Adding PheValuator to HADES

OHDSI · Dec 5, 2022 · 13d2b5a · 13d2b5a
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diff --git 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", , "[email protected]", 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
@@ -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
@@ -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
@@ -29,6 +29,7 @@ Below are the packages included in HADES. For each package a link is provided wi
 <li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/CohortGenerator">CohortGenerator</a></h4>Instantiating cohorts in a database based on a set of cohort definitions.</br><a href="https://ohdsi.github.io/CohortGenerator">Learn more...</a></li>
 <li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/PhenotypeLibrary">PhenotypeLibrary</a></h4>The OHDSI Phenotype Library: a collection of community-maintained pre-definined cohorts.</br><a href="https://ohdsi.github.io/PhenotypeLibrary">Learn more...</a></li>
 <li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/CohortDiagnostics">CohortDiagnostics</a></h4>Generate a wide set of diagnostics to evaluate cohort definitions against databases in the CDM.</br><a href="https://ohdsi.github.io/CohortDiagnostics">Learn more...</a></li>
+<li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/PheValuator">PheValuator</a></h4>Semi-automated evaluation of cohorts, producing metrics suchs as sensitivity, specificity, and positive and negative preditive value.</br><a href="https://ohdsi.github.io/PheValuator">Learn more...</a></li>
 <li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/CohortExplorer">CohortExplorer</a></h4>Visually explore all individual-level data of patients in a cohort</br><a href="https://ohdsi.github.io/CohortExplorer">Learn more...</a></li>
 </ul>
 <h2 id="pkg_header">Evidence Quality</h2>

diff --git 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
@@ -491,6 +491,8 @@ <h1>Package milestones</h1>
 <script>addMileStones('PatientLevelPrediction')</script>
 <p id='PhenotypeLibrary'/>
 <script>addMileStones('PhenotypeLibrary')</script>
+<p id='PheValuator'/>
+<script>addMileStones('PheValuator')</script>
 <p id='ROhdsiWebApi'/>
 <script>addMileStones('ROhdsiWebApi')</script>
 <p id='SelfControlledCaseSeries'/>

diff --git a/docs/packageStatuses.html b/docs/packageStatuses.html
@@ -630,6 +630,16 @@ <h1 class="title toc-ignore">Package statuses</h1>
 <td align="center"><a href="https://codecov.io/github/OHDSI/PhenotypeLibrary?branch=main"><img src="https://codecov.io/github/OHDSI/PhenotypeLibrary/coverage.svg?branch=main" alt="codecov.io" /></a></td>
 </tr>
 <tr class="even">
+<td align="left"><a href="https://github.com/OHDSI/PheValuator">PheValuator</a></td>
+<td align="center"><a href="https://ohdsi.github.io/PheValuator/"><img src="https://img.shields.io/github/r-package/v/ohdsi/PheValuator?label=%20" alt="Version" /></a></td>
+<td align="left">Joel Swerdel</td>
+<td align="center">GitHub</td>
+<td align="center"><a href="https://github.com/OHDSI/PheValuator/issues"><img src="https://img.shields.io/github/issues-raw/OHDSI/PheValuator?label=%20" alt="Open issues" /></a></td>
+<td align="center"><a href="https://github.com/OHDSI/PheValuator/pulls"><img src="https://img.shields.io/github/issues-pr-raw/OHDSI/PheValuator?label=%20" alt="Open pull-requests" /></a></td>
+<td align="center"><a href="https://github.com/OHDSI/PheValuator/actions?query=workflow%3AR-CMD-check"><img src="https://github.com/OHDSI/PheValuator/workflows/R-CMD-check/badge.svg" alt="Build Status" /></a></td>
+<td align="center"><a href="https://codecov.io/github/OHDSI/PheValuator?branch=main"><img src="https://codecov.io/github/OHDSI/PheValuator/coverage.svg?branch=main" alt="codecov.io" /></a></td>
+</tr>
+<tr class="odd">
 <td align="left"><a href="https://github.com/OHDSI/ROhdsiWebApi">ROhdsiWebApi</a></td>
 <td align="center"><a href="https://ohdsi.github.io/ROhdsiWebApi/"><img src="https://img.shields.io/github/r-package/v/ohdsi/ROhdsiWebApi?label=%20" alt="Version" /></a></td>
 <td align="left">Gowtham Rao</td>
@@ -639,7 +649,7 @@ <h1 class="title toc-ignore">Package statuses</h1>
 <td align="center"><a href="https://github.com/OHDSI/ROhdsiWebApi/actions?query=workflow%3AR-CMD-check"><img src="https://github.com/OHDSI/ROhdsiWebApi/workflows/R-CMD-check/badge.svg" alt="Build Status" /></a></td>
 <td align="center"><a href="https://codecov.io/github/OHDSI/ROhdsiWebApi?branch=main"><img src="https://codecov.io/github/OHDSI/ROhdsiWebApi/coverage.svg?branch=main" alt="codecov.io" /></a></td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="left"><a href="https://github.com/OHDSI/SelfControlledCaseSeries">SelfControlledCaseSeries</a></td>
 <td align="center"><a href="https://ohdsi.github.io/SelfControlledCaseSeries/"><img src="https://img.shields.io/github/r-package/v/ohdsi/SelfControlledCaseSeries?label=%20" alt="Version" /></a></td>
 <td align="left">Martijn Schuemie</td>
@@ -649,7 +659,7 @@ <h1 class="title toc-ignore">Package statuses</h1>
 <td align="center"><a href="https://github.com/OHDSI/SelfControlledCaseSeries/actions?query=workflow%3AR-CMD-check"><img src="https://github.com/OHDSI/SelfControlledCaseSeries/workflows/R-CMD-check/badge.svg" alt="Build Status" /></a></td>
 <td align="center"><a href="https://codecov.io/github/OHDSI/SelfControlledCaseSeries?branch=main"><img src="https://codecov.io/github/OHDSI/SelfControlledCaseSeries/coverage.svg?branch=main" alt="codecov.io" /></a></td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td align="left"><a href="https://github.com/OHDSI/SelfControlledCohort">SelfControlledCohort</a></td>
 <td align="center"><a href="https://ohdsi.github.io/SelfControlledCohort/"><img src="https://img.shields.io/github/r-package/v/ohdsi/SelfControlledCohort?label=%20" alt="Version" /></a></td>
 <td align="left">Jamie Gilbert</td>
@@ -659,7 +669,7 @@ <h1 class="title toc-ignore">Package statuses</h1>
 <td align="center"><a href="https://github.com/OHDSI/SelfControlledCohort/actions?query=workflow%3AR-CMD-check"><img src="https://github.com/OHDSI/SelfControlledCohort/workflows/R-CMD-check/badge.svg" alt="Build Status" /></a></td>
 <td align="center"><a href="https://codecov.io/github/OHDSI/SelfControlledCohort?branch=main"><img src="https://codecov.io/github/OHDSI/SelfControlledCohort/coverage.svg?branch=main" alt="codecov.io" /></a></td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="left"><a href="https://github.com/OHDSI/SqlRender">SqlRender</a></td>
 <td align="center"><a href="https://ohdsi.github.io/SqlRender/"><img src="https://img.shields.io/github/r-package/v/ohdsi/SqlRender?label=%20" alt="Version" /></a></td>
 <td align="left">Martijn Schuemie</td>

diff --git a/docs/packages.html b/docs/packages.html
@@ -531,6 +531,12 @@ <h4>
 </li>
 <li>
 <h4>
+<i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/PheValuator">PheValuator</a>
+</h4>
+Semi-automated evaluation of cohorts, producing metrics suchs as sensitivity, specificity, and positive and negative preditive value.</br><a href="https://ohdsi.github.io/PheValuator">Learn more…</a>
+</li>
+<li>
+<h4>
 <i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/CohortExplorer">CohortExplorer</a>
 </h4>
 Visually explore all individual-level data of patients in a cohort</br><a href="https://ohdsi.github.io/CohortExplorer">Learn more…</a>

diff --git a/docs/support.html b/docs/support.html
@@ -472,6 +472,7 @@ <h1>Bug reports</h1>
 <li><p><a href="https://github.com/OHDSI/ParallelLogger/issues">ParallelLogger issue tracker</a></p></li>
 <li><p><a href="https://github.com/OHDSI/PatientLevelPrediction/issues">PatientLevelPrediction issue tracker</a></p></li>
 <li><p><a href="https://github.com/OHDSI/PhenotypeLibrary/issues">PhenotypeLibrary issue tracker</a></p></li>
+<li><p><a href="https://github.com/OHDSI/PheValuator/issues">PheValuator issue tracker</a></p></li>
 <li><p><a href="https://github.com/OHDSI/ROhdsiWebApi/issues">ROhdsiWebApi issue tracker</a></p></li>
 <li><p><a href="https://github.com/OHDSI/SelfControlledCaseSeries/issues">SelfControlledCaseSeries issue tracker</a></p></li>
 <li><p><a href="https://github.com/OHDSI/SelfControlledCohort/issues">SelfControlledCohort issue tracker</a></p></li>

diff --git 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