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Adding Keeper to HADES
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schuemie committed Jun 18, 2024
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9 changes: 5 additions & 4 deletions DESCRIPTION
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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", , "[email protected]", role = c("aut", "cre")),
person("Observational Health Data Science and Informatics", role = c("cph"))
Expand Down Expand Up @@ -47,7 +47,8 @@ Imports:
ShinyAppBuilder,
DataQualityDashboard,
BrokenAdaptiveRidge,
Achilles
Achilles,
Keeper
Remotes:
ohdsi/BigKnn,
ohdsi/ROhdsiWebApi,
Expand All @@ -71,7 +72,7 @@ Remotes:
ohdsi/Characterization,
ohdsi/ShinyAppBuilder,
ohdsi/DataQualityDashboard,
ohdsi/Achilles
ohdsi/Keeper
LazyData: false
RoxygenNote: 7.2.0
Encoding: UTF-8
6 changes: 6 additions & 0 deletions NEWS.md
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HADES 1.14.0
============

- Adding Keeper to HADES


HADES 1.13.1
============

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1 change: 1 addition & 0 deletions Rmd/packageStatuses.Rmd
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Expand Up @@ -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)
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1 change: 1 addition & 0 deletions Rmd/packages.Rmd
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Expand Up @@ -35,6 +35,7 @@ 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/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>
<li><h4><i class="fas fa-cube "></i> <a href="https://ohdsi.github.io/Keeper">Keeper</a></h4>Knowledge-Enhanced Electronic Profile Review</br><a href="https://ohdsi.github.io/Keeper">Learn more...</a></li>
</ul>
<h2 id="pkg_header">Evidence Quality</h2>
<ul id="pkg">
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2 changes: 2 additions & 0 deletions Rmd/support.Rmd
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Expand Up @@ -58,6 +58,8 @@ Bug reports should be files using the issue tracker of the misbehaving package:

- [IterativeHardThresholding issue tracker](https://github.com/OHDSI/IterativeHardThresholding/issues)

- [Keeper issue tracker](https://github.com/OHDSI/Keeper/issues)

- [MethodEvaluation issue tracker](https://github.com/OHDSI/MethodEvaluation/issues)

- [OhdsiSharing issue tracker](https://github.com/OHDSI/OhdsiSharing/issues)
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<title>Code Style</title>

<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
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<title>Development Community</title>

<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
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<title>Connecting to a Database</title>

<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
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<title>Contribute</title>

<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>Developer Guidelines</title>

<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>Development Roadmap</title>

<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
Expand Down Expand Up @@ -494,6 +494,8 @@ <h1>Package milestones</h1>
<script>addMileStones('Hydra')</script>
<p id='IterativeHardThresholding'/>
<script>addMileStones('IterativeHardThresholding')</script>
<p id='Keeper'/>
<script>addMileStones('Keeper')</script>
<p id='MethodEvaluation'/>
<script>addMileStones('MethodEvaluation')</script>
<p id='OhdsiSharing'/>
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2 changes: 1 addition & 1 deletion docs/index.html
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<title>HADES</title>

<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
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2 changes: 1 addition & 1 deletion docs/installingHades.html
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<title>Installing HADES</title>

<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>HADES Package Requirements</title>

<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
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<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
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<title>Package statuses</title>

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<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
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Expand Down Expand Up @@ -1013,6 +1013,31 @@ <h1 class="title toc-ignore">Package statuses</h1>
</tr>
<tr class="odd">
<td align="left"><a
href="https://github.com/OHDSI/Keeper">Keeper</a></td>
<td align="center"><a href="https://ohdsi.github.io/Keeper/"><img
src="https://img.shields.io/github/r-package/v/ohdsi/Keeper?label=%20"
alt="Version" /></a></td>
<td align="left">Anna Ostropolets</td>
<td align="center">GitHub</td>
<td align="center"><a href="https://github.com/OHDSI/Keeper/issues"><img
src="https://img.shields.io/github/issues-raw/OHDSI/Keeper?label=%20"
alt="Open issues" /></a></td>
<td align="center"><a href="https://github.com/OHDSI/Keeper/pulls"><img
src="https://img.shields.io/github/issues-pr-raw/OHDSI/Keeper?label=%20"
alt="Open pull-requests" /></a></td>
<td align="center"><a
href="https://github.com/OHDSI/Keeper/actions/workflows/R_CMD_check_main_weekly.yaml"><img
src="https://github.com/ohdsi/Keeper/actions/workflows/R_CMD_check_main_weekly.yaml/badge.svg"
alt="Build Status" /></a></td>
<td align="center"><a
href="https://codecov.io/github/OHDSI/Keeper?branch=main"><img
src="https://codecov.io/github/OHDSI/Keeper/coverage.svg?branch=main"
alt="codecov.io" /></a></td>
<td align="left"><a
href="https://ohdsi.github.io/HadesFiles/pare_reports/Keeper.html">Report</a></td>
</tr>
<tr class="even">
<td align="left"><a
href="https://github.com/OHDSI/MethodEvaluation">MethodEvaluation</a></td>
<td align="center"><a
href="https://ohdsi.github.io/MethodEvaluation/"><img
Expand All @@ -1039,7 +1064,7 @@ <h1 class="title toc-ignore">Package statuses</h1>
<td align="left"><a
href="https://ohdsi.github.io/HadesFiles/pare_reports/MethodEvaluation.html">Report</a></td>
</tr>
<tr class="even">
<tr class="odd">
<td align="left"><a
href="https://github.com/OHDSI/OhdsiSharing">OhdsiSharing</a></td>
<td align="center"><a href="https://ohdsi.github.io/OhdsiSharing/"><img
Expand All @@ -1066,7 +1091,7 @@ <h1 class="title toc-ignore">Package statuses</h1>
<td align="left"><a
href="https://ohdsi.github.io/HadesFiles/pare_reports/OhdsiSharing.html">Report</a></td>
</tr>
<tr class="odd">
<tr class="even">
<td align="left"><a
href="https://github.com/OHDSI/OhdsiShinyModules">OhdsiShinyModules</a></td>
<td align="center"><a
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<td align="left"><a
href="https://ohdsi.github.io/HadesFiles/pare_reports/OhdsiShinyModules.html">Report</a></td>
</tr>
<tr class="even">
<tr class="odd">
<td align="left"><a
href="https://github.com/OHDSI/ParallelLogger">ParallelLogger</a></td>
<td align="center"><a
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<td align="left"><a
href="https://ohdsi.github.io/HadesFiles/pare_reports/ParallelLogger.html">Report</a></td>
</tr>
<tr class="odd">
<tr class="even">
<td align="left"><a
href="https://github.com/OHDSI/PatientLevelPrediction">PatientLevelPrediction</a></td>
<td align="center"><a
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<td align="left"><a
href="https://ohdsi.github.io/HadesFiles/pare_reports/PatientLevelPrediction.html">Report</a></td>
</tr>
<tr class="even">
<tr class="odd">
<td align="left"><a
href="https://github.com/OHDSI/PhenotypeLibrary">PhenotypeLibrary</a></td>
<td align="center"><a
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<td align="left"><a
href="https://ohdsi.github.io/HadesFiles/pare_reports/PhenotypeLibrary.html">Report</a></td>
</tr>
<tr class="odd">
<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
Expand All @@ -1205,7 +1230,7 @@ <h1 class="title toc-ignore">Package statuses</h1>
<td align="left"><a
href="https://ohdsi.github.io/HadesFiles/pare_reports/PheValuator.html">Report</a></td>
</tr>
<tr class="even">
<tr class="odd">
<td align="left"><a
href="https://github.com/OHDSI/ResultModelManager">ResultModelManager</a></td>
<td align="center"><a
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<td align="left"><a
href="https://ohdsi.github.io/HadesFiles/pare_reports/ResultModelManager.html">Report</a></td>
</tr>
<tr class="odd">
<tr class="even">
<td align="left"><a
href="https://github.com/OHDSI/ROhdsiWebApi">ROhdsiWebApi</a></td>
<td align="center"><a href="https://ohdsi.github.io/ROhdsiWebApi/"><img
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<td align="left"><a
href="https://ohdsi.github.io/HadesFiles/pare_reports/ROhdsiWebApi.html">Report</a></td>
</tr>
<tr class="even">
<tr class="odd">
<td align="left"><a
href="https://github.com/OHDSI/SelfControlledCaseSeries">SelfControlledCaseSeries</a></td>
<td align="center"><a
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<td align="left"><a
href="https://ohdsi.github.io/HadesFiles/pare_reports/SelfControlledCaseSeries.html">Report</a></td>
</tr>
<tr class="odd">
<tr class="even">
<td align="left"><a
href="https://github.com/OHDSI/SelfControlledCohort">SelfControlledCohort</a></td>
<td align="center"><a
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<td align="left"><a
href="https://ohdsi.github.io/HadesFiles/pare_reports/SelfControlledCohort.html">Report</a></td>
</tr>
<tr class="even">
<tr class="odd">
<td align="left"><a
href="https://github.com/OHDSI/ShinyAppBuilder">ShinyAppBuilder</a></td>
<td align="center"><a
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<td align="left"><a
href="https://ohdsi.github.io/HadesFiles/pare_reports/ShinyAppBuilder.html">Report</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
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10 changes: 9 additions & 1 deletion docs/packages.html
Original file line number Diff line number Diff line change
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<title>Packages</title>

<script src="site_libs/header-attrs-2.26/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.27/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
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cohort</br><a href="https://ohdsi.github.io/CohortExplorer">Learn
more…</a>
</li>
<li>
<h4>
<i class="fas fa-cube "></i>
<a href="https://ohdsi.github.io/Keeper">Keeper</a>
</h4>
Knowledge-Enhanced Electronic Profile
Review</br><a href="https://ohdsi.github.io/Keeper">Learn more…</a>
</li>
</ul>
<h2 id="pkg_header">
Evidence Quality
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