dsBase/docs/index.html at 69e0bf65a4e7ab6bdeb7a20299972fa62759fafe · StuartWheater/dsBase · GitHub

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<meta property="og:description" content='Base DataSHIELD functions for the server side. DataSHIELD is a software package which allows you to do non-disclosive federated analysis on sensitive data. DataSHIELD analytic functions have been designed to only share non disclosive summary statistics, with built in automated output checking based on statistical disclosure control. With data sites setting the threshold values for the automated output checks. For more details, see citation("dsBase").'>
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<div class="section level2">
<h2 id="dsbase-datashield-server-side-base-functions">dsBase: ‘DataSHIELD’ Server Side Base Functions<a class="anchor" aria-label="anchor" href="#dsbase-datashield-server-side-base-functions"></a>
</h2>
<p><a href="https://www.gnu.org/licenses/gpl-3.0.html" class="external-link"><img src="https://img.shields.io/badge/License-GPLv3-blue.svg" alt="License"></a> <a href="https://cran.r-project.org/package=dsBase" class="external-link"><img src="https://www.r-pkg.org/badges/version/dsBase?color=black"></a> <a href="https://github.com/datashield/dsBase/actions" class="external-link"><img src="https://github.com/datashield/dsBase/workflows/R-CMD-check/badge.svg" alt="R build status"></a> <a href="https://app.codecov.io/gh/datashield/dsBase" class="external-link"><img src="https://codecov.io/gh/datashield/dsBase/graph/badge.svg" alt="Codecov test coverage"></a></p>
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<div class="section level2">
<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
</h2>
<p>You can install the released version of dsBase from <a href="https://cran.r-project.org/package=dsBase" class="external-link">CRAN</a> with:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"dsBase"</span><span class="op">)</span></span></code></pre></div>
<p>And the development version from <a href="https://github.com/datashield/dsBase/" class="external-link">GitHub</a> with: <!-- You can install the development version from [GitHub](https://github.com/) with: --></p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span></span>
<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"datashield/dsBase"</span>, <span class="st">"&lt;BRANCH&gt;"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Install v6.3.4 with the following</span></span>
<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"datashield/dsBase"</span>, <span class="st">"6.3.4"</span><span class="op">)</span></span></code></pre></div>
<p>For a full list of development branches, checkout <a href="https://github.com/datashield/dsBase/branches" class="external-link uri">https://github.com/datashield/dsBase/branches</a></p>
</div>
<div class="section level2">
<h2 id="about">About<a class="anchor" aria-label="anchor" href="#about"></a>
</h2>
<p>DataSHIELD is a software package which allows you to do non-disclosive federated analysis on sensitive data. Our website (<a href="https://www.datashield.org" class="external-link uri">https://www.datashield.org</a>) has in depth descriptions of what it is, how it works and how to install it. A key point to highlight is that DataSHIELD has a client-server infrastructure, so the dsBase package (<a href="https://github.com/datashield/dsBase" class="external-link uri">https://github.com/datashield/dsBase</a>) needs to be used in conjunction with the dsBaseClient package (<a href="https://github.com/datashield/dsBaseClient" class="external-link uri">https://github.com/datashield/dsBaseClient</a>) - trying to use one without the other makes no sense.</p>
<p>Detailed instructions on how to install DataSHIELD are at <a href="https://wiki.datashield.org/" class="external-link uri">https://wiki.datashield.org/</a>. The code here is organised as:</p>
<table class="table">
<colgroup>
<col width="70%">
<col width="30%">
</colgroup>
<thead><tr class="header">
<th>Location</th>
<th>What is it?</th>
</tr></thead>
<tbody>
<tr class="odd">
<td>obiba CRAN</td>
<td>Where you probably should install DataSHIELD from.</td>
</tr>
<tr class="even">
<td>releases</td>
<td>Stable releases.</td>
</tr>
<tr class="odd">
<td>master branch</td>
<td>Mostly in sync with the latest release, changes rarely.</td>
</tr>
</tbody>
</table>
</div>
<div class="section level2">
<h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a>
</h2>
<p>[1] Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Bishop T, Gaye A, Escribà Montagut X, Wheater S (2025). <em>dsBase: ‘DataSHIELD’ Server Side Base Functions</em>. R package version 6.3.4. <a href="https://doi.org/10.32614/CRAN.package.dsBase" class="external-link uri">https://doi.org/10.32614/CRAN.package.dsBase</a>.</p>
<p>[2] Gaye A, Marcon Y, Isaeva J, LaFlamme P, Turner A, Jones E, Minion J, Boyd A, Newby C, Nuotio M, Wilson R, Butters O, Murtagh B, Demir I, Doiron D, Giepmans L, Wallace S, Budin-Ljøsne I, Oliver Schmidt C, Boffetta P, Boniol M, Bota M, Carter K, deKlerk N, Dibben C, Francis R, Hiekkalinna T, Hveem K, Kvaløy K, Millar S, Perry I, Peters A, Phillips C, Popham F, Raab G, Reischl E, Sheehan N, Waldenberger M, Perola M, van den Heuvel E, Macleod J, Knoppers B, Stolk R, Fortier I, Harris J, Woffenbuttel B, Murtagh M, Ferretti V, Burton P (2014). “DataSHIELD: taking the analysis to the data, not the data to the analysis.” <em>International Journal of Epidemiology</em>, <em>43</em>(6), 1929-1944. <a href="https://doi.org/10.1093/ije/dyu188" class="external-link uri">https://doi.org/10.1093/ije/dyu188</a>.</p>
<p>[3] Wilson R, W. Butters O, Avraam D, Baker J, Tedds J, Turner A, Murtagh M, R. Burton P (2017). “DataSHIELD – New Directions and Dimensions.” <em>Data Science Journal</em>, <em>16</em>(21), 1-21. <a href="https://doi.org/10.5334/dsj-2017-021" class="external-link uri">https://doi.org/10.5334/dsj-2017-021</a>.</p>
<p>[4] Avraam D, Wilson R, Aguirre Chan N, Banerjee S, Bishop T, Butters O, Cadman T, Cederkvist L, Duijts L, Escribà Montagut X, Garner H, Gonçalves G, González J, Haakma S, Hartlev M, Hasenauer J, Huth M, Hyde E, Jaddoe V, Marcon Y, Mayrhofer M, Molnar-Gabor F, Morgan A, Murtagh M, Nestor M, Nybo Andersen A, Parker S, Pinot de Moira A, Schwarz F, Strandberg-Larsen K, Swertz M, Welten M, Wheater S, Burton P (2024). “DataSHIELD: mitigating disclosure risk in a multi-site federated analysis platform.” <em>Bioinformatics Advances</em>, <em>5</em>(1), 1-21. <a href="https://doi.org/10.1093/bioadv/vbaf046" class="external-link uri">https://doi.org/10.1093/bioadv/vbaf046</a>.</p>
<blockquote>
<p><strong><em>Note:</em></strong> Apple Mx architecture users, please be aware that there are some numerical limitations on this platform, which leads to unexpected results when using base R packages, like stats.</p>
<p>x &lt;- c(0, 3, 7)</p>
<p>1 - cor(x, x)</p>
<p>The above should result in a value of zero.</p>
<p><em>Also See:</em> For more details see <a href="https://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f" class="external-link uri">https://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f</a> and the bug report: <a href="https://bugs.r-project.org/show_bug.cgi?id=18941" class="external-link uri">https://bugs.r-project.org/show_bug.cgi?id=18941</a></p>
</blockquote>
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<li><a href="authors.html#citation">Citing dsBase</a></li>
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<h2 data-toc-skip>Developers</h2>
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<li>Paul Burton <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0001-5799-9634" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>  </li>
<li>Rebecca Wilson <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0003-2294-593X" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>  </li>
<li>Olly Butters <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0003-0354-8461" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>  </li>
<li>Patricia Ryser-Welch <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0002-0070-0264" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>  </li>
<li>Alex Westerberg <br><small class="roles"> Author </small>   </li>
<li>Leire Abarrategui <br><small class="roles"> Author </small>   </li>
<li>Roberto Villegas-Diaz <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0001-5036-8661" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>  </li>
<li>Demetris Avraam <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0001-8908-2441" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>  </li>
<li>Yannick Marcon <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0003-0138-2023" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>  </li>
<li>Tom Bishop <br><small class="roles"> Author </small>   </li>
<li>Amadou Gaye <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0002-1180-2792" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>  </li>
<li>Xavier Escribà-Montagut <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0003-2888-8948" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>  </li>
<li>Stuart Wheater <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0009-0003-2419-1964" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>  </li>
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<p>Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Tom Bishop, Amadou Gaye, Xavier Escribà-Montagut, Stuart Wheater.</p>
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