Make tutorial page at ropensci.github.io/neotoma

[sckott]

Actually, we want to start moving in another direction. Still making tutorials, but putting them in different places. So since R v3, R supports R Markdown vignettes. It would be great to have vignettes in each of our packages, and then we can parse these (since they are written in Markdown) to html pages for our website. So when you have time, do the following:

• Write a vignette in R Markdown, and
• Store the R Markdown file in /inst/doc/ with filename packagename_vignette.Rmd (i.e., neotoma_vignette.Rmd)
• Put the following line in your Description file VignetteBuilder: knitr

Whenever you install neotoma the vignette will run and build a document that users can look at. You can also knit the vignette from .Rmd to a .pdf or .html, etc. for whatever other uses you want.

We don't have it solved yet, but will then parse the .Rmd vignette to a page on our website at ropensci.org/tutorials/

[sckott]

@SimonGoring Here's an example of a vignette in Rmd https://github.com/ropensci/rbison/blob/master/inst/doc/rbison_vignette.Rmd

[sckott]

@SimonGoring Here's some help from Yihui himself https://github.com/yihui/knitr/blob/master/inst/doc/knitr-markdown.Rmd

[karthik]

Simon, let us know if you need help. You can also drop it in whatever format and we can help integrate the first round.

On Friday, July 12, 2013 at 8:01 PM, Scott Chamberlain wrote:

@SimonGoring (https://github.com/SimonGoring) Here's some help from Yihui himself https://github.com/yihui/knitr/blob/master/inst/doc/knitr-markdown.Rmd

— Reply to this email directly or view it on GitHub (https://github.com/ropensci/neotoma/issues/5#issuecomment-20879886).

[SimonGoring]

Just going through these now. @karthik @sckott, can I stick the neotoma paper into the inst/doc folder then and use it as the vignette? If so I'll just copy it directly across and stick a little header at the top with the proper citation.

[karthik]

Sounds good. You'll need to turn it into html first and stick it in the root of the gh-pages repo.

[SimonGoring]

Not sure where that is @karthik. Is it an ropensci repository?

[karthik]

sorry, by gh-pages repo I meant the branch.

So create a new branch called gh-pages checkout that branch then copy the vignette into the root of the folder as index.html

[gavinsimpson]

@SimonGoring You really don't want to do this! The code takes hours to run and so each time we test we'd have to turn off checking of vignettes (which is easy; but then we don't benefit from the test!).

CRAN won't allow you to turn off the creating etc of vignettes so there would be no hope of getting this on CRAN.

[SimonGoring]

@ucfgals I was going to just put the compiled md/html file up there, not the whole Rmd. I assume that will work.

On Wed, Jan 7, 2015 at 4:39 PM, Gavin Simpson notifications@github.com wrote:

@SimonGoring https://github.com/SimonGoring You really don't want to do this! The code takes hours to run and so each time we test we'd have to turn off checking of vignettes (which is easy; but then we don't benefit from the test!).

CRAN won't allow you to turn off the creating etc of vignettes so there would be no hope of getting this on CRAN.

— Reply to this email directly or view it on GitHub https://github.com/ropensci/neotoma/issues/5#issuecomment-69105649.

[gavinsimpson]

@SimonGoring That would be OK, but I would include a rendered PDF file and a rendered html. FYI, this would not be considered a vignette in formal R-pkg sense as the sources would not be available nor checked by R CMD check. Arbitrary documentation is fine in inst/doc, however.

Would be good to include a link to the actual paper on the OQ site once we have that available.