bioinformatics: use subject_section in header

[stephenturner]

fixes #414

To contribute a new article template to this package, please make sure you have done the following things (note that journalname_article below is only an example name):

• [ ] This project uses a Contributor Licence Agreement (CLA) that you'll be asked to sign when opening a PR. This is required for a significant pull request (it is fine not to sign it if a PR is only intended to fix a few typos). We use a tool called CLA assistant for that.
  You could also, unless you have done it in any other RStudio's projects before, sign the individual or corporate contributor agreement. You can send the signed copy to jj@rstudio.com.

• [ ] Add the journalname_article() function to R/article.R if the output format is simple enough, otherwise create a separate R/journalname_article.R.

• [ ] Add the Pandoc LaTeX template inst/rmarkdown/templates/journalname/resources/template.tex.

• [ ] Add a skeleton article inst/rmarkdown/templates/journalname/skeleton/skeleton.Rmd.

• [ ] Add a description of the template inst/rmarkdown/templates/journalname/template.yaml.

• [ ] Please include the document class file (*.cls) if needed, but please do not include standard LaTeX packages (*.sty) that can be downloaded from CTAN. If you are using TinyTeX or TeX Live, you can verify if a package is available on CTAN via tinytex::parse_packages(files = "FILENAME"") (e.g., when FILENAME is plain.bst, it should return "bibtex", which means this file is from a standard CTAN package). Please keep the number of new files absolutely minimal (e.g., do not include PDF output files), and also make examples minimal (e.g., if you need a .bib example, try to only leave one or two bibliography entries in it, and don't include too many items in it without using all of them).

• [ ] Update Rd and namespace (could be done by devtools::document()).

• [ ] Update NEWS.

• [ ] Update README with a link to the newly supported journal. Please add your Github username and the full name of the journal (follow other examples in the list).

• [ ] Add a test to tests/testit/test-formats.R by adding a line test_format("journalname"). We try to keep them in alphabetical order.

• [ ] Add your name to the list of authors Authors@R in DESCRIPTION. You don't need to bump the package version in DESCRIPTION.

Lastly, please try your best to do only one thing per pull request (e.g., if you want to add two output formats, do them in two separate pull requests), and refrain from making cosmetic changes in the code base: https://yihui.name/en/2018/02/bite-sized-pull-requests/

Thank you!

[CLAassistant]

All committers have signed the CLA.

[cderv]

Thanks for the contribution !

Should it really be set as the same value as subtitle ?

We could also introduce a new variable to set in YAML like category or manuscript_category and set it to subject_section if not set maybe.

I don't know this journal but we could try do what is more flexible maybe ?

What do you think ?

[stephenturner]

You're right - these are separate things. Looking at a recent application note:

The header shows Application note as the category, with Genome Analysis as the subject

[stephenturner]

So, yes, does seem like these should be two separate variables!

[cderv]

You can adapt this PR then and it will be ready to merge! You can add a NEWS bullet also with the new variable. Please add it also in the skeleton Rmd to see how it should be set.

Thanks !

[cderv]

Also, I think the category that should be used are the one in Type of Manuscript in https://academic.oup.com/bioinformatics/pages/instructions_for_authors

right ?

Maybe we should document this too.

[stephenturner]

I think this is fixed and documented in comments in 453e5eb

[stephenturner]

NEWS updated in ce82131