Format for AAAS Science Journal #373

sasank89 · 2021-02-11T08:07:42Z

This is in reference to issue #320 . I have tried to do what I can. I do have some doubts which are given in /templates/science/resources/doubts.md. I have added my doubts in detail to the individual things below.

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.

Have done this bit. I am not sure how to word the function. Is this the function that is responsible for generating the output. I am not clearly understanding how the data is flowing through this.

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

Added. I also included the original template from the Science website

Add a skeleton article inst/rmarkdown/templates/journalname/skeleton/skeleton.Rmd.

Added. Might update this as rest changes.

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).

Not yet done.

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

Not yet done. Will do once the template etc is finalised.

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

Not yet done.

Thank you so much for any guidance to improve this and help me close this PR.

CLAassistant · 2021-02-11T08:07:48Z

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cderv

Hi,

Thank you for this first draft!

I tried to answer most of your questions.

With there special workflow to not include images, this is not an easy template. One the workflow is correctly known and understood, I believe setting some knitr option and maybe pre/post processor for rmarkdown would do the job.

This could be tricky to automate maybe. so the idea of the after_body content to be written in another file manually could be simpler.

I let you see what you want to do with all this.

Thanks.

inst/rmarkdown/templates/science/template.yaml

cderv · 2021-02-15T10:34:38Z

inst/rmarkdown/templates/science/resources/doubts.md

@@ -0,0 +1,5 @@
+1. Need a help to figure out how to create a pandoc template for the author's section
+2. Is there a way to get Pandoc to render all images at the end? 


What do you mean by that exactly ? Not sure to understand.

It would not be Pandoc but knitr or rmarkdown. Maybe this format would require a more advanced pre process and post process as other formats in the rticles package. If so, this would be done on the R side.

If you explain more precisely I can guide you.

The journal requirements for figures are as follows -

If the manuscript is an initial submission, you should include figures within the PDF file that you upload, preferably at the end of the text.
For the final submission (after peer review)- Save your figures as separate files, using Science's guidelines for preparing figures, and upload the figures separately with figure captions at the end of your LaTeX file as ordinary text (i.e., do not use the {figure} environment)

Science - Authoring articles with LaTeX

So, my thought was to let the author set a variable to either "Draft" or "Final" in the YAML header and then compile the document as needed without having to change the primary rmarkdown file.

This is a good thought. I hope this will be possible to do so. You may try. I think it will need to be in the R function that would set or unset a value of a knitr option. It could also be a variable set in the setup chunk to use in chunks with figures. This variable would modify the value of the chunk option accordingly. I let you try what you think is better.

But Pandoc itself won't be able to do that (unless maybe using a Lua filter, but it seems too much)

cderv · 2021-02-15T10:39:34Z

inst/rmarkdown/templates/science/resources/doubts.md

+3. Problem is that they want figures rendered for the initial draft / peer review, but no figures included for the final version - 
+- potential solution - get pandoc variable "figures:true" to decide if images should be included in the PDF or not


This would need to be controlled by knitr options I think. For example fig.show = "hide" would generate the figure but not include them in the document.

What should the output document look like ? No figure inside the document but what in replacement ?

cderv · 2021-02-15T10:43:44Z

inst/rmarkdown/templates/science/resources/doubts.md

+2. Is there a way to get Pandoc to render all images at the end? 
+3. Problem is that they want figures rendered for the initial draft / peer review, but no figures included for the final version - 
+- potential solution - get pandoc variable "figures:true" to decide if images should be included in the PDF or not
+4. In which format does science want references? is there a custom csl file - There only appears to be Science.bst file?


.bst file is enough for the style. This command in the template

\bibliographystyle{Science}

is the one that should set the style.

cderv · 2021-02-15T11:44:08Z

inst/rmarkdown/templates/science/skeleton/skeleton.Rmd

+type: REVIEW/ARTICLE
+figures: true / false [required to decide initial submission vs final draft]


Not sure this is needed either.

If you need to show examples in the Rmd, do not use a this / that syntax. It should be valid YAML

figures: true # use false to ...

R/article.R

cderv · 2021-02-15T11:48:39Z

R/article.R

+#' @export
+#' @rdname article
+science_article <- function(
+ ..., keep_tex = TRUE, md_extensions = c("-autolink_bare_uris")


Just curious why this extension needs to be unset ?

inst/rmarkdown/templates/science/resources/template.tex

cderv · 2021-02-15T12:00:38Z

R/article.R

+ ..., keep_tex = TRUE, md_extensions = c("-autolink_bare_uris")
+) {
+ pdf_document_format(
+ "science", md_extensions = md_extensions, ...


keep_tex is defined above but is missing

Suggested change

"science", md_extensions = md_extensions, ...

"science", keep_tex = keep_tex, md_extensions = md_extensions, ...

Co-authored-by: Christophe Dervieux <[email protected]>

cderv · 2021-09-07T13:24:34Z

Hi @sasank89 !

Just a friendly ping. Are you planning to keep working on this branch to add the AAAS template ?

Just in order to know what are the plan on this one.

Thanks.

cderv · 2021-11-29T15:22:25Z

Hi @sasank89,

I have merge master branch into this PR so that it is easier to start on better grounds next time you'll work on this.

Do you plan to continue this PR any time soon ?

No rush, just to know the status on this.

cderv · 2021-11-29T22:35:46Z

inst/rmarkdown/templates/science/resources/science_latex_template.tex

+\author
+{John Smith,$^{1\ast}$ Jane Doe,$^{1}$ Joe Scientist$^{2}$\\
+\\
+\normalsize{$^{1}$Department of Chemistry, University of Wherever,}\\
+\normalsize{An Unknown Address, Wherever, ST 00000, USA}\\
+\normalsize{$^{2}$Another Unknown Address, Palookaville, ST 99999, USA}\\
+\\
+\normalsize{$^\ast$To whom correspondence should be addressed; E-mail: [email protected].}
+}
+


I think we have CI error because of this here: $ cant be used as is in the template because it has special meanings. You need to escape that as Pandoc expects it: https://pandoc.org/MANUAL.html#delimiters

sasank89 · 2022-01-01T23:30:50Z

Hi @cderv ,

So sorry I dropped off for a few months. Unfortunately, I did not get much time to work on this the past few months. I do want to work on it and complete it. Hopefully, I will be able to do more in the coming months.

cderv · 2022-01-03T12:20:14Z

Hi @sasank89,

No problem. Take your time on it, I am in no hurry. I'll just continue to ping once in a while to get status update so that I know if this becomes stale or not.

Happy to help in any way, so please do ping me for anything that I could help with to add this article format.

Thanks for your time and work on this !

cderv · 2022-08-25T14:16:30Z

@sasank89 Just to share that there is another try at this in #486

sasank89 and others added 22 commits January 23, 2021 19:03

Added science_article to article.R

5ed75a7

Copied template from scifile.tex

334ae43

Create skeleton.Rmd

0501308

Create template.yaml

ef25e65

Added science to test-formats.R

b615e8e

Create scibib.bib

96b0e8d

Create scicite.sty

2fa4bc4

Create Science.bst

6d9f081

Update skeleton.Rmd

11e2fa9

Post running roxygen

54d4f99

Modified the template files

ba51e60

Updated skeleton.Rmd

3db9797

Adding the custom template

4a2b13a

Create doubts.md

3effeab

renamed science template

3ab5be3

renamed template

a87d002

Added section on pandoc citation processing

50c7529

Added doubt on authors

942e790

Update doubts.md

b952db1

Update template.tex

a637feb

Update skeleton.Rmd

c611783

Update article.R

ecb331a

sasank89 closed this Feb 12, 2021

sasank89 reopened this Feb 12, 2021

cderv requested changes Feb 15, 2021

View reviewed changes

sasank89 and others added 4 commits February 16, 2021 13:33

Update inst/rmarkdown/templates/science/template.yaml

ef1e004

Co-authored-by: Christophe Dervieux <[email protected]>

Update inst/rmarkdown/templates/science/template.yaml

4268ce1

Co-authored-by: Christophe Dervieux <[email protected]>

Update inst/rmarkdown/templates/science/resources/template.tex

59d9e87

Co-authored-by: Christophe Dervieux <[email protected]>

Update R/article.R

46fcc80

Co-authored-by: Christophe Dervieux <[email protected]>

Merge branch 'master' into sasank89-aaas-science

2b6b60b

Fix CI issues

138f90a

cderv requested changes Nov 29, 2021

View reviewed changes

cderv added the WIP label Apr 19, 2023

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Format for AAAS Science Journal #373

Format for AAAS Science Journal #373

sasank89 commented Feb 11, 2021 •

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sasank89 commented Jan 1, 2022

cderv commented Jan 3, 2022

cderv commented Aug 25, 2022

		@@ -0,0 +1,5 @@
		1. Need a help to figure out how to create a pandoc template for the author's section
		2. Is there a way to get Pandoc to render all images at the end?

		3. Problem is that they want figures rendered for the initial draft / peer review, but no figures included for the final version -
		- potential solution - get pandoc variable "figures:true" to decide if images should be included in the PDF or not

		type: REVIEW/ARTICLE
		figures: true / false [required to decide initial submission vs final draft]

	"science", md_extensions = md_extensions, ...
	"science", keep_tex = keep_tex, md_extensions = md_extensions, ...

Format for AAAS Science Journal #373

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Format for AAAS Science Journal #373

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