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Fixing build status badge and link on package status page
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schuemie committed Oct 9, 2023
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70 changes: 35 additions & 35 deletions Rmd/packageStatuses.Rmd
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128 changes: 95 additions & 33 deletions docs/codeStyle.html
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42 changes: 29 additions & 13 deletions docs/community.html
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<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" />
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<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-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">
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</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>

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23 changes: 17 additions & 6 deletions docs/connecting.html
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<title>Connecting to a Database</title>

<script src="site_libs/header-attrs-2.23/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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<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
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</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>


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32 changes: 25 additions & 7 deletions docs/contribute.html
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<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>
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<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
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<link href="site_libs/font-awesome-6.4.0/css/all.min.css" rel="stylesheet" />
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<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' />

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</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>


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