Report and Cite Packages"
In report: Automated Reporting of Results and Statistical Models

knitr::opts_chunk$set(
  collapse = TRUE,
  message = FALSE,
  warning = FALSE,
  comment = "#"
)

options(
  knitr.kable.NA = "",
  width = 60
)

if (!requireNamespace("dplyr", quietly = TRUE)) {
  knitr::opts_chunk$set(eval = FALSE)
}

Citing the packages, modules and software you used for your analysis is important to acknowledge the time and effort spent by people who create theses tools (sometimes in their free-time, or at the expense of their own research), but also for reproducibility. Indeed, statistical routines are often implemented in different ways by different packages, which can lead to possible discrepancies in the results. Explicitly mentioning that "I did this using this function from that package version 1.2.3" is a way of protecting yourself by being transparent about what you have found doing what you have done.

But, understandably, you must have a lot of questions-

That's great, but how to actually cite them?

I used about 100 packages, should I cite them all?

How should I report the system (the OS, the R version, etc.)?

We attempt to answer these questions below :)

What should I cite?

Ideally, you should indeed cite all the packages that you used. However, it's often not possible to cite them all in the manuscript body. Therefore, we would recommend the following guidelines:

1. Cite the main/important packages in the manuscript

This should be done for the packages that were central to your specific study (i.e., that got you the results that you reported) rather than data manipulation tools (even though these are as much, if not more, important). For example:

Statistical analysis were carried out using R 4.1.0 (R Core Team, 2021), the rstanarm (v2.13.1; Gabry \& Goodrich, 2016) and the report (v0.2.0; Makowski, Patil, \& Lüdecke, 2019) packages. The full reproducible code is available in Supplementary Materials.

2. Present everything in Supplementary Materials

Then, in Supplementary Materials, you can show all the packages and functions you used. To do it quickly, explicitly and in a reproducible fashion, we recommend writing the Supplementary Materials with R Markdown, which can generate docs and pdf files that you can submit along with your manuscript. Moreover, if you're using R, you can include (usually at the end) every used package's citation using the cite_packages() function from the report package. For example:

library(report)

cite_packages()

Where

Finding the right citation information is sometimes complicated. In R, this process is made quite easy, you simply run citation("packagename"). For instance, citation("bayestestR"):

To cite bayestestR in publications use:

  Makowski, D., Ben-Shachar, M., \& Lüdecke, D. (2019). bayestestR:
  Describing Effects and their Uncertainty, Existence and Significance
  within the Bayesian Framework. Journal of Open Source Software,
  4(40), 1541. doi:10.21105/joss.01541

A BibTeX entry for LaTeX users is

  @Article{,
    title = {bayestestR: Describing Effects and their Uncertainty, Existence and Significance within the Bayesian Framework.},
    author = {Dominique Makowski and Mattan S. Ben-Shachar and Daniel Lüdecke},
    journal = {Journal of Open Source Software},
    doi = {10.21105/joss.01541},
    year = {2019},
    number = {40},
    volume = {4},
    pages = {1541},
    url = {https://joss.theoj.org/papers/10.21105/joss.01541},
  }

For other languages, such as Python or Julia, it might be a little trickier, but a quick search on Google (or github) should provide you with all the necessary information (version, authors and date).

Keep in mind that it's better to have a slightly incomplete citation than no citation at all.