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(This article was first published on <strong><a href="https://neuropsychology.github.io/psycho.R//2018/08/31/cite_packages.html"> Dominique Makowski</a></strong>, and kindly contributed to <a rel="nofollow" href="https://www.r-bloggers.com/">R-bloggers)</a> </div>
<ul>
<li><a rel="nofollow" href="https://neuropsychology.github.io/psycho.R//2018/08/31/cite_packages.html#what-should-i-cite" target="_blank">What should I cite?</a></li>
<li><a rel="nofollow" href="https://neuropsychology.github.io/psycho.R//2018/08/31/cite_packages.html#how-should-i-cite-it" target="_blank">How should I cite it?</a></li>
<li><a rel="nofollow" href="https://neuropsychology.github.io/psycho.R//2018/08/31/cite_packages.html#previous-blogposts" target="_blank">Previous blogposts</a></li>
</ul>
<p><strong>Citing the packages, modules and softwares you used for your analysis is important</strong>, both from a <strong>reproducibility perspective</strong> (statistical routines are often implemented in different ways by different packages, which could explain slight discrepancies in the results. Saying &quot;<em>I did this using this function from that package version 1.2.3</em>â€� is a way of protecting yourself by being clear about what you have found doing what you have done) but also for <strong>acknowledging</strong> the work and time that people spent creating tools for others (sometimes at the expense of their own research).</p>
<ul>
<li><strong>That's great, but how to <em>actually</em> cite them?</strong></li>
<li><strong>I used about 100 packages, should I cite them <em>all</em>?</strong></li>
</ul>
<h1>What should I cite?</h1>
<p>Ideally, you should indeed cite all the packages that you used. However, it's not very diegetic. Therefore, I would recommand the following:</p>
<ol>
<li>Cite the main / important packages in the manuscript</li>
</ol>
<p>This should be done for the packages that were central to your specific analysis (<em>i.e.,</em> that got you the results that you reported) rather than data manipulation tools (even though these are as much important).</p>
<p>For example:</p>
<blockquote>
<p>Statistics were done using R 3.5.0 (R Core Team, 2018), the <em>rstanarm</em> (<em>v2.13.1</em>; Gabry &amp; Goodrich, 2016) and the <em>psycho</em> (<em>v0.3.4</em>; Makowski, 2018) packages. The full reproducible code is available in <strong>Supplementary Materials</strong>.</p>
</blockquote>
<ol>
<li>Present everything in Supplementary Materials</li>
</ol>
<p>Then, in Supplementary Materials, you show the packages and functions you used. Moreover, in R, you can include (usually at the end) every used package and their version using the <code>sessionInfo()</code> function.</p>
<h1>How should I cite it?</h1>
<p>Finding the right citation information is sometimes complicated. In R, this process is made quite easy, you simply run <code>citation(&quot;packagename&quot;)</code>. For instance, <code>citation(&quot;dplyr&quot;)</code>:</p>
<div>
<div>
<pre><code>To cite â€˜dplyr' in publications use:

  Hadley Wickham, Romain FranÃ§ois, Lionel Henry and Kirill MÃ¼ller (2018). dplyr: A Grammar of Data Manipulation. R package version
  0.7.6. https://CRAN.R-project.org/package=dplyr

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {dplyr: A Grammar of Data Manipulation},
    author = {Hadley Wickham and Romain FranÃ§ois and Lionel Henry and Kirill MÃ¼ller},
    year = {2018},
    note = {R package version 0.7.6},
    url = {https://CRAN.R-project.org/package=dplyr},
  }
</code></pre>
</div>
</div>
<p>For other languages, such as Python or Julia, it might be a little trickier, but a <strong>quick search on google (<em>or github</em>)</strong> should provide you with all the necessary information (version, authors, date). <strong>It's better to have a slightly incomplete citation than no citation at all.</strong></p>
<h1>Previous blogposts</h1>
<ul>
<li><a rel="nofollow" href="https://neuropsychology.github.io/psycho.R/2018/07/20/analyze_anova.html" target="_blank">The end of errors in ANOVA reporting</a></li>
<li><a rel="nofollow" href="https://neuropsychology.github.io/psycho.R/2018/07/14/standardize_grouped_df.html" target="_blank">Variable vs. Participant-wise Standardization</a></li>
<li><a rel="nofollow" href="https://neuropsychology.github.io/psycho.R/2018/06/28/analyze_correlation.html" target="_blank">Formatted Correlation with Effect Size</a></li>
<li><a rel="nofollow" href="https://neuropsychology.github.io/psycho.R/2018/06/25/refdata.html" target="_blank">Extracting a Reference Grid of your Data for Machine Learning Models Visualization</a></li>
<li><a rel="nofollow" href="https://neuropsychology.github.io/psycho.R/2018/06/19/analyze_ttest.html" target="_blank">Copy/paste t-tests Directly to Manuscripts</a></li>
<li><a rel="nofollow" href="https://neuropsychology.github.io/psycho.R/2018/06/11/bayesian_correlation.html" target="_blank">Easy APA Formatted Bayesian Correlation</a></li>
<li><a rel="nofollow" href="https://neuropsychology.github.io/psycho.R/2018/06/03/plot_bayesian_model.html" target="_blank">Fancy Plot (with Posterior Samples) for Bayesian Regressions</a></li>
<li><a rel="nofollow" href="https://neuropsychology.github.io/psycho.R/2018/05/24/n_factors.html" target="_blank">How Many Factors to Retain in Factor Analysis</a></li>
<li><a rel="nofollow" href="https://neuropsychology.github.io/psycho.R/2018/05/20/correlation.html" target="_blank">Beautiful and Powerful Correlation Tables</a></li>
<li><a rel="nofollow" href="https://neuropsychology.github.io/psycho.R/2018/05/10/interpret_mixed_models.html" target="_blank">Format and Interpret Linear Mixed Models</a></li>
<li><a rel="nofollow" href="https://neuropsychology.github.io/psycho.R/2018/05/01/repeated_measure_anovas.html" target="_blank">How to do Repeated Measures ANOVAs</a></li>
<li><a rel="nofollow" href="https://neuropsychology.github.io/psycho.R/2018/03/29/standardize.html" target="_blank">Standardize (Z-score) a dataframe</a></li>
<li><a rel="nofollow" href="https://neuropsychology.github.io/psycho.R/2018/03/29/SDT.html" target="_blank">Compute Signal Detection Theory Indices</a></li>
<li><a rel="nofollow" href="https://neuropsychology.github.io/psycho.R/2018/03/21/installingR.html" target="_blank">Installing R, R Studio and psycho</a></li>
</ul>
	<p>
<div>
<div>To <strong>leave a comment</strong> for the author, please follow the link and comment on their blog: <strong><a href="https://neuropsychology.github.io/psycho.R//2018/08/31/cite_packages.html"> Dominique Makowski</a></strong>.</div>
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