Update manuscript to reference correct object names and paper_id

[egouldo]

• Manuscript has been updated to reference the anonymised paper ID's and names to old supp. data objects have been changed to reflect current names.
• Manuscript files moved to ./vignettes/, BUT, I can't get the vignette to register when calling browseVignettes(package = "aggreCAT"). @psychtek can you please make any necessary changes to the draft PR so the vignette is included in the package build?

[psychtek]

@egouldo No worries ill jump in and get this branch rolling 🥼

[psychtek]

Ok so I am getting conflicting information when I start digging around as to where to put manuscript docs. Seems that the vignettes is for package reference vignettes? Manuscripts go into sub folder in inst/docs. Confused 😅
https://stackoverflow.com/questions/59645828/how-to-properly-organise-vignettes-and-inst-folders-when-creating-new-r-package

We might need to create a reference pdf of the package anyway?

My understanding is that we create the rmd in the vignettes folder.
then devtools::build_vignettes() which does a bunch of fancy stuff:

ℹ Copying vignettes
ℹ Moving manuscript.html and manuscript.R to doc/
ℹ Copying manuscript.Rmd to doc/
ℹ Building vignette index

But this is for html.

@egouldo But the manuscript is printing to pdf and html correct?

If all we need is the pdf then theres info here about just placing the pdf and asis inside the vignettes.

Also, unless theres a more up to date link Quarto isnt currently supported for vignettes (at least for CRAN approval): r-lib/pkgdown#2154
EMODnet/EMODnetWCS#11
So we might need to change it back to Rmd format.

Good summary about vignettes and pdf articles here

[egouldo]

Hmmm, sounds like there's also a difference between 'reference manual' and a 'vignette'. I think reference manual is cobbled together document of all the R man for the package, and vignette is a separate long-form document yet again.

[egouldo]

For now, simplest way forward is to include the knitted quarto PDF of the manuscript rather than trying to build the .qmd document in the package building workflow.

See: https://cran.r-project.org/web/packages/R.rsp/vignettes/R_packages-Static_PDF_and_HTML_vignettes.pdf

• Elliot to include PDF of manuscript as PDF

[egouldo]

Ok @psychtek , so package builds locally, but fails check because r.sp is not specified as the package builder (had to change it from knitr to r.sp (See 9a79e4f, file: DESCRIPTION). That's the vignette builder we need to include PDF as pkg vignette.

Log L#30: https://github.com/metamelb-repliCATS/aggreCAT/runs/8199741340?check_suite_focus=true#step:5:31

[psychtek]

Creeping every so closely 😄

[egouldo]

Creeping every so closely 😄

😅 Do we need to update GH actions file or docker to make the checks work?

[psychtek]

Nah its neeeearly there! I have set it up to flag when warnings are present

checking for portable file names ... WARNING
  Found the following files with non-portable file names:
    inst/ms/_extensions/jss/_extensions/quarto-ext/fancy-text/_extension 2.yml
    inst/ms/_extensions/jss/_extensions/quarto-ext/fancy-text/fancy-text 2.lua

if these arent needed for ms build then add to .buildignore ?

[egouldo]

ping @psychtek ready for review, we all ✅ on Rcmdcheck

[psychtek]

      - name: vignette-builder
        run:  install.packages("R.rsp"); remotes::install_deps(dependencies = TRUE)
        shell: Rscript {0}

Ill bake this into the image at a later date.

[egouldo]

Also adding this reference to the mix here: - https://www.jstatsoft.org/style - how to incorporate JSS manuscript as vignette in package I’ll have a look at those other refs shortly.

…

Sent from my iPhone On 6 Sep 2022, at 10:58 am, Aaron ***@***.***> wrote:  Ok so I am getting conflicting information when I start digging around as to where to put manuscript docs. Seems that the vignettes is for package reference vignettes<https://stackoverflow.com/questions/69570632/is-there-a-special-rmd-template-to-create-r-package-vignette-in-pdf>? Manuscripts go into sub folder in inst/docs. Confused 😅 https://stackoverflow.com/questions/59645828/how-to-properly-organise-vignettes-and-inst-folders-when-creating-new-r-package<https://stackoverflow.com/questions/59645828/how-to-properly-organise-vignettes-and-inst-folders-when-creating-new-r-package> We might need to create a reference<https://stackoverflow.com/questions/16986422/r-create-reference-manual-with-r-cmd-check?noredirect=1&lq=1> pdf of the package anyway? My understanding is that we create the rmd in the vignettes folder. then devtools::build_vignettes() which does a bunch of fancy stuff: ℹ Copying vignettes ℹ Moving manuscript.html and manuscript.R to doc/ ℹ Copying manuscript.Rmd to doc/ ℹ Building vignette index But this is for html. @egouldo<https://github.com/egouldo> But the manuscript is printing to pdf and html correct? If all we need is the pdf then theres info here<https://cran.r-project.org/web/packages/R.rsp/vignettes/R_packages-Static_PDF_and_HTML_vignettes.pdf> about just placing the pdf and asis inside the vignettes. Also, unless theres a more up to date link Quarto isnt currently supported for vignettes (at least for CRAN approval): r-lib/pkgdown#2154<r-lib/pkgdown#2154> EMODnet/EMODnetWCS#11<EMODnet/EMODnetWCS#11> So we might need to change it back to Rmd format. Good summary about vignettes and pdf articles here<https://blog.r-hub.io/2020/06/03/vignettes> — Reply to this email directly, view it on GitHub<#11 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACAC6KQOWSCQI4ERS6CU6B3V42JK5ANCNFSM6AAAAAAQEWHYJU>. You are receiving this because you were mentioned.Message ID: ***@***.***>