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I'm sure we need to pay credit to every R package developer. Just in line with this post.

My question is, how better to integrate the citations of R packages into my paper. Should it be part of the methodological part? I saw papers that just throw the citations into the reference list. But it just doest not seem right.

There is a similar question on Academia. My focus is on the way one should incorporate the actual citations into the paper.

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3 Answers 3

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You should cite the software packages that you use just like any other piece of scientific work that you build on. If they are significant enough to make it to your main narrative, then cite them there just like the other key techniques you build upon. If they are useful but uninteresting methodological detail (e.g., equivalent to a microscope model or reagent brand) then they should in just the same way be relegated to an equivalent methods section, appendix, or other piece of supplemental material.

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  • How would you cite ggplot2?
    – ikashnitsky
    Commented Sep 12, 2015 at 21:48
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    @Ilya Honestly, I don't think I would, unless there was something fundamental about ggplot2 that enabled the analysis.
    – Fomite
    Commented Sep 12, 2015 at 22:23
  • @Fomite I don't agree. It is crucial to pay credit to those who contributed their time helping others. Also, I think, you should mention all the packages used for reproducibility.
    – ikashnitsky
    Commented Sep 17, 2015 at 9:16
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    @Ilya Except this will rapidly become cumbersome. Do I cite Git? matplotlib? Numpy, because I really like their CSV export function? Requests, because its how I pull down a config file off Github to make sure I'm always using the current one?
    – Fomite
    Commented Sep 18, 2015 at 3:27
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    @Ilya Yet you could obtain the figure using base graphics - a scatter plot is a scatter plot.
    – Fomite
    Commented Sep 19, 2015 at 5:00
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This should be included in your Methods section towards the end of the section.

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The analysis/statistics section of your manuscript would be the appropriate location. It is here that you should mention what R version, what additional packages were used, etc.

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