From 13d2b5ae0c02b9f47ea1d433c42bd84e7df22366 Mon Sep 17 00:00:00 2001 From: Schuemie Date: Mon, 5 Dec 2022 13:20:15 +0100 Subject: [PATCH] Adding PheValuator to HADES --- DESCRIPTION | 6 ++++-- NEWS.md | 7 +++++++ Rmd/packageStatuses.Rmd | 1 + Rmd/packages.Rmd | 1 + Rmd/support.Rmd | 2 ++ docs/developmentRoadmap.html | 2 ++ docs/packageStatuses.html | 16 +++++++++++++--- docs/packages.html | 6 ++++++ docs/support.html | 1 + extras/packages.csv | 1 + 10 files changed, 38 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index d9da99b..5e82a89 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: Hades Type: Package Title: Health Analytics Data-to-Evidence Suite -Version: 1.5.0 -Date: 2022-11-18 +Version: 1.6.0 +Date: 2022-12-05 Authors@R: c( person("Martijn", "Schuemie", , "schuemie@ohdsi.org", role = c("aut", "cre")), person("Observational Health Data Science and Informatics", role = c("cph")) @@ -36,6 +36,7 @@ Imports: SelfControlledCohort, PatientLevelPrediction, PhenotypeLibrary, + PheValuator, MethodEvaluation, OhdsiSharing, Hydra, @@ -53,6 +54,7 @@ Remotes: ohdsi/MethodEvaluation, ohdsi/OhdsiSharing, ohdsi/PhenotypeLibrary, + ohdsi/PheValuator, ohdsi/Hydra, ohdsi/CirceR, ohdsi/Capr, diff --git a/NEWS.md b/NEWS.md index 69c45bf..e7d13b9 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ +HADES 1.6.0 +=========== + +Changes + +- Adding PheValuator to HADES + HADES 1.5.0 =========== diff --git a/Rmd/packageStatuses.Rmd b/Rmd/packageStatuses.Rmd index bc07f21..766ce40 100644 --- a/Rmd/packageStatuses.Rmd +++ b/Rmd/packageStatuses.Rmd @@ -41,6 +41,7 @@ The table below lists, for each of the HADES packages, the following details: | [ParallelLogger](https://github.com/OHDSI/ParallelLogger) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/ParallelLogger?label=%20)](https://ohdsi.github.io/ParallelLogger/) | Martijn Schuemie | CRAN | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/ParallelLogger?label=%20)](https://github.com/OHDSI/ParallelLogger/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/ParallelLogger?label=%20)](https://github.com/OHDSI/ParallelLogger/pulls) | [![Build Status](https://github.com/OHDSI/ParallelLogger/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/ParallelLogger/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/ParallelLogger/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/ParallelLogger?branch=main) | | [PatientLevelPrediction](https://github.com/OHDSI/PatientLevelPrediction) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/PatientLevelPrediction?label=%20)](https://ohdsi.github.io/PatientLevelPrediction/) | Jenna Reps & Peter Rijnbeek | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/PatientLevelPrediction?label=%20)](https://github.com/OHDSI/PatientLevelPrediction/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/PatientLevelPrediction?label=%20)](https://github.com/OHDSI/PatientLevelPrediction/pulls) | [![Build Status](https://github.com/OHDSI/PatientLevelPrediction/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/PatientLevelPrediction/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/PatientLevelPrediction/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/PatientLevelPrediction?branch=main) | | [PhenotypeLibrary](https://github.com/OHDSI/PhenotypeLibrary) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/PhenotypeLibrary?label=%20)](https://ohdsi.github.io/PhenotypeLibrary/) | Gowtham Rao | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/PhenotypeLibrary?label=%20)](https://github.com/OHDSI/PhenotypeLibrary/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/PhenotypeLibrary?label=%20)](https://github.com/OHDSI/PhenotypeLibrary/pulls) | [![Build Status](https://github.com/OHDSI/PhenotypeLibrary/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/PhenotypeLibrary/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/PhenotypeLibrary/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/PhenotypeLibrary?branch=main) | +| [PheValuator](https://github.com/OHDSI/PheValuator) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/PheValuator?label=%20)](https://ohdsi.github.io/PheValuator/) | Joel Swerdel | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/PheValuator?label=%20)](https://github.com/OHDSI/PheValuator/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/PheValuator?label=%20)](https://github.com/OHDSI/PheValuator/pulls) | [![Build Status](https://github.com/OHDSI/PheValuator/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/PheValuator/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/PheValuator/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/PheValuator?branch=main) | | [ROhdsiWebApi](https://github.com/OHDSI/ROhdsiWebApi) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/ROhdsiWebApi?label=%20)](https://ohdsi.github.io/ROhdsiWebApi/) | Gowtham Rao | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/ROhdsiWebApi?label=%20)](https://github.com/OHDSI/ROhdsiWebApi/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/ROhdsiWebApi?label=%20)](https://github.com/OHDSI/ROhdsiWebApi/pulls) | [![Build Status](https://github.com/OHDSI/ROhdsiWebApi/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/ROhdsiWebApi/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/ROhdsiWebApi/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/ROhdsiWebApi?branch=main) | | [SelfControlledCaseSeries](https://github.com/OHDSI/SelfControlledCaseSeries) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/SelfControlledCaseSeries?label=%20)](https://ohdsi.github.io/SelfControlledCaseSeries/) | Martijn Schuemie | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/SelfControlledCaseSeries?label=%20)](https://github.com/OHDSI/SelfControlledCaseSeries/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/SelfControlledCaseSeries?label=%20)](https://github.com/OHDSI/SelfControlledCaseSeries/pulls) | [![Build Status](https://github.com/OHDSI/SelfControlledCaseSeries/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/SelfControlledCaseSeries/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/SelfControlledCaseSeries/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/SelfControlledCaseSeries?branch=main) | | [SelfControlledCohort](https://github.com/OHDSI/SelfControlledCohort) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/SelfControlledCohort?label=%20)](https://ohdsi.github.io/SelfControlledCohort/) | Jamie Gilbert | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/SelfControlledCohort?label=%20)](https://github.com/OHDSI/SelfControlledCohort/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/SelfControlledCohort?label=%20)](https://github.com/OHDSI/SelfControlledCohort/pulls) | [![Build Status](https://github.com/OHDSI/SelfControlledCohort/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/SelfControlledCohort/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/SelfControlledCohort/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/SelfControlledCohort?branch=main) | diff --git a/Rmd/packages.Rmd b/Rmd/packages.Rmd index 6cc29a0..684512d 100644 --- a/Rmd/packages.Rmd +++ b/Rmd/packages.Rmd @@ -29,6 +29,7 @@ Below are the packages included in HADES. For each package a link is provided wi

  • CohortGenerator

    Instantiating cohorts in a database based on a set of cohort definitions.
    Learn more...

  • PhenotypeLibrary

    The OHDSI Phenotype Library: a collection of community-maintained pre-definined cohorts.
    Learn more...

  • 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...

    • Evidence Quality

    diff --git a/Rmd/support.Rmd b/Rmd/support.Rmd index 8fbca21..4aabe07 100644 --- a/Rmd/support.Rmd +++ b/Rmd/support.Rmd @@ -60,6 +60,8 @@ Bug reports should be files using the issue tracker of the misbehaving package: - [PhenotypeLibrary issue tracker](https://github.com/OHDSI/PhenotypeLibrary/issues) +- [PheValuator issue tracker](https://github.com/OHDSI/PheValuator/issues) + - [ROhdsiWebApi issue tracker](https://github.com/OHDSI/ROhdsiWebApi/issues) - [SelfControlledCaseSeries issue tracker](https://github.com/OHDSI/SelfControlledCaseSeries/issues) diff --git a/docs/developmentRoadmap.html b/docs/developmentRoadmap.html index 7352cff..146f9f6 100644 --- a/docs/developmentRoadmap.html +++ b/docs/developmentRoadmap.html @@ -491,6 +491,8 @@

    Package milestones

    +

    +

    diff --git a/docs/packageStatuses.html b/docs/packageStatuses.html index e61f299..0049c5b 100644 --- a/docs/packageStatuses.html +++ b/docs/packageStatuses.html @@ -630,6 +630,16 @@

    Package statuses

    codecov.io +PheValuator +Version +Joel Swerdel +GitHub +Open issues +Open pull-requests +Build Status +codecov.io + + ROhdsiWebApi Version Gowtham Rao @@ -639,7 +649,7 @@

    Package statuses

    Build Status codecov.io - + SelfControlledCaseSeries Version Martijn Schuemie @@ -649,7 +659,7 @@

    Package statuses

    Build Status codecov.io - + SelfControlledCohort Version Jamie Gilbert @@ -659,7 +669,7 @@

    Package statuses

    Build Status codecov.io - + SqlRender Version Martijn Schuemie diff --git a/docs/packages.html b/docs/packages.html index 4d84b89..af86c9e 100644 --- a/docs/packages.html +++ b/docs/packages.html @@ -531,6 +531,12 @@

  • + 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… diff --git a/docs/support.html b/docs/support.html index 3a4a988..299ac06 100644 --- a/docs/support.html +++ b/docs/support.html @@ -472,6 +472,7 @@

    Bug reports

  • ParallelLogger issue tracker

  • PatientLevelPrediction issue tracker

  • PhenotypeLibrary issue tracker

    • +

  • PheValuator issue tracker

  • ROhdsiWebApi issue tracker

  • SelfControlledCaseSeries issue tracker

  • SelfControlledCohort issue tracker

    • diff --git a/extras/packages.csv b/extras/packages.csv index 51fe223..bc924d4 100644 --- a/extras/packages.csv +++ b/extras/packages.csv @@ -11,6 +11,7 @@ order,name,section,description,inCran,pages,maintainers 10,CohortGenerator,Cohort construction and evaluation,Instantiating cohorts in a database based on a set of cohort definitions.,FALSE,TRUE,Anthony Sena 11,PhenotypeLibrary,Cohort construction and evaluation,The OHDSI Phenotype Library: a collection of community-maintained pre-definined cohorts.,FALSE,TRUE,Gowtham Rao 12,CohortDiagnostics,Cohort construction and evaluation,Generate a wide set of diagnostics to evaluate cohort definitions against databases in the CDM.,FALSE,TRUE,Jamie Gilbert +13,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 13,CohortExplorer,Cohort construction and evaluation,Visually explore all individual-level data of patients in a cohort,FALSE,TRUE,Gowtham Rao 14,EmpiricalCalibration,Evidence Quality,Use negative control exposure-outcome pairs to profile and calibrate a particular analysis design.,TRUE,TRUE,Martijn Schuemie 15,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