diff --git a/DESCRIPTION b/DESCRIPTION index b125fab..5e90163 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: Hades Type: Package Title: Health Analytics Data-to-Evidence Suite -Version: 1.13.0 -Date: 2023-05-19 +Version: 1.13.1 +Date: 2024-05-08 Authors@R: c( person("Martijn", "Schuemie", , "schuemie@ohdsi.org", role = c("aut", "cre")), person("Observational Health Data Science and Informatics", role = c("cph")) @@ -52,7 +52,6 @@ Remotes: ohdsi/BigKnn, ohdsi/ROhdsiWebApi, ohdsi/EnsemblePatientLevelPrediction, - ohdsi/FeatureExtraction, ohdsi/CohortDiagnostics, ohdsi/CohortMethod, ohdsi/SelfControlledCaseSeries, @@ -63,9 +62,7 @@ Remotes: ohdsi/PhenotypeLibrary, ohdsi/PheValuator, ohdsi/Hydra, - ohdsi/CirceR, ohdsi/Capr, - ohdsi/Eunomia, ohdsi/CohortGenerator, ohdsi/DeepPatientLevelPrediction, ohdsi/CohortExplorer, diff --git a/NEWS.md b/NEWS.md index c1d38c5..999597c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +HADES 1.13.1 +============ + +- CirceR, Eunomia, and FeatureExtraction are now in CRAN. Removing reference to Github repos. + HADES 1.13.0 ============ diff --git a/Rmd/images/downloadJavaWindows.png b/Rmd/images/downloadJavaWindows.png index 77249dc..40cb197 100644 Binary files a/Rmd/images/downloadJavaWindows.png and b/Rmd/images/downloadJavaWindows.png differ diff --git a/Rmd/packageStatuses.Rmd b/Rmd/packageStatuses.Rmd index bc52391..e500a1b 100644 --- a/Rmd/packageStatuses.Rmd +++ b/Rmd/packageStatuses.Rmd @@ -24,7 +24,7 @@ The table below lists, for each of the HADES packages, the following details: | [BrokenAdaptiveRidge](https://github.com/OHDSI/BrokenAdaptiveRidge) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/BrokenAdaptiveRidge?label=%20)](https://ohdsi.github.io/BrokenAdaptiveRidge/) | Marc Suchard | CRAN | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/BrokenAdaptiveRidge?label=%20)](https://github.com/OHDSI/BrokenAdaptiveRidge/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/BrokenAdaptiveRidge?label=%20)](https://github.com/OHDSI/BrokenAdaptiveRidge/pulls) | [![Build Status](https://github.com/ohdsi/BrokenAdaptiveRidge/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/BrokenAdaptiveRidge/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/BrokenAdaptiveRidge/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/BrokenAdaptiveRidge?branch=main) | [Report](pare_reports/BrokenAdaptiveRidge.html) | [Capr](https://github.com/OHDSI/Capr) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/Capr?label=%20)](https://ohdsi.github.io/Capr/) | Martin Lavallee | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/Capr?label=%20)](https://github.com/OHDSI/Capr/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/Capr?label=%20)](https://github.com/OHDSI/Capr/pulls) | [![Build Status](https://github.com/ohdsi/Capr/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/Capr/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/Capr/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/Capr?branch=main) | [Report](pare_reports/Capr.html) | [Characterization](https://github.com/OHDSI/Characterization) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/Characterization?label=%20)](https://ohdsi.github.io/Characterization/) | Jenna Reps | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/Characterization?label=%20)](https://github.com/OHDSI/Characterization/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/Characterization?label=%20)](https://github.com/OHDSI/Characterization/pulls) | [![Build Status](https://github.com/ohdsi/Characterization/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/Characterization/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/Characterization/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/Characterization?branch=main) | [Report](pare_reports/Characterization.html) -| [CirceR](https://github.com/OHDSI/CirceR) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/CirceR?label=%20)](https://ohdsi.github.io/CirceR/) | Chris Knoll | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/CirceR?label=%20)](https://github.com/OHDSI/CirceR/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/CirceR?label=%20)](https://github.com/OHDSI/CirceR/pulls) | [![Build Status](https://github.com/ohdsi/CirceR/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/CirceR/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/CirceR/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/CirceR?branch=main) | [Report](pare_reports/CirceR.html) +| [CirceR](https://github.com/OHDSI/CirceR) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/CirceR?label=%20)](https://ohdsi.github.io/CirceR/) | Chris Knoll | CRAN | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/CirceR?label=%20)](https://github.com/OHDSI/CirceR/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/CirceR?label=%20)](https://github.com/OHDSI/CirceR/pulls) | [![Build Status](https://github.com/ohdsi/CirceR/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/CirceR/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/CirceR/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/CirceR?branch=main) | [Report](pare_reports/CirceR.html) | [CohortDiagnostics](https://github.com/OHDSI/CohortDiagnostics) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/CohortDiagnostics?label=%20)](https://ohdsi.github.io/CohortDiagnostics/) | Jamie Gilbert | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/CohortDiagnostics?label=%20)](https://github.com/OHDSI/CohortDiagnostics/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/CohortDiagnostics?label=%20)](https://github.com/OHDSI/CohortDiagnostics/pulls) | [![Build Status](https://github.com/ohdsi/CohortDiagnostics/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/CohortDiagnostics/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/CohortDiagnostics/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/CohortDiagnostics?branch=main) | [Report](pare_reports/CohortDiagnostics.html) | [CohortExplorer](https://github.com/OHDSI/CohortExplorer) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/CohortExplorer?label=%20)](https://ohdsi.github.io/CohortExplorer/) | Gowtham Rao | CRAN | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/CohortExplorer?label=%20)](https://github.com/OHDSI/CohortExplorer/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/CohortExplorer?label=%20)](https://github.com/OHDSI/CohortExplorer/pulls) | [![Build Status](https://github.com/ohdsi/CohortExplorer/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/CohortExplorer/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/CohortExplorer/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/CohortExplorer?branch=main) | [Report](pare_reports/CohortExplorer.html) | [CohortGenerator](https://github.com/OHDSI/CohortGenerator) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/CohortGenerator?label=%20)](https://ohdsi.github.io/CohortGenerator/) | Anthony Sena | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/CohortGenerator?label=%20)](https://github.com/OHDSI/CohortGenerator/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/CohortGenerator?label=%20)](https://github.com/OHDSI/CohortGenerator/pulls) | [![Build Status](https://github.com/ohdsi/CohortGenerator/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/CohortGenerator/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/CohortGenerator/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/CohortGenerator?branch=main) | [Report](pare_reports/CohortGenerator.html) @@ -35,9 +35,9 @@ The table below lists, for each of the HADES packages, the following details: | [DeepPatientLevelPrediction](https://github.com/OHDSI/DeepPatientLevelPrediction) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/DeepPatientLevelPrediction?label=%20)](https://ohdsi.github.io/DeepPatientLevelPrediction/) | Egill Fridgeirsson | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/DeepPatientLevelPrediction?label=%20)](https://github.com/OHDSI/DeepPatientLevelPrediction/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/DeepPatientLevelPrediction?label=%20)](https://github.com/OHDSI/DeepPatientLevelPrediction/pulls) | [![Build Status](https://github.com/ohdsi/DeepPatientLevelPrediction/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/DeepPatientLevelPrediction/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/DeepPatientLevelPrediction/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/DeepPatientLevelPrediction?branch=main) | [Report](pare_reports/DeepPatientLevelPrediction.html) | [EmpiricalCalibration](https://github.com/OHDSI/EmpiricalCalibration) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/EmpiricalCalibration?label=%20)](https://ohdsi.github.io/EmpiricalCalibration/) | Martijn Schuemie | CRAN | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/EmpiricalCalibration?label=%20)](https://github.com/OHDSI/EmpiricalCalibration/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/EmpiricalCalibration?label=%20)](https://github.com/OHDSI/EmpiricalCalibration/pulls) | [![Build Status](https://github.com/ohdsi/EmpiricalCalibration/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/EmpiricalCalibration/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/EmpiricalCalibration/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/EmpiricalCalibration?branch=main) | [Report](pare_reports/EmpiricalCalibration.html) | [EnsemblePatientLevelPrediction](https://github.com/OHDSI/EnsemblePatientLevelPrediction) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/EnsemblePatientLevelPrediction?label=%20)](https://ohdsi.github.io/EnsemblePatientLevelPrediction/) | Jenna Reps | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/EnsemblePatientLevelPrediction?label=%20)](https://github.com/OHDSI/EnsemblePatientLevelPrediction/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/EnsemblePatientLevelPrediction?label=%20)](https://github.com/OHDSI/EnsemblePatientLevelPrediction/pulls) | [![Build Status](https://github.com/ohdsi/EnsemblePatientLevelPrediction/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/EnsemblePatientLevelPrediction/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/EnsemblePatientLevelPrediction/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/EnsemblePatientLevelPrediction?branch=main) | [Report](pare_reports/EnsemblePatientLevelPrediction.html) -| [Eunomia](https://github.com/OHDSI/Eunomia) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/Eunomia?label=%20)](https://ohdsi.github.io/Eunomia/) | Frank DeFalco | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/Eunomia?label=%20)](https://github.com/OHDSI/Eunomia/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/Eunomia?label=%20)](https://github.com/OHDSI/Eunomia/pulls) | [![Build Status](https://github.com/ohdsi/Eunomia/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/Eunomia/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/Eunomia/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/Eunomia?branch=main) | [Report](pare_reports/Eunomia.html) +| [Eunomia](https://github.com/OHDSI/Eunomia) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/Eunomia?label=%20)](https://ohdsi.github.io/Eunomia/) | Frank DeFalco | CRAN | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/Eunomia?label=%20)](https://github.com/OHDSI/Eunomia/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/Eunomia?label=%20)](https://github.com/OHDSI/Eunomia/pulls) | [![Build Status](https://github.com/ohdsi/Eunomia/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/Eunomia/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/Eunomia/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/Eunomia?branch=main) | [Report](pare_reports/Eunomia.html) | [EvidenceSynthesis](https://github.com/OHDSI/EvidenceSynthesis) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/EvidenceSynthesis?label=%20)](https://ohdsi.github.io/EvidenceSynthesis/) | Martijn Schuemie | CRAN | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/EvidenceSynthesis?label=%20)](https://github.com/OHDSI/EvidenceSynthesis/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/EvidenceSynthesis?label=%20)](https://github.com/OHDSI/EvidenceSynthesis/pulls) | [![Build Status](https://github.com/ohdsi/EvidenceSynthesis/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/EvidenceSynthesis/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/EvidenceSynthesis/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/EvidenceSynthesis?branch=main) | [Report](pare_reports/EvidenceSynthesis.html) -| [FeatureExtraction](https://github.com/OHDSI/FeatureExtraction) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/FeatureExtraction?label=%20)](https://ohdsi.github.io/FeatureExtraction/) | Anthony Sena | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/FeatureExtraction?label=%20)](https://github.com/OHDSI/FeatureExtraction/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/FeatureExtraction?label=%20)](https://github.com/OHDSI/FeatureExtraction/pulls) | [![Build Status](https://github.com/ohdsi/FeatureExtraction/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/FeatureExtraction/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/FeatureExtraction/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/FeatureExtraction?branch=main) | [Report](pare_reports/FeatureExtraction.html) +| [FeatureExtraction](https://github.com/OHDSI/FeatureExtraction) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/FeatureExtraction?label=%20)](https://ohdsi.github.io/FeatureExtraction/) | Ger Inberg | CRAN | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/FeatureExtraction?label=%20)](https://github.com/OHDSI/FeatureExtraction/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/FeatureExtraction?label=%20)](https://github.com/OHDSI/FeatureExtraction/pulls) | [![Build Status](https://github.com/ohdsi/FeatureExtraction/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/FeatureExtraction/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/FeatureExtraction/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/FeatureExtraction?branch=main) | [Report](pare_reports/FeatureExtraction.html) | [Hydra](https://github.com/OHDSI/Hydra) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/Hydra?label=%20)](https://ohdsi.github.io/Hydra/) | Anthony Sena | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/Hydra?label=%20)](https://github.com/OHDSI/Hydra/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/Hydra?label=%20)](https://github.com/OHDSI/Hydra/pulls) | [![Build Status](https://github.com/ohdsi/Hydra/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/Hydra/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/Hydra/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/Hydra?branch=main) | [Report](pare_reports/Hydra.html) | [IterativeHardThresholding](https://github.com/OHDSI/IterativeHardThresholding) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/IterativeHardThresholding?label=%20)](https://ohdsi.github.io/IterativeHardThresholding/) | Marc Suchard | CRAN | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/IterativeHardThresholding?label=%20)](https://github.com/OHDSI/IterativeHardThresholding/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/IterativeHardThresholding?label=%20)](https://github.com/OHDSI/IterativeHardThresholding/pulls) | [![Build Status](https://github.com/ohdsi/IterativeHardThresholding/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/IterativeHardThresholding/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/IterativeHardThresholding/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/IterativeHardThresholding?branch=main) | [Report](pare_reports/IterativeHardThresholding.html) | [MethodEvaluation](https://github.com/OHDSI/MethodEvaluation) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/MethodEvaluation?label=%20)](https://ohdsi.github.io/MethodEvaluation/) | Martijn Schuemie | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/MethodEvaluation?label=%20)](https://github.com/OHDSI/MethodEvaluation/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/MethodEvaluation?label=%20)](https://github.com/OHDSI/MethodEvaluation/pulls) | [![Build Status](https://github.com/ohdsi/MethodEvaluation/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/MethodEvaluation/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/MethodEvaluation/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/MethodEvaluation?branch=main) | [Report](pare_reports/MethodEvaluation.html) diff --git a/Rmd/rSetup.Rmd b/Rmd/rSetup.Rmd index ccd07ea..92502b2 100644 --- a/Rmd/rSetup.Rmd +++ b/Rmd/rSetup.Rmd @@ -62,7 +62,7 @@ rToolsUrl <- sprintf("https://cran.r-project.org/bin/windows/Rtools/rtools%s/rto ## Installing Java -1. Go to , and select the Windows 64-bit JRE installer as highlighted below. ![](images/downloadJavaWindows.png) +1. Go to , and select the Windows 64-bit JDK installer as highlighted below. ![](images/downloadJavaWindows.png) 2. After downloading just run the installer. diff --git a/Rmd/validation.Rmd b/Rmd/validation.Rmd index 742f22a..1049ea4 100644 --- a/Rmd/validation.Rmd +++ b/Rmd/validation.Rmd @@ -8,7 +8,10 @@ output: # Validation -Coming soon... +For validation, HADES mostly relies on an extensive set of unit tests executed as part of its continuous integration. This assures validity on a continuous basis, at every release. A good reference would be our recent HADES paper: + +- Schuemie M, Reps J, Black A, et al. [Health-Analytics Data to Evidence Suite (HADES): Open-Source Software for Observational Research](https://ebooks.iospress.nl/doi/10.3233/SHTI231108) Studies in health technology and informatics. 2024 Jan 25:310:966-970. + # Evaluation diff --git a/docs/images/downloadJavaWindows.png b/docs/images/downloadJavaWindows.png index 77249dc..40cb197 100644 Binary files a/docs/images/downloadJavaWindows.png and b/docs/images/downloadJavaWindows.png differ diff --git a/docs/packageStatuses.html b/docs/packageStatuses.html index c2d05d6..7df7d9b 100644 --- a/docs/packageStatuses.html +++ b/docs/packageStatuses.html @@ -578,7 +578,7 @@

Package statuses

src="https://img.shields.io/github/r-package/v/ohdsi/CirceR?label=%20" alt="Version" /> Chris Knoll -GitHub +CRAN Open issues @@ -878,7 +878,7 @@

Package statuses

src="https://img.shields.io/github/r-package/v/ohdsi/Eunomia?label=%20" alt="Version" /> Frank DeFalco -GitHub +CRAN Package statuses href="https://ohdsi.github.io/FeatureExtraction/">Version -Anthony Sena -GitHub +Ger Inberg +CRAN Installing Java

  • Go to https://docs.aws.amazon.com/corretto/latest/corretto-8-ug/downloads-list.html, -and select the Windows 64-bit JRE installer as highlighted below.

  • After downloading just run the installer.

  • The default maximum Java heap space is very small (only 512MB), diff --git a/docs/validation.html b/docs/validation.html index 98768a6..1a01593 100644 --- a/docs/validation.html +++ b/docs/validation.html @@ -446,7 +446,17 @@

    Validation & Evaluation

    Validation

    -

    Coming soon…

    +

    For validation, HADES mostly relies on an extensive set of unit tests +executed as part of its continuous integration. This assures validity on +a continuous basis, at every release. A good reference would be our +recent HADES paper:

    +

    Evaluation

    diff --git a/extras/GeneratePackagesPage.R b/extras/GeneratePackagesPage.R index 0f1ce50..474732f 100644 --- a/extras/GeneratePackagesPage.R +++ b/extras/GeneratePackagesPage.R @@ -1,4 +1,4 @@ -setwd("C:/Temp/Git/Hades") +# setwd("C:/Temp/Git/Hades") packages <- read.csv("extras/packages.csv", stringsAsFactors = FALSE) # sections <- read.csv("extras/sections.csv", stringsAsFactors = FALSE) diff --git a/extras/packages.csv b/extras/packages.csv index 1dedb34..507bcef 100644 --- a/extras/packages.csv +++ b/extras/packages.csv @@ -8,7 +8,7 @@ order,name,section,description,inCran,pages,maintainers,CRON 7,EnsemblePatientLevelPrediction,Patient-level prediction,Building and validating ensemble patient-level predictive models.,FALSE,TRUE,Jenna Reps,0 14 * * 6 8,Characterization,Characterization,Various types of characterizations of a target and outcome cohort.,FALSE,TRUE,Jenna Reps,0 14 * * 0 9,Capr,Cohort construction and evaluation,Develop and manipulate complex cohort definitions in R,FALSE,TRUE,Martin Lavallee,0 15 * * 6 -10,CirceR,Cohort construction and evaluation,"An R wrapper for Circe, a library for creating cohort definitions, expressing them as JSON, SQL, or Markdown.",FALSE,TRUE,Chris Knoll,0 16 * * 6 +10,CirceR,Cohort construction and evaluation,"An R wrapper for Circe, a library for creating cohort definitions, expressing them as JSON, SQL, or Markdown.",TRUE,TRUE,Chris Knoll,0 16 * * 6 11,CohortGenerator,Cohort construction and evaluation,Instantiating cohorts in a database based on a set of cohort definitions.,FALSE,TRUE,Anthony Sena,0 17 * * 6 12,PhenotypeLibrary,Cohort construction and evaluation,The OHDSI Phenotype Library: a collection of community-maintained pre-definined cohorts.,FALSE,TRUE,Gowtham Rao,0 18 * * 6 13,CohortDiagnostics,Cohort construction and evaluation,Generate a wide set of diagnostics to evaluate cohort definitions against databases in the CDM.,FALSE,TRUE,Jamie Gilbert,0 19 * * 6 @@ -18,13 +18,13 @@ order,name,section,description,inCran,pages,maintainers,CRON 17,DataQualityDashboard,Evidence Quality,Expose and evaluate observational data quality.,FALSE,TRUE,Katy Sadowksi,0 17 * * 0 18,EmpiricalCalibration,Evidence Quality,Use negative control exposure-outcome pairs to profile and calibrate a particular analysis design.,TRUE,TRUE,Martijn Schuemie,0 22 * * 6 19,MethodEvaluation,Evidence Quality,Use real data and established reference sets as well as simulations injected in real data to evaluate the performance of methods.,FALSE,TRUE,Martijn Schuemie ,0 23 * * 6 -20,Andromeda,Supporting packages,"Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.",TRUE,TRUE,Adam Black,0 0 * * 0 +20,Andromeda,Supporting packages,"Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.",TRUE,TRUE,Martijn Schuemie,0 0 * * 0 21,BigKnn,Supporting packages,A large scale k-nearest neighbor classifier using the Lucene search engine.,FALSE,TRUE,Martijn Schuemie ,0 1 * * 0 22,BrokenAdaptiveRidge,Supporting packages,Broken Adaptive Ridge Regression with Cyclops.,TRUE,TRUE,Marc Suchard,0 18 * * 0 23,Cyclops,Supporting packages,"Highly efficient implementation of regularized logistic, Poisson and Cox regression.",TRUE,TRUE,Marc Suchard,0 2 * * 0 24,DatabaseConnector,Supporting packages,"Connect directly to a wide range of database platforms, including SQL Server, Oracle, and PostgreSQL.",TRUE,TRUE,Martijn Schuemie ,0 3 * * 0 -25,Eunomia,Supporting packages,A standard CDM dataset for testing and demonstration purposes that runs on an embedded SQLite database.,FALSE,TRUE,Frank DeFalco,0 4 * * 0 -26,FeatureExtraction,Supporting packages,Automatically extract large sets of features for user-specified cohorts using data in the CDM.,FALSE,TRUE,Anthony Sena,0 5 * * 0 +25,Eunomia,Supporting packages,A standard CDM dataset for testing and demonstration purposes that runs on an embedded SQLite database.,TRUE,TRUE,Frank DeFalco,0 4 * * 0 +26,FeatureExtraction,Supporting packages,Automatically extract large sets of features for user-specified cohorts using data in the CDM.,TRUE,TRUE,Ger Inberg,0 5 * * 0 27,Hydra,Supporting packages,Hydrating package skeletons into executable R study packages based on specifications in JSON format.,FALSE,TRUE,Anthony Sena ,0 6 * * 0 28,IterativeHardThresholding,Supporting packages,Performing L0-based regressions using Cyclops,TRUE,TRUE,Marc Suchard,0 7 * * 0 29,OhdsiSharing,Supporting packages,Securely sharing (large) files between OHDSI collaborators.,FALSE,TRUE,Lee Evans,0 8 * * 0