Adding ACHILLES

OHDSI · May 19, 2023 · 8904a27 · 8904a27
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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: 1.12.0
-Date: 2023-04-13
+Version: 1.13.0
+Date: 2023-05-19
 Authors@R: c(
   person("Martijn", "Schuemie", , "[email protected]", role = c("aut", "cre")),
   person("Observational Health Data Science and Informatics", role = c("cph"))
@@ -46,7 +46,8 @@ Imports:
   Characterization,
   ShinyAppBuilder,
   DataQualityDashboard,
-  BrokenAdaptiveRidge
+  BrokenAdaptiveRidge,
+  Achilles
 Remotes:
   ohdsi/BigKnn,
   ohdsi/ROhdsiWebApi,
@@ -72,7 +73,8 @@ Remotes:
   ohdsi/ResultModelManager,
   ohdsi/Characterization,
   ohdsi/ShinyAppBuilder,
-  ohdsi/DataQualityDashboard
+  ohdsi/DataQualityDashboard,
+  ohdsi/Achilles
 LazyData: false
 RoxygenNote: 7.2.0
 Encoding: UTF-8
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+HADES 1.13.0
+============
+
+- Adding Achilles to HADES
+
 HADES 1.12.0
 ============
 

diff --git a/Rmd/packageStatuses.Rmd b/Rmd/packageStatuses.Rmd
@@ -18,6 +18,7 @@ The table below lists, for each of the HADES packages, the following details:
 
 | Package            | Version | Maintainer(s)   | Availability | Open issues | Open pull-requests | Build status | Coverage   |
 | :----------------- | :----: |:--------------- | :------: | :------: | :------: | :------------: | :----------: |
+| [Achilles](https://github.com/OHDSI/Achilles) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/Achilles?label=%20)](https://ohdsi.github.io/Achilles/) | Frank DeFalco | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/Achilles?label=%20)](https://github.com/OHDSI/Achilles/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/Achilles?label=%20)](https://github.com/OHDSI/Achilles/pulls) | [![Build Status](https://github.com/OHDSI/Achilles/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/Achilles/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/Achilles/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/Achilles?branch=main) |
 | [Andromeda](https://github.com/OHDSI/Andromeda) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/Andromeda?label=%20)](https://ohdsi.github.io/Andromeda/) | Adam Black | CRAN | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/Andromeda?label=%20)](https://github.com/OHDSI/Andromeda/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/Andromeda?label=%20)](https://github.com/OHDSI/Andromeda/pulls) | [![Build Status](https://github.com/OHDSI/Andromeda/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/Andromeda/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/Andromeda/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/Andromeda?branch=main) |
 | [BigKnn](https://github.com/OHDSI/BigKnn) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/BigKnn?label=%20)](https://ohdsi.github.io/BigKnn/) | Martijn Schuemie  | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/BigKnn?label=%20)](https://github.com/OHDSI/BigKnn/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/BigKnn?label=%20)](https://github.com/OHDSI/BigKnn/pulls) | [![Build Status](https://github.com/OHDSI/BigKnn/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/BigKnn/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/BigKnn/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/BigKnn?branch=main) |
 | [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/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/BrokenAdaptiveRidge/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/BrokenAdaptiveRidge/coverage.svg?branch=main)](https://codecov.io/github/OHDSI/BrokenAdaptiveRidge?branch=main) |

diff --git a/Rmd/packages.Rmd b/Rmd/packages.Rmd
@@ -38,6 +38,7 @@ Below are the packages included in HADES. For each package a link is provided wi
 </ul>
 <h2 id="pkg_header">Evidence Quality</h2>
 <ul id="pkg">
+<li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/Achilles">Achilles</a></h4>Generate descriptive statistics on an entire OMOP CDM database</br><a href="https://ohdsi.github.io/Achilles">Learn more...</a></li>
 <li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/DataQualityDashboard">DataQualityDashboard</a></h4>Expose and evaluate observational data quality.</br><a href="https://ohdsi.github.io/DataQualityDashboard">Learn more...</a></li>
 <li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/EmpiricalCalibration">EmpiricalCalibration</a></h4>Use negative control exposure-outcome pairs to profile and calibrate a particular analysis design.</br><a href="https://ohdsi.github.io/EmpiricalCalibration">Learn more...</a></li>
 <li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/MethodEvaluation">MethodEvaluation</a></h4>Use real data and established reference sets as well as simulations injected in real data to evaluate the performance of methods.</br><a href="https://ohdsi.github.io/MethodEvaluation">Learn more...</a></li>

diff --git a/Rmd/support.Rmd b/Rmd/support.Rmd
@@ -14,6 +14,8 @@ Questions about HADES can be asked on the [OHDSI Forums](http://forums.ohdsi.org
 
 Bug reports should be files using the issue tracker of the misbehaving package:
 
+- [Achilles issue tracker](https://github.com/OHDSI/Achilles/issues)
+
 - [Andromeda issue tracker](https://github.com/OHDSI/Andromeda/issues)
 
 - [BigKnn issue tracker](https://github.com/OHDSI/BigKnn/issues)

diff --git a/docs/codeStyle.html b/docs/codeStyle.html
@@ -13,7 +13,7 @@
 
 <title>Code Style</title>
 
-<script src="site_libs/header-attrs-2.20/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.21/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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@@ -35,8 +35,8 @@
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 <script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
-<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
-<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.0/css/all.min.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.0/css/v4-shims.min.css" rel="stylesheet" />
 <link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
 
 <style type="text/css">

diff --git a/docs/community.html b/docs/community.html
@@ -13,7 +13,7 @@
 
 <title>Development Community</title>
 
-<script src="site_libs/header-attrs-2.20/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.21/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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@@ -35,8 +35,8 @@
 <script src="site_libs/navigation-1.1/tabsets.js"></script>
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 <script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
-<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
-<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.0/css/all.min.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.0/css/v4-shims.min.css" rel="stylesheet" />
 <link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
 
 <style type="text/css">

diff --git a/docs/connecting.html b/docs/connecting.html
@@ -13,7 +13,7 @@
 
 <title>Connecting to a Database</title>
 
-<script src="site_libs/header-attrs-2.20/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.21/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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@@ -35,8 +35,8 @@
 <script src="site_libs/navigation-1.1/tabsets.js"></script>
 <link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
 <script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
-<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
-<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.0/css/all.min.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.0/css/v4-shims.min.css" rel="stylesheet" />
 <link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
 
 <style type="text/css">

diff --git a/docs/contribute.html b/docs/contribute.html
@@ -13,7 +13,7 @@
 
 <title>Contribute</title>
 
-<script src="site_libs/header-attrs-2.20/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.21/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" />
@@ -35,8 +35,8 @@
 <script src="site_libs/navigation-1.1/tabsets.js"></script>
 <link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
 <script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
-<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
-<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.0/css/all.min.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.0/css/v4-shims.min.css" rel="stylesheet" />
 <link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
 
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diff --git a/docs/developerGuidelines.html b/docs/developerGuidelines.html
@@ -13,7 +13,7 @@
 
 <title>Developer Guidelines</title>
 
-<script src="site_libs/header-attrs-2.20/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.21/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" />
@@ -35,8 +35,8 @@
 <script src="site_libs/navigation-1.1/tabsets.js"></script>
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 <script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
-<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
-<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.0/css/all.min.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.0/css/v4-shims.min.css" rel="stylesheet" />
 <link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
 
 <style type="text/css">

diff --git a/docs/developmentRoadmap.html b/docs/developmentRoadmap.html
@@ -13,7 +13,7 @@
 
 <title>Development Roadmap</title>
 
-<script src="site_libs/header-attrs-2.20/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.21/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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@@ -35,8 +35,8 @@
 <script src="site_libs/navigation-1.1/tabsets.js"></script>
 <link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
 <script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
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-<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.0/css/all.min.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.0/css/v4-shims.min.css" rel="stylesheet" />
 <link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
 
 <style type="text/css">
@@ -442,6 +442,8 @@ <h1 class="title toc-ignore">Development Roadmap</h1>
 <h1>Package milestones</h1>
 <p>For each of the HADES packages we try to define milestones corresponding to future releases. Here’s an overview of these milestones:</p>
 <script src="milestones.js"></script>
+<p id='Achilles'/>
+<script>addMileStones('Achilles')</script>
 <p id='Andromeda'/>
 <script>addMileStones('Andromeda')</script>
 <p id='BigKnn'/>

diff --git a/docs/index.html b/docs/index.html
@@ -13,7 +13,7 @@
 
 <title>HADES</title>
 
-<script src="site_libs/header-attrs-2.20/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.21/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" />
@@ -35,8 +35,8 @@
 <script src="site_libs/navigation-1.1/tabsets.js"></script>
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 <script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
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-<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.0/css/all.min.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.0/css/v4-shims.min.css" rel="stylesheet" />
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 <style type="text/css">

diff --git a/docs/installingHades.html b/docs/installingHades.html
@@ -13,7 +13,7 @@
 
 <title>Installing HADES</title>
 
-<script src="site_libs/header-attrs-2.20/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.21/header-attrs.js"></script>
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 <meta name="viewport" content="width=device-width, initial-scale=1" />
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@@ -35,8 +35,8 @@
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+<link href="site_libs/font-awesome-6.4.0/css/all.min.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.0/css/v4-shims.min.css" rel="stylesheet" />
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diff --git a/docs/packageRequirements.html b/docs/packageRequirements.html
@@ -13,7 +13,7 @@
 
 <title>HADES Package Requirements</title>
 
-<script src="site_libs/header-attrs-2.20/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.21/header-attrs.js"></script>
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@@ -35,8 +35,8 @@
 <script src="site_libs/navigation-1.1/tabsets.js"></script>
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-<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.0/css/all.min.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.0/css/v4-shims.min.css" rel="stylesheet" />
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 <style type="text/css">