Merge branch 'main' into main

Rmd/index.Rmd

@@ -24,7 +24,7 @@ See the Support section for instructions on [setting up the R environment](rSetu
 
 ## Technology
 
-HADES is a set of R packages that execute against data in a database server. HADES supports traditional database systems (PostgreSQL, Microsoft SQL Server, and Oracle), parallel data warehouses (Microsoft APS, IBM Netezza, and Amazon RedShift), as well as 'Big Data' platforms (Hadoop through Apache Impala, Apache Spark, and Google BigQuery). HADES does *not* support MySQL. 
+HADES is a set of R packages that execute against data in a database server. HADES supports traditional database systems (PostgreSQL, Microsoft SQL Server, and Oracle), parallel data warehouses (e.g. Amazon RedShift), as well as 'Big Data' platforms (e.g. Google BigQuery). HADES does *not* support MySQL. The full list of supported database platforms can be found [here](supportedPlatforms.html).
 
 ## License
 

Rmd/installingHades.Rmd

@@ -35,4 +35,21 @@ options(install.packages.compile.from.source = "never")
 
 library(remotes)
 update_packages()
-```
+```
+
+# HADES-wide releases
+
+At the end of quarter 1 and 3 of each year a HADES-wide release is created. This is a snapshot of all HADES packages and their dependencies at one point in time. Additional checks are executed to ensure all packages and their dependencies work together. As such, these HADES-wide releases form a stable foundation for studies that may not require the absolute cutting-edge in HADES functionality.
+
+These releases are currently captured as [renv](https://rstudio.github.io/renv/articles/renv.html) lock files. The following releases are available:
+
+- 2023Q1: [renv lock file](https://raw.githubusercontent.com/OHDSI/Hades/main/hadesWideReleases/2023Q1/renv.lock)
+- 2023Q3: [renv lock file](https://raw.githubusercontent.com/OHDSI/Hades/main/hadesWideReleases/2023Q3/renv.lock)
+
+To build the R library corresponding to the latest release in your current RStudio project, you can use:
+
+```r
+download.file("https://raw.githubusercontent.com/OHDSI/Hades/main/hadesWideReleases/2023Q3/renv.lock", "renv.lock")
+install.packages("renv")
+renv::restore()
+```

docs/community.html

@@ -13,7 +13,7 @@
 
 <title>Development Community</title>
 
-<script src="site_libs/header-attrs-2.23/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.25/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-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 href="site_libs/font-awesome-6.4.2/css/all.min.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet" />
 <link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
 
 <style type="text/css">
@@ -441,34 +441,50 @@ <h1 class="title toc-ignore">Development Community</h1>
 </div>
 
 
-<p>HADES is developed and maintained by the HADES Workgroup of the OHDSI community.</p>
+<p>HADES is developed and maintained by the HADES Workgroup of the OHDSI
+community.</p>
 <div id="online-discussions" class="section level1">
 <h1>Online discussions</h1>
-<p>Online discussions can take place in the <a href="https://teams.microsoft.com/l/team/19%3ac0ff168a04954dc28c18c260133baa3c%40thread.tacv2/conversations?groupId=e6ddb436-9789-468e-820e-defbb0f1a11b&amp;tenantId=a30f0094-9120-4aab-ba4c-e5509023b2d5">HADES Teams</a> or on the <a href="https://forums.ohdsi.org/">OHDSI forums</a>.</p>
+<p>Online discussions can take place in the <a
+href="https://teams.microsoft.com/l/team/19%3ac0ff168a04954dc28c18c260133baa3c%40thread.tacv2/conversations?groupId=e6ddb436-9789-468e-820e-defbb0f1a11b&amp;tenantId=a30f0094-9120-4aab-ba4c-e5509023b2d5">HADES
+Teams</a> or on the <a href="https://forums.ohdsi.org/">OHDSI
+forums</a>.</p>
 </div>
 <div id="meetings" class="section level1">
 <h1>Meetings</h1>
-<p>The HADES workgroup has regular meetings. Meetings are open to all, and will be held on the third Thursday of the month. Time (DST where appropriate):</p>
+<p>The HADES workgroup has regular meetings. Meetings are open to all,
+and will be held on the third Thursday of the month. Time (DST where
+appropriate):</p>
 <ul>
 <li><strong>6pm Central European time</strong></li>
 <li><strong>5pm UK time</strong></li>
-<li><strong>12pm (noon) Eastern Time</strong> (New York / New Jersey / Pennsylvania)</li>
+<li><strong>12pm (noon) Eastern Time</strong> (New York / New Jersey /
+Pennsylvania)</li>
 <li><strong>9am Pacific Time</strong> (Los Angeles / Stanford)</li>
 </ul>
 <p>Teams meeting details:</p>
-<p>URL: <a href="https://teams.microsoft.com/l/meetup-join/19%3ac0ff168a04954dc28c18c260133baa3c%40thread.tacv2/1602145307087?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%22dac1472c-1cc6-41dc-9cc7-c4720f7798de%22%7d">Join Microsoft Teams Meeting</a></p>
+<p>URL: <a
+href="https://teams.microsoft.com/l/meetup-join/19%3ac0ff168a04954dc28c18c260133baa3c%40thread.tacv2/1602145307087?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%22dac1472c-1cc6-41dc-9cc7-c4720f7798de%22%7d">Join
+Microsoft Teams Meeting</a></p>
 </div>
 <div id="package-maintainers" class="section level1">
 <h1>Package maintainers</h1>
-<p>Each package in HADES has one or two maintainers. These maintainers have the final responsibility and authority over their package. These are the expectations of package maintainers:</p>
+<p>Each package in HADES has one or two maintainers. These maintainers
+have the final responsibility and authority over their package. These
+are the expectations of package maintainers:</p>
 <ul>
 <li>Represent the package in the HADES group discussions.</li>
 <li>Ensure that issues are resolved in a timely manner.</li>
 <li>Review and merge pull requests.</li>
-<li>Create releases (and communicate upcoming releases to those that need to know).</li>
-<li>Adapt the package to changes in its dependencies (including R packages, R itself, and the infrastructure).</li>
-<li>Develop new functionality depending on the needs of the community.</li>
-<li>Adhere to and enforce the HADES standards, such as the <a href="developerGuidelines.html">Developer Guidelines</a> and <a href="codeStyle.html">Code Style Guide</a>.</li>
+<li>Create releases (and communicate upcoming releases to those that
+need to know).</li>
+<li>Adapt the package to changes in its dependencies (including R
+packages, R itself, and the infrastructure).</li>
+<li>Develop new functionality depending on the needs of the
+community.</li>
+<li>Adhere to and enforce the HADES standards, such as the <a
+href="developerGuidelines.html">Developer Guidelines</a> and <a
+href="codeStyle.html">Code Style Guide</a>.</li>
 </ul>
 </div>
 

docs/connecting.html

@@ -13,7 +13,7 @@
 
 <title>Connecting to a Database</title>
 
-<script src="site_libs/header-attrs-2.23/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.25/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-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 href="site_libs/font-awesome-6.4.2/css/all.min.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet" />
 <link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
 
 <style type="text/css">
@@ -441,15 +441,26 @@ <h1 class="title toc-ignore">Connecting to a Database</h1>
 </div>
 
 
-<p>Most HADES packages will need to interact with a database, for example a database containing healthcare data in the <a href="https://ohdsi.github.io/CommonDataModel/">Common Data Model</a>. HADES provides the <code>DatabaseConnector</code> package to make these connections.</p>
+<p>Most HADES packages will need to interact with a database, for
+example a database containing healthcare data in the <a
+href="https://ohdsi.github.io/CommonDataModel/">Common Data Model</a>.
+HADES provides the <code>DatabaseConnector</code> package to make these
+connections.</p>
 <div id="installing-databaseconnector" class="section level2">
 <h2>Installing DatabaseConnector</h2>
-<p>To connect to a database, you must first make sure the <code>DatabaseConnector</code> is installed. If you have <a href="installingHades.html">installed all of HADES</a> you will already have installed <code>DatabaseConnector</code>. Otherwise, you can install <code>DatabaseConnector</code> from CRAN using:</p>
+<p>To connect to a database, you must first make sure the
+<code>DatabaseConnector</code> is installed. If you have <a
+href="installingHades.html">installed all of HADES</a> you will already
+have installed <code>DatabaseConnector</code>. Otherwise, you can
+install <code>DatabaseConnector</code> from CRAN using:</p>
 <pre class="r"><code>install.package(&quot;DatabaseConnector&quot;)</code></pre>
 </div>
 <div id="configuring-your-connection" class="section level2">
 <h2>Configuring your connection</h2>
-<p>After <code>DatabaseConnector</code> is installed, several steps will need to be taken to configure the connection to your database. See <a href="http://ohdsi.github.io/DatabaseConnector/articles/Connecting.html">this vignette</a> for instructions.</p>
+<p>After <code>DatabaseConnector</code> is installed, several steps will
+need to be taken to configure the connection to your database. See <a
+href="http://ohdsi.github.io/DatabaseConnector/articles/Connecting.html">this
+vignette</a> for instructions.</p>
 </div>
 
 

docs/contribute.html

@@ -13,7 +13,7 @@
 
 <title>Contribute</title>
 
-<script src="site_libs/header-attrs-2.23/header-attrs.js"></script>
+<script src="site_libs/header-attrs-2.25/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-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 href="site_libs/font-awesome-6.4.2/css/all.min.css" rel="stylesheet" />
+<link href="site_libs/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet" />
 <link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
 
 <style type="text/css">
@@ -441,18 +441,36 @@ <h1 class="title toc-ignore">Contribute</h1>
 </div>
 
 
-<p>HADES is built by the community for the community. No matter what you skill level, there is always a way for you to contribute:</p>
+<p>HADES is built by the community for the community. No matter what you
+skill level, there is always a way for you to contribute:</p>
 <div id="file-bug-reports" class="section level1">
 <h1>File bug reports</h1>
-<p>If you’ve found a bug you can help out by filing a bug report. Each package has an issue tracker where you can create a new issue. Try and be as specific as possible. What error message occurs? Can you provide a simple example to reproduce the problem? What versions of the various packages are you running?</p>
+<p>If you’ve found a bug you can help out by filing a bug report. Each
+package has an issue tracker where you can create a new issue. Try and
+be as specific as possible. What error message occurs? Can you provide a
+simple example to reproduce the problem? What versions of the various
+packages are you running?</p>
 </div>
 <div id="write-help-files" class="section level1">
 <h1>Write help files</h1>
-<p>If you’re a bit more experienced with HADES and are looking to improve your open source development skills, the next step up is to contribute a pull request to a HADES package. The most important thing to know is that HADES packages use <a href="https://github.com/klutometis/roxygen">roxygen2</a>: this means that documentation is found in the R code close to the source of each function.</p>
+<p>If you’re a bit more experienced with HADES and are looking to
+improve your open source development skills, the next step up is to
+contribute a pull request to a HADES package. The most important thing
+to know is that HADES packages use <a
+href="https://github.com/klutometis/roxygen">roxygen2</a>: this means
+that documentation is found in the R code close to the source of each
+function.</p>
 </div>
 <div id="write-unit-tests" class="section level1">
 <h1>Write unit tests</h1>
-<p>An important part of validating the methods in the library is unit testing. A unit test is a small program that tests a specific function in the library. For example, there are <a href="https://github.com/OHDSI/CohortMethod/blob/main/tests/testthat/test-psFunctions.R#L5">several unit tests</a> that make sure the propensity score matching works correctly. We can never have enough unit tests, and writing unit tests is an excellent way to learn how HADES packages work under the hood. Make sure you read through the Develops section first!</p>
+<p>An important part of validating the methods in the library is unit
+testing. A unit test is a small program that tests a specific function
+in the library. For example, there are <a
+href="https://github.com/OHDSI/CohortMethod/blob/main/tests/testthat/test-psFunctions.R#L5">several
+unit tests</a> that make sure the propensity score matching works
+correctly. We can never have enough unit tests, and writing unit tests
+is an excellent way to learn how HADES packages work under the hood.
+Make sure you read through the Develops section first!</p>
 </div>