluation.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_113/plpResult/prediction.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/analysisRef.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/covariateSummary.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/executionSummary.rds
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validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/model/attributes.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/model/cohortId.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/model/covariateMap.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/model/dense.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/model/hyperParamSearch.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/model/index.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/model/metaData.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/model/model.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/model/modelSettings.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/model/outcomeId.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/model/populationSettings.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/model/trainCVAuc.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/model/trainingTime.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/model/transform.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/model/varImp.rds
validationPackage/EhdenRaPredictionValidation/inst/plp_models/Analysis_13/plpResult/performanceEvaluation.rds
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validationPackage/EhdenRaPredictionValidation/readme.md
validationPackage/EhdenRaPredictionValidation/vignettes/UsingSkeletonPredictionValidationPackage.rmd
vignettes/Figure1.png
vignettes/UsingSkeletonPackage.Rmd
