From 4781f77b1844101e86e65c3ecf17371bf7cdf4cd Mon Sep 17 00:00:00 2001 From: schuemie Date: Tue, 18 Jun 2024 13:19:56 +0200 Subject: [PATCH] Adding Keeper to HADES --- DESCRIPTION | 9 ++-- NEWS.md | 6 +++ Rmd/packageStatuses.Rmd | 1 + Rmd/packages.Rmd | 1 + Rmd/support.Rmd | 2 + docs/codeStyle.html | 2 +- docs/community.html | 2 +- docs/connecting.html | 2 +- docs/contribute.html | 2 +- docs/developerGuidelines.html | 2 +- docs/developmentRoadmap.html | 4 +- docs/index.html | 2 +- docs/installingHades.html | 2 +- docs/packageRequirements.html | 2 +- docs/packageStatuses.html | 51 ++++++++++++++----- docs/packages.html | 10 +++- docs/publications.html | 2 +- docs/rSetup.html | 2 +- docs/releaseProcess.html | 2 +- docs/renv.html | 2 +- .../header-attrs.js | 0 docs/support.html | 4 +- docs/supportedPlatforms.html | 2 +- docs/testServerUsage.html | 2 +- docs/validation.html | 2 +- extras/GenerateSupportPage.R | 2 +- extras/packages.csv | 41 +++++++-------- 27 files changed, 105 insertions(+), 56 deletions(-) rename docs/site_libs/{header-attrs-2.26 => header-attrs-2.27}/header-attrs.js (100%) diff --git a/DESCRIPTION b/DESCRIPTION index 5e90163..85b8d7e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: Hades Type: Package Title: Health Analytics Data-to-Evidence Suite -Version: 1.13.1 -Date: 2024-05-08 +Version: 1.14.0 +Date: 2024-06-18 Authors@R: c( person("Martijn", "Schuemie", , "schuemie@ohdsi.org", role = c("aut", "cre")), person("Observational Health Data Science and Informatics", role = c("cph")) @@ -47,7 +47,8 @@ Imports: ShinyAppBuilder, DataQualityDashboard, BrokenAdaptiveRidge, - Achilles + Achilles, + Keeper Remotes: ohdsi/BigKnn, ohdsi/ROhdsiWebApi, @@ -71,7 +72,7 @@ Remotes: ohdsi/Characterization, ohdsi/ShinyAppBuilder, ohdsi/DataQualityDashboard, - ohdsi/Achilles + ohdsi/Keeper LazyData: false RoxygenNote: 7.2.0 Encoding: UTF-8 diff --git a/NEWS.md b/NEWS.md index 999597c..ee1fe10 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +HADES 1.14.0 +============ + +- Adding Keeper to HADES + + HADES 1.13.1 ============ diff --git a/Rmd/packageStatuses.Rmd b/Rmd/packageStatuses.Rmd index 0955048..fc87189 100644 --- a/Rmd/packageStatuses.Rmd +++ b/Rmd/packageStatuses.Rmd @@ -40,6 +40,7 @@ The table below lists, for each of the HADES packages, the following details: | [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](https://ohdsi.github.io/HadesFiles/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](https://ohdsi.github.io/HadesFiles/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](https://ohdsi.github.io/HadesFiles/pare_reports/IterativeHardThresholding.html) +| [Keeper](https://github.com/OHDSI/Keeper) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/Keeper?label=%20)](https://ohdsi.github.io/Keeper/) | Anna Ostropolets | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/Keeper?label=%20)](https://github.com/OHDSI/Keeper/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/Keeper?label=%20)](https://github.com/OHDSI/Keeper/pulls) | [![Build Status](https://github.com/ohdsi/Keeper/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/Keeper/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/Keeper/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/Keeper?branch=main) | [Report](https://ohdsi.github.io/HadesFiles/pare_reports/Keeper.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](https://ohdsi.github.io/HadesFiles/pare_reports/MethodEvaluation.html) | [OhdsiSharing](https://github.com/OHDSI/OhdsiSharing) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/OhdsiSharing?label=%20)](https://ohdsi.github.io/OhdsiSharing/) | Lee Evans | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/OhdsiSharing?label=%20)](https://github.com/OHDSI/OhdsiSharing/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/OhdsiSharing?label=%20)](https://github.com/OHDSI/OhdsiSharing/pulls) | [![Build Status](https://github.com/ohdsi/OhdsiSharing/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/OhdsiSharing/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/OhdsiSharing/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/OhdsiSharing?branch=main) | [Report](https://ohdsi.github.io/HadesFiles/pare_reports/OhdsiSharing.html) | [OhdsiShinyModules](https://github.com/OHDSI/OhdsiShinyModules) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/OhdsiShinyModules?label=%20)](https://ohdsi.github.io/OhdsiShinyModules/) | Jenna Reps | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/OhdsiShinyModules?label=%20)](https://github.com/OHDSI/OhdsiShinyModules/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/OhdsiShinyModules?label=%20)](https://github.com/OHDSI/OhdsiShinyModules/pulls) | [![Build Status](https://github.com/ohdsi/OhdsiShinyModules/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg)](https://github.com/OHDSI/OhdsiShinyModules/actions/workflows/R_CMD_check_main_weekly.yaml) | [![codecov.io](https://codecov.io/github/OHDSI/OhdsiShinyModules/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/OhdsiShinyModules?branch=main) | [Report](https://ohdsi.github.io/HadesFiles/pare_reports/OhdsiShinyModules.html) diff --git a/Rmd/packages.Rmd b/Rmd/packages.Rmd index fa20f1d..20ca7d6 100644 --- a/Rmd/packages.Rmd +++ b/Rmd/packages.Rmd @@ -35,6 +35,7 @@ Below are the packages included in HADES. For each package a link is provided wi

  • CohortDiagnostics

    Generate a wide set of diagnostics to evaluate cohort definitions against databases in the CDM.
    Learn more...

  • PheValuator

    Semi-automated evaluation of cohorts, producing metrics suchs as sensitivity, specificity, and positive and negative preditive value.
    Learn more...

  • CohortExplorer

    Visually explore all individual-level data of patients in a cohort
    Learn more...
    • +

  • Keeper

    Knowledge-Enhanced Electronic Profile Review
    Learn more...

    • Evidence Quality

    Evidence Quality diff --git a/docs/publications.html b/docs/publications.html index 80ae423..8f94235 100644 --- a/docs/publications.html +++ b/docs/publications.html @@ -13,7 +13,7 @@ Publications - + diff --git a/docs/rSetup.html b/docs/rSetup.html index efc4db4..edffdab 100644 --- a/docs/rSetup.html +++ b/docs/rSetup.html @@ -13,7 +13,7 @@ Setting up the R environment - + diff --git a/docs/releaseProcess.html b/docs/releaseProcess.html index 0a04b3a..b20ffb2 100644 --- a/docs/releaseProcess.html +++ b/docs/releaseProcess.html @@ -13,7 +13,7 @@ Release Process - + diff --git a/docs/renv.html b/docs/renv.html index 947e52c..e0d7a7b 100644 --- a/docs/renv.html +++ b/docs/renv.html @@ -13,7 +13,7 @@ Using Renv for Dependencies - + diff --git a/docs/site_libs/header-attrs-2.26/header-attrs.js b/docs/site_libs/header-attrs-2.27/header-attrs.js similarity index 100% rename from docs/site_libs/header-attrs-2.26/header-attrs.js rename to docs/site_libs/header-attrs-2.27/header-attrs.js diff --git a/docs/support.html b/docs/support.html index 23d6b41..52deded 100644 --- a/docs/support.html +++ b/docs/support.html @@ -13,7 +13,7 @@ Questions and Bug Reports - + @@ -512,6 +512,8 @@

    Bug reports

  • IterativeHardThresholding issue tracker

    • +

  • Keeper issue +tracker

  • MethodEvaluation issue tracker

    • diff --git a/docs/supportedPlatforms.html b/docs/supportedPlatforms.html index 7652abe..fd6856d 100644 --- a/docs/supportedPlatforms.html +++ b/docs/supportedPlatforms.html @@ -13,7 +13,7 @@ Supported Database Platforms - + diff --git a/docs/testServerUsage.html b/docs/testServerUsage.html index a0664e1..ec6e7cb 100644 --- a/docs/testServerUsage.html +++ b/docs/testServerUsage.html @@ -13,7 +13,7 @@ Test server usage - + diff --git a/docs/validation.html b/docs/validation.html index 1a01593..e8fb4ea 100644 --- a/docs/validation.html +++ b/docs/validation.html @@ -13,7 +13,7 @@ Validation & Evaluation - + diff --git a/extras/GenerateSupportPage.R b/extras/GenerateSupportPage.R index 981b001..6cf0cd0 100644 --- a/extras/GenerateSupportPage.R +++ b/extras/GenerateSupportPage.R @@ -1,4 +1,4 @@ -setwd("C:/Temp/Git/Hades") +# setwd("C:/Temp/Git/Hades") packages <- read.csv("extras/packages.csv", stringsAsFactors = FALSE) packages <- packages[order(packages$name), ] diff --git a/extras/packages.csv b/extras/packages.csv index 507bcef..bd67491 100644 --- a/extras/packages.csv +++ b/extras/packages.csv @@ -14,23 +14,24 @@ order,name,section,description,inCran,pages,maintainers,CRON 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 14,PheValuator,Cohort construction and evaluation,"Semi-automated evaluation of cohorts, producing metrics suchs as sensitivity, specificity, and positive and negative preditive value.",FALSE,TRUE,Joel Swerdel,0 20 * * 6 15,CohortExplorer,Cohort construction and evaluation,Visually explore all individual-level data of patients in a cohort,TRUE,TRUE,Gowtham Rao,0 21 * * 6 -16,Achilles,Evidence Quality,Generate descriptive statistics on an entire OMOP CDM database,TRUE,TRUE,Frank DeFalco,0 19 * * 0 -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,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.,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 -30,OhdsiShinyModules,Supporting packages,Contains shiny modules that can be used within shiny result interfaces,FALSE,TRUE,Jenna Reps,0 9 * * 0 -31,ParallelLogger,Supporting packages,"Support for parallel computation with logging to console, disk, or e-mail.",TRUE,TRUE,Martijn Schuemie ,0 10 * * 0 -32,ResultModelManager,Supporting packages,A lightweight utility for data migrations allowing old results to work with new shiny apps and data visualisations.,FALSE,TRUE,Jamie Gilbert,0 13 * * 0 -33,ROhdsiWebApi,Supporting packages,Interact with OHDSI WebAPI web services.,FALSE,TRUE,Gowtham Rao,0 11 * * 0 -34,ShinyAppBuilder,Supporting packages,Interactively view analysis results across different types of analyses.,FALSE,TRUE,Jenna Reps,0 15 * * 0 -35,SqlRender,Supporting packages,Generate SQL on the fly for the various SQL dialects.,TRUE,TRUE,Martijn Schuemie ,0 12 * * 0 +16,Keeper,Cohort construction and evaluation,Knowledge-Enhanced Electronic Profile Review,FALSE,TRUE,Anna Ostropolets,0 3 * * 0 +17,Achilles,Evidence Quality,Generate descriptive statistics on an entire OMOP CDM database,TRUE,TRUE,Frank DeFalco,0 19 * * 0 +18,DataQualityDashboard,Evidence Quality,Expose and evaluate observational data quality.,FALSE,TRUE,Katy Sadowksi,0 17 * * 0 +19,EmpiricalCalibration,Evidence Quality,Use negative control exposure-outcome pairs to profile and calibrate a particular analysis design.,TRUE,TRUE,Martijn Schuemie,0 22 * * 6 +20,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 +21,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 +22,BigKnn,Supporting packages,A large scale k-nearest neighbor classifier using the Lucene search engine.,FALSE,TRUE,Martijn Schuemie ,0 1 * * 0 +23,BrokenAdaptiveRidge,Supporting packages,Broken Adaptive Ridge Regression with Cyclops.,TRUE,TRUE,Marc Suchard,0 18 * * 0 +24,Cyclops,Supporting packages,"Highly efficient implementation of regularized logistic, Poisson and Cox regression.",TRUE,TRUE,Marc Suchard,0 2 * * 0 +25,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 +26,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 +27,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 +28,Hydra,Supporting packages,Hydrating package skeletons into executable R study packages based on specifications in JSON format.,FALSE,TRUE,Anthony Sena ,0 6 * * 0 +29,IterativeHardThresholding,Supporting packages,Performing L0-based regressions using Cyclops,TRUE,TRUE,Marc Suchard,0 7 * * 0 +30,OhdsiSharing,Supporting packages,Securely sharing (large) files between OHDSI collaborators.,FALSE,TRUE,Lee Evans,0 8 * * 0 +31,OhdsiShinyModules,Supporting packages,Contains shiny modules that can be used within shiny result interfaces,FALSE,TRUE,Jenna Reps,0 9 * * 0 +32,ParallelLogger,Supporting packages,"Support for parallel computation with logging to console, disk, or e-mail.",TRUE,TRUE,Martijn Schuemie ,0 10 * * 0 +33,ResultModelManager,Supporting packages,A lightweight utility for data migrations allowing old results to work with new shiny apps and data visualisations.,FALSE,TRUE,Jamie Gilbert,0 13 * * 0 +34,ROhdsiWebApi,Supporting packages,Interact with OHDSI WebAPI web services.,FALSE,TRUE,Gowtham Rao,0 11 * * 0 +35,ShinyAppBuilder,Supporting packages,Interactively view analysis results across different types of analyses.,FALSE,TRUE,Jenna Reps,0 15 * * 0 +36,SqlRender,Supporting packages,Generate SQL on the fly for the various SQL dialects.,TRUE,TRUE,Martijn Schuemie ,0 12 * * 0