Adding CohortGenerator as HADES package

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: Hades
 Type: Package
 Title: Health Analytics Data-to-Evidence Suite
-Version: 1.0.1
-Date: 2021-12-14
+Version: 1.1.0
+Date: 2021-12-17
 Authors@R: c(
   person("Martijn", "Schuemie", , "[email protected]", role = c("aut", "cre")),
   person("Observational Health Data Science and Informatics", role = c("cph"))
@@ -27,6 +27,7 @@ Imports:
   FeatureExtraction,
   CohortDiagnostics,
   CohortMethod,
+  CohortGenerator,
   SelfControlledCaseSeries,
   SelfControlledCohort,
   PatientLevelPrediction,
@@ -46,7 +47,8 @@ Remotes:
   ohdsi/OhdsiSharing,
   ohdsi/Hydra,
   ohdsi/CirceR,
-  ohdsi/Eunomia
+  ohdsi/Eunomia,
+  ohdsi/CohortGenerator
 LazyData: false
 RoxygenNote: 7.1.1
 Encoding: UTF-8

Rmd/packageStatuses.Rmd

@@ -22,6 +22,7 @@ The table below lists, for each of the HADES packages, the following details:
 | [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=master)](https://codecov.io/github/OHDSI/BigKnn?branch=master) |
 | [CirceR](https://github.com/OHDSI/CirceR) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/CirceR?label=%20)](https://ohdsi.github.io/CirceR/) | Chris Knoll | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/CirceR?label=%20)](https://github.com/OHDSI/CirceR/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/CirceR?label=%20)](https://github.com/OHDSI/CirceR/pulls) | [![Build Status](https://github.com/OHDSI/CirceR/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/CirceR/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/CirceR/coverage.svg?branch=master)](https://codecov.io/github/OHDSI/CirceR?branch=master) |
 | [CohortDiagnostics](https://github.com/OHDSI/CohortDiagnostics) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/CohortDiagnostics?label=%20)](https://ohdsi.github.io/CohortDiagnostics/) | Gowtham Rao | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/CohortDiagnostics?label=%20)](https://github.com/OHDSI/CohortDiagnostics/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/CohortDiagnostics?label=%20)](https://github.com/OHDSI/CohortDiagnostics/pulls) | [![Build Status](https://github.com/OHDSI/CohortDiagnostics/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/CohortDiagnostics/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/CohortDiagnostics/coverage.svg?branch=master)](https://codecov.io/github/OHDSI/CohortDiagnostics?branch=master) |
+| [CohortGenerator](https://github.com/OHDSI/CohortGenerator) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/CohortGenerator?label=%20)](https://ohdsi.github.io/CohortGenerator/) | Anthony Sena | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/CohortGenerator?label=%20)](https://github.com/OHDSI/CohortGenerator/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/CohortGenerator?label=%20)](https://github.com/OHDSI/CohortGenerator/pulls) | [![Build Status](https://github.com/OHDSI/CohortGenerator/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/CohortGenerator/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/CohortGenerator/coverage.svg?branch=master)](https://codecov.io/github/OHDSI/CohortGenerator?branch=master) |
 | [CohortMethod](https://github.com/OHDSI/CohortMethod) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/CohortMethod?label=%20)](https://ohdsi.github.io/CohortMethod/) | Martijn Schuemie  | GitHub | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/CohortMethod?label=%20)](https://github.com/OHDSI/CohortMethod/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/CohortMethod?label=%20)](https://github.com/OHDSI/CohortMethod/pulls) | [![Build Status](https://github.com/OHDSI/CohortMethod/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/CohortMethod/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/CohortMethod/coverage.svg?branch=master)](https://codecov.io/github/OHDSI/CohortMethod?branch=master) |
 | [Cyclops](https://github.com/OHDSI/Cyclops) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/Cyclops?label=%20)](https://ohdsi.github.io/Cyclops/) | Marc Suchard | CRAN | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/Cyclops?label=%20)](https://github.com/OHDSI/Cyclops/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/Cyclops?label=%20)](https://github.com/OHDSI/Cyclops/pulls) | [![Build Status](https://github.com/OHDSI/Cyclops/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/Cyclops/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/Cyclops/coverage.svg?branch=master)](https://codecov.io/github/OHDSI/Cyclops?branch=master) |
 | [DatabaseConnector](https://github.com/OHDSI/DatabaseConnector) | [![Version](https://img.shields.io/github/r-package/v/ohdsi/DatabaseConnector?label=%20)](https://ohdsi.github.io/DatabaseConnector/) | Martijn Schuemie  | CRAN | [![Open issues](https://img.shields.io/github/issues-raw/OHDSI/DatabaseConnector?label=%20)](https://github.com/OHDSI/DatabaseConnector/issues) | [![Open pull-requests](https://img.shields.io/github/issues-pr-raw/OHDSI/DatabaseConnector?label=%20)](https://github.com/OHDSI/DatabaseConnector/pulls) | [![Build Status](https://github.com/OHDSI/DatabaseConnector/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/DatabaseConnector/actions?query=workflow%3AR-CMD-check) | [![codecov.io](https://codecov.io/github/OHDSI/DatabaseConnector/coverage.svg?branch=master)](https://codecov.io/github/OHDSI/DatabaseConnector?branch=master) |

Rmd/packages.Rmd

@@ -28,16 +28,17 @@ Below are the packages included in HADES. For each package a link is provided wi
 </ul>
 <h2 id="pkg_header">Supporting packages</h2>
 <ul id="pkg">
+<li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/Andromeda">Andromeda</a></h4>Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.</br><a href="https://ohdsi.github.io/Andromeda">Learn more...</a></li>
+<li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/BigKnn">BigKnn</a></h4>A large scale k-nearest neighbor classifier using the Lucene search engine.</br><a href="https://ohdsi.github.io/BigKnn">Learn more...</a></li>
+<li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/CirceR">CirceR</a></h4>An R wrapper for Circe, a library for creating cohort definitions, expressing them as JSON, SQL, or Markdown.</br><a href="https://ohdsi.github.io/CirceR">Learn more...</a></li>
+<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/Cyclops">Cyclops</a></h4>Highly efficient implementation of regularized logistic, Poisson and Cox regression.</br><a href="https://ohdsi.github.io/Cyclops">Learn more...</a></li>
 <li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/DatabaseConnector">DatabaseConnector</a></h4>Connect directly to a wide range of database platforms, including SQL Server, Oracle, and PostgreSQL.</br><a href="https://ohdsi.github.io/DatabaseConnector">Learn more...</a></li>
-<li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/SqlRender">SqlRender</a></h4>Generate SQL on the fly for the various SQL dialects.</br><a href="https://ohdsi.github.io/SqlRender">Learn more...</a></li>
-<li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/ParallelLogger">ParallelLogger</a></h4>Support for parallel computation with logging to console, disk, or e-mail.</br><a href="https://ohdsi.github.io/ParallelLogger">Learn more...</a></li>
+<li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/Eunomia">Eunomia</a></h4>A standard CDM dataset for testing and demonstration purposes that runs on an embedded SQLite database.</br><a href="https://ohdsi.github.io/Eunomia">Learn more...</a></li>
 <li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/FeatureExtraction">FeatureExtraction</a></h4>Automatically extract large sets of features for user-specified cohorts using data in the CDM.</br><a href="https://ohdsi.github.io/FeatureExtraction">Learn more...</a></li>
-<li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/Andromeda">Andromeda</a></h4>Storing very large data objects on a local drive, while still making it possible to manipulate the data in an efficient manner.</br><a href="https://ohdsi.github.io/Andromeda">Learn more...</a></li>
-<li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/BigKnn">BigKnn</a></h4>A large scale k-nearest neighbor classifier using the Lucene search engine.</br><a href="https://ohdsi.github.io/BigKnn">Learn more...</a></li>
-<li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/ROhdsiWebApi">ROhdsiWebApi</a></h4>Interact with OHDSI WebAPI web services.</br><a href="https://ohdsi.github.io/ROhdsiWebApi">Learn more...</a></li>
-<li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/OhdsiSharing">OhdsiSharing</a></h4>Securely sharing (large) files between OHDSI collaborators.</br><a href="https://ohdsi.github.io/OhdsiSharing">Learn more...</a></li>
 <li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/Hydra">Hydra</a></h4>Hydrating package skeletons into executable R study packages based on specifications in JSON format.</br><a href="https://ohdsi.github.io/Hydra">Learn more...</a></li>
-<li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/Eunomia">Eunomia</a></h4>A standard CDM dataset for testing and demonstration purposes that runs on an embedded SQLite database.</br><a href="https://ohdsi.github.io/Eunomia">Learn more...</a></li>
-<li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/CirceR">CirceR</a></h4>An R wrapper for Circe, a library for creating cohort definitions, expressing them as JSON, SQL, or Markdown.</br><a href="https://ohdsi.github.io/CirceR">Learn more...</a></li>
+<li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/OhdsiSharing">OhdsiSharing</a></h4>Securely sharing (large) files between OHDSI collaborators.</br><a href="https://ohdsi.github.io/OhdsiSharing">Learn more...</a></li>
+<li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/ParallelLogger">ParallelLogger</a></h4>Support for parallel computation with logging to console, disk, or e-mail.</br><a href="https://ohdsi.github.io/ParallelLogger">Learn more...</a></li>
+<li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/ROhdsiWebApi">ROhdsiWebApi</a></h4>Interact with OHDSI WebAPI web services.</br><a href="https://ohdsi.github.io/ROhdsiWebApi">Learn more...</a></li>
+<li><h4><i class="fas  fa-cube "></i> <a href="https://ohdsi.github.io/SqlRender">SqlRender</a></h4>Generate SQL on the fly for the various SQL dialects.</br><a href="https://ohdsi.github.io/SqlRender">Learn more...</a></li>
 </ul>

Rmd/support.Rmd

@@ -22,6 +22,8 @@ Bug reports should be files using the issue tracker of the misbehaving package:
 
 - [CohortDiagnostics issue tracker](https://github.com/OHDSI/CohortDiagnostics/issues)
 
+- [CohortGenerator issue tracker](https://github.com/OHDSI/CohortGenerator/issues)
+
 - [CohortMethod issue tracker](https://github.com/OHDSI/CohortMethod/issues)
 
 - [Cyclops issue tracker](https://github.com/OHDSI/Cyclops/issues)