Josis

[Robinlovelace]

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 [email protected].

• 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]

Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you all sign our Contributor License Agreement before we can accept your contribution.
1 out of 2 committers have signed the CLA.

✅ cderv
❌ Robinlovelace
_{You have signed the CLA already but the status is still pending? Let us recheck it.}

[Robinlovelace]

First pass, let's see what happens! Any feedback v. welcome.

[Robinlovelace]

Heads-up @cderv I think this is ready to be reviewed/merged as appropriate. The template generates nice outputs as can be seen here in this in-progress paper I'm working on: https://github.com/zonebuilders/zonebuilder/releases/download/0.0.1/zonebuilder-paper.pdf

[cderv]

Thanks I'll add it in the review todo 😅
I should go back to rticles next week I believe.

[cderv]

Thanks for your contribution.

See my comments below. There are a few things that I believe are not working as expected.

And other comments are about improvement that could be made if you want, like t Markdown syntax for example that you could use more in the skeleton.

[cderv]

Maybe we need to add this checklist (or adapt it) somewhere in the documentation accessible to author from R ?

Like in the R help section for the format or in the skeleton ?

[cderv]

As these are suggested, should it be make optional through a YAML option to use one or all of these ?

Using Pandoc variable can help with that as in other template.

For example, a R user won't be able to uncomment %\usepackage{algorithmic} for its Rmd file.

Or maybe should all be activated by default as it does not harm really ?

[cderv]

booktabs is already loaded before.
https://github.com/rstudio/rticles/pull/382/files#diff-7242a8d3731225c175e35b36ec39868cee3b909d2a0c3234030cd9939d8382c8R45
I don't know if this is an issue to load it twice. Probably not

[cderv]

Same as above, does this needs to be activated somehow ?

If so, then a variables should be added so that it could be included in the output.

[cderv]

For author template this is usually below a single authors field which is usual for a Rmd.

See examples in other templates:

rticles/inst/rmarkdown/templates/aea/skeleton/skeleton.Rmd

Lines 15 to 25 in 84a8fb4

	author:
	- name: Alice Anonymous
	firstname: Alice
	surname: Anonymous
	email: [email protected]
	affiliation: Some Institute of Technology
	- name: Bob Security
	firstname: Bob
	surname: Security
	email: [email protected]
	affiliation: Another University

if this could work here too, it would be better. This requires change in the pandoc template with a for loop I guess. I know some templates use this like you did but it would also not be extensible to more then two.

In the future we plan to standardize this more: #324

[cderv]

You show table above with knitr : is this interested to keep ?

[cderv]

This would be header 1 in Markdown as the other above, wouldn't it ?

[cderv]

FYI in Pandoc's markdown this would be

# Acknowledgement {-}

or

# Acknowledgement {.unnumbered}

[cderv]

I believe this syntax requires to use natbib as citation processing engine.
Currently, your format sets "default" meaning use Pandoc processing and biliography seems to be added twice.
See

See this is because one of the reference is done using Pandoc's syntax (https://pandoc.org/MANUAL.html#citations) and the others are made using \cite I believe so Pandoc
does not process them.

So maybe you need to default to "natbib" for this format.

Usually with Pandoc a CSL is used by I don't see one for ACM Josis

• https://bookdown.org/yihui/rmarkdown-cookbook/bibliography.html
• https://www.zotero.org/styles?q=ACM

[cderv]

See commend about bibliography in template: I believe it should be natbib here not default

[Robinlovelace]

Thanks for all the feedback @cderv this is great and highly educational. Will look to update the PR and respond to your comments in due course.

[cderv]

I forgot to mention that this needs to be extended. I believe CI error are because of this See for example

rticles/inst/rmarkdown/templates/acm/resources/template.tex

Lines 66 to 93 in fbb332f

	$if(csl-refs)$
	\newlength{\csllabelwidth}
	\setlength{\csllabelwidth}{3em}
	\newlength{\cslhangindent}
	\setlength{\cslhangindent}{1.5em}
	% for Pandoc 2.8 to 2.10.1
	\newenvironment{cslreferences}%
	{$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
	\everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
	{\par}
	% For Pandoc 2.11+
	\newenvironment{CSLReferences}[2] % #1 hanging-ident, #2 entry spacing
	{% don't indent paragraphs
	\setlength{\parindent}{0pt}
	% turn on hanging indent if param 1 is 1
	\ifodd #1 \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces\fi
	% set entry spacing
	\ifnum #2 > 0
	\setlength{\parskip}{#2\baselineskip}
	\fi
	}%
	{}
	\usepackage{calc} % for calculating minipage widths
	\newcommand{\CSLBlock}[1]{#1\hfill\break}
	\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
	\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break}
	\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
	$endif$

The part for ealier Pandoc version needs to be added

Suggested change

	$if(csl-refs)$
	\newlength{\cslhangindent}
	\setlength{\cslhangindent}{1.5em}
	\newlength{\csllabelwidth}
	\setlength{\csllabelwidth}{3em}
	\newenvironment{CSLReferences}[2] % #1 hanging-ident, #2 entry spacing
	{% don't indent paragraphs
	\setlength{\parindent}{0pt}
	% turn on hanging indent if param 1 is 1
	\ifodd #1 \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces\fi
	% set entry spacing
	\ifnum #2 > 0
	\setlength{\parskip}{#2\baselineskip}
	\fi
	}%
	{}
	\usepackage{calc}
	\newcommand{\CSLBlock}[1]{#1\hfill\break}
	\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
	\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break}
	\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
	$endif$
	$if(csl-refs)$
	\newlength{\csllabelwidth}
	\setlength{\csllabelwidth}{3em}
	\newlength{\cslhangindent}
	\setlength{\cslhangindent}{1.5em}
	% for Pandoc 2.8 to 2.10.1
	\newenvironment{cslreferences}%
	{$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
	\everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
	{\par}
	% For Pandoc 2.11+
	\newenvironment{CSLReferences}[2] % #1 hanging-ident, #2 entry spacing
	{% don't indent paragraphs
	\setlength{\parindent}{0pt}
	% turn on hanging indent if param 1 is 1
	\ifodd #1 \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces\fi
	% set entry spacing
	\ifnum #2 > 0
	\setlength{\parskip}{#2\baselineskip}
	\fi
	}%
	{}
	\usepackage{calc} % for calculating minipage widths
	\newcommand{\CSLBlock}[1]{#1\hfill\break}
	\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
	\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break}
	\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
	$endif$

[cderv]

Hi @Robinlovelace,

Friendly ping as I am going through PR for next version.

Is this something you are still planning to spend a bit of time off ?

No hurry. I just want to check the status of this PR. Thanks !

[Robinlovelace]

Sorry for slow reply. I still plan to do this but may be ~1 month before I get the dedicated time needed to move this forward. Looking forward to that time as it will be a learning experience!

[cderv]

Hi @Robinlovelace ,

Just to inform you that I took the time to merge master in this PR and fix the conflicts so that you can start on a better basis when you'll find time to continue the work.

Cheers,

[nuest]

Hi @Robinlovelace ! Just came across this while looking for another PR. Big JOSIS fan, so if you're still not seeing a window to take another look, I'll find time before the end of the year.

[Robinlovelace]

Many thanks @nuest let's do this. The PR is almost there but year, needs a bit of TLC. FYI the editors are aware and in support of this effort.

[cderv]

@nuest @Robinlovelace just a friendly ping to see if this is still a project. If you need my help to make JOSIS format happens, happy to schedule some time on this.

[Robinlovelace]

May need some help. Thanks for patience @cderv, will be worth it! JOSIS is a great open access journal and we're almost there. I will try to get some of the editorial team involved who my have comments also.