Address citation of software and data

literature.bib

@@ -675,4 +675,42 @@ @book{Fowler1999
 	publisher = {Addison-Wesley},
 	author = {Fowler, Martin and Beck, Kent and Opdyke, William and Roberts, Don},
 	date = {1999},
+}
+@misc{Brown2016,
+  author       = {Brown, Louise and
+                  Crusoe, Michael R. and
+                  Miļajevs, Dmitrijs and
+                  Romanowska, Iza},
+  title        = {{Should you cite this particular piece of software?}},
+  year         = 2016,
+  doi          = {10.5281/zenodo.2559142},
+  url          = {https://mr-c.github.io/shouldacite/},
+	howpublished = {\url{https://mr-c.github.io/shouldacite/}}
+}
+@article{Starr2015,
+	title = {Achieving human and machine accessibility of cited data in scholarly publications},
+	volume = {1},
+	issn = {2376-5992},
+	doi = {10.7717/peerj-cs.1},
+	pages = {e1},
+	journaltitle = {{PeerJ} Computer Science},
+	author = {Starr, Joan and Castro, Eleni and Crosas, Mercè and Dumontier, Michel and Downs, Robert R. and Duerr, Ruth and Haak, Laurel L. and Haendel, Melissa and Herman, Ivan and Hodson, Simon and Hourclé, Joe and Kratz, John Ernest and Lin, Jennifer and Nielsen, Lars Holm and Nurnberger, Amy and Proell, Stefan and Rauber, Andreas and Sacchi, Simone and Smith, Arthur and Taylor, Mike and Clark, Tim},
+	urldate = {2024-11-28},
+	date = {2015-05-27},
+	langid = {english},
+}
+@article{Smith2016,
+	title = {Software citation principles},
+	volume = {2},
+	rights = {http://creativecommons.org/licenses/by/4.0/},
+	issn = {2376-5992},
+	url = {https://peerj.com/articles/cs-86},
+	doi = {10.7717/peerj-cs.86},
+	abstract = {Software is a critical part of modern research and yet there is little support across the scholarly ecosystem for its acknowledgement and citation. Inspired by the activities of the {FORCE}11 working group focused on data citation, this document summarizes the recommendations of the {FORCE}11 Software Citation Working Group and its activities between June 2015 and April 2016. Based on a review of existing community practices, the goal of the working group was to produce a consolidated set of citation principles that may encourage broad adoption of a consistent policy for software citation across disciplines and venues. Our work is presented here as a set of software citation principles, a discussion of the motivations for developing the principles, reviews of existing community practice, and a discussion of the requirements these principles would place upon different stakeholders. Working examples and possible technical solutions for how these principles can be implemented will be discussed in a separate paper.},
+	pages = {e86},
+	journaltitle = {{PeerJ} Computer Science},
+	author = {Smith, Arfon M. and Katz, Daniel S. and Niemeyer, Kyle E. and {FORCE11 Software Citation Working Group}},
+	urldate = {2024-11-28},
+	date = {2016-09-19},
+	langid = {english},
 }

setup.qmd

@@ -427,6 +427,51 @@ This is only a brief summary and there is much more to be learned about coding p
 > 
 > --- @Fowler1999, p. 15
 
+## Citing Software and Data
+
+If you rely on software or data by others in your research, the question arises whether and how to cite it in your publications. Put simply, all data relied upon should be cited to allow for precise identification and access. From the "eight core principles of data citation" [@Starr2015, licensed under [CC0\ 1.0](https://creativecommons.org/publicdomain/zero/1.0/)]:
+
+> **Principle 1 – Importance**: "Data should be considered legitimate, citable products of research. Data citations should be accorded the same importance in the scholarly record as citations of other research objects, such as publications."
+> 
+> **Principle 3 – Evidence**: "In scholarly literature, whenever and wherever a claim relies upon data, the corresponding data should be cited."
+> 
+> **Principle 5 – Access**: "Data citations should facilitate access to the data themselves and to such associated metadata, documentation, code, and other materials, as are necessary for both humans and machines to make informed use of the referenced data."
+> 
+> **Principle 7 – Specificity and Verifiability**: "Data citations should facilitate identification of, access to, and verification of the specific data that support a claim. Citations or citation metadata should include information about provenance and fixity sufficient to facilitate verifying that the specific time slice, version and/or granular portion of data retrieved subsequently is the same as was originally cited."
+
+When it comes to software, the answer is a little more nuanced – you can consult @fig-software-citation for advice whether to cite it. As with data, citations should allow for exact identification and access. From the "software citation principles" [@Smith2016]:
+
+> **1\. Importance**: Software should be considered a legitimate and citable product of research. Software citations should be accorded the same importance in the scholarly record as citations of other research products, such as publications and data; they should be included in the metadata of the citing work, for example in the reference list of a journal article, and should not be omitted or separated. Software should be cited on the same basis as any other research product such as a paper or a book, that is, authors should cite the appropriate set of software products just as they cite the appropriate set of papers.
+> 
+> **5\. Accessibility**: Software citations should facilitate access to the software itself and to its associated metadata, documentation, data, and other materials necessary for both humans and machines to make informed use of the referenced software.
+> 
+> **6\. Specificity**: Software citations should facilitate identification of, and access to, the specific version of software that was used. Software identification should be as specific as necessary, such as using version numbers, revision numbers, or variants such as platforms.
+
+To help with generating the citation, you can use the [CiteAs](https://citeas.org/) service.
+
+::: {#fig-software-citation}
+```{mermaid}
+flowchart TB
+  asks_for_citation("Does the software<br>ask you to cite it?")
+  critical_or_unique_contribution("Did the software<br>play a critical part<br>in or contributed<br>something unique<br>to your research?")
+  manipulate("Did the software<br>manipulate or create<br>your data, software,<br>or other outputs?")
+  relies_on_credit("Do the authors of<br>the software rely<br>on academic credit<br>for funding?")
+  cite[Cite!]
+  nocite[Don't cite!]
+
+  asks_for_citation --"Yes"--> cite
+  asks_for_citation --"No"--> critical_or_unique_contribution
+  critical_or_unique_contribution --"Yes"--> cite
+  critical_or_unique_contribution --"No"--> manipulate
+  manipulate --"Yes"--> cite
+  manipulate --"No"--> relies_on_credit
+  relies_on_credit --"Yes"--> cite
+  relies_on_credit --"No"--> nocite
+```
+
+"Should I cite the software?" by @Brown2016 licensed under [CC\ BY-SA\ 4.0](https://creativecommons.org/licenses/by-sa/4.0/). Simplified from original.
+:::
+
 ## The Last Mile
 
 `renv` only records the versions of R packages and of R itself. This means that potential system dependencies of R packages and other tools utilized in the project are not documented anywhere, including Quarto.^[As of August 2024, a proposal to record the version of Quarto has not been implemented, see [rstudio/renv#1143](https://github.com/rstudio/renv/issues/1143).] We will manually write them down when [creating a README](make_readme.qmd). For now, however, there is one simple step you can take to record the version of Quarto (and a few other dependencies). Do run the following: