Simple document format #68

jimhester · 2014-10-07T18:24:24Z

This is a major restructuring of the package embracing rmarkdown fully. It has two main features,

fully support rmarkdown, building knitrBootstrap off of html_document()
simplify the code by removing features
- style and code theme choosers
- global toggles

It aims to do as little work in javascript as possible, namely no DOM restructuring (other than highlighting).

znmeb · 2014-10-07T21:57:16Z

Thanks!! Once that's done will it upgrade cleanly to Bootstrap 3.2.0?

znmeb · 2014-10-08T07:49:33Z

If I want to test this, can I just do devtools::install_github('jimhester/knitrBootstrap', ref = 'rmarkdown_template')?

jimhester · 2014-10-08T12:22:20Z

Yes you can do either

# to install from the rmarkdown_template branch
devtools::install_github('jimhester/knitrBootstrap', ref = 'rmarkdown_template')
# or
devtools::install_github('jimhester/knitrBootstrap@rmarkdown_template')

# To install directly from this pull request
devtools::install_github('jimhester/knitrBootstrap#68')

Let me know if you have issues, or if you miss features I took out. I can add some back if they are things people liked.

The easiest way to get started is to use the rmarkdown templates in Rstudio.

znmeb · 2014-10-09T03:10:28Z

OK - I'll be testing it tonight!! Do you have your own rmarkdown templates? I've been using the "Mosaic Fancy" template from https://github.com/rpruim/mosaic as a template and it works great once I figured out the MathJax code for in-line math.

znmeb · 2014-10-09T03:38:38Z

I did a "new file" from the "knitrBootstrap" template in RStudio. That creates a directory with an Rmd file and a js and css folder. Doing a "knit" in RStudio gives an error -

Error in (function (css = NULL, theme = NULL, highlight = NULL, ...)  : 
  could not find function "%||%"
Calls: <Anonymous> -> create_output_format -> do.call -> <Anonymous>
Execution halted

So does running "rmarkdown::render" in the console:

> getwd()
[1] "/data/Projects/journal-source/stories/knitrBootstrap"
> rmarkdown::render('knitrBootstrap.Rmd')
Error in (function (css = NULL, theme = NULL, highlight = NULL, ...)  : 
  could not find function "%||%"
>

znmeb · 2014-10-09T03:54:12Z

It looks like there aren't any vignettes now - at least only 'DESCRIPTION' and 'NEWS' are showing in the help panel. The install appears to have worked.

> devtools::install_github('jimhester/knitrBootstrap@rmarkdown_template')
Downloading github repo jimhester/knitrBootstrap@rmarkdown_template
Installing knitrBootstrap
'/usr/lib64/R/bin/R' --vanilla CMD INSTALL  \
  '/tmp/RtmpG1nI5K/devtools28ca7e37c723/jimhester-knitrBootstrap-25924a2'  \
  --library='/usr/lib64/R/library' --install-tests 

* installing *source* package ‘knitrBootstrap’ ...
** R
** exec
** inst
** preparing package for lazy loading
** help
No man pages found in package  ‘knitrBootstrap’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (knitrBootstrap)
Making 'packages.html' ... done
>

znmeb · 2014-10-09T03:55:17Z

Here's what's in the library after the install:

/usr/lib64/R/library/knitrBootstrap:
total 48
-rw-r--r--. 1 root root  984 Oct  8 20:45 DESCRIPTION
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 examples
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 exec
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 help
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 html
-rw-r--r--. 1 root root   40 Oct  8 20:45 LICENSE
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 Meta
-rw-r--r--. 1 root root  159 Oct  8 20:45 NAMESPACE
-rw-r--r--. 1 root root 2202 Oct  8 20:45 NEWS
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 R
drwxr-xr-x. 4 root root 4096 Oct  8 20:45 rmarkdown
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 templates

/usr/lib64/R/library/knitrBootstrap/examples:
total 3448
-rw-r--r--. 1 root root 3067595 Oct  8 20:45 all.html
-rw-r--r--. 1 root root     489 Oct  8 20:45 all.Rmd
-rw-r--r--. 1 root root  440344 Oct  8 20:45 engines.html
-rw-r--r--. 1 root root    3590 Oct  8 20:45 engines.Rmd
-rw-r--r--. 1 root root    6394 Oct  8 20:45 messages.html
-rw-r--r--. 1 root root     630 Oct  8 20:45 messages.Rmd

/usr/lib64/R/library/knitrBootstrap/exec:
total 4
-rwxr-xr-x. 1 root root 3010 Oct  8 20:45 encode.pl

/usr/lib64/R/library/knitrBootstrap/help:
total 12
-rw-r--r--. 1 root root  60 Oct  8 20:45 aliases.rds
-rw-r--r--. 1 root root   0 Oct  8 20:45 AnIndex
-rw-r--r--. 1 root root   0 Oct  8 20:45 knitrBootstrap.rdb
-rw-r--r--. 1 root root 113 Oct  8 20:45 knitrBootstrap.rdx
-rw-r--r--. 1 root root  64 Oct  8 20:45 paths.rds

/usr/lib64/R/library/knitrBootstrap/html:
total 8
-rw-r--r--. 1 root root  920 Oct  8 20:45 00Index.html
-rw-r--r--. 1 root root 1179 Oct  8 20:45 R.css

/usr/lib64/R/library/knitrBootstrap/Meta:
total 20
-rw-r--r--. 1 root root  190 Oct  8 20:45 hsearch.rds
-rw-r--r--. 1 root root   38 Oct  8 20:45 links.rds
-rw-r--r--. 1 root root  228 Oct  8 20:45 nsInfo.rds
-rw-r--r--. 1 root root 1020 Oct  8 20:45 package.rds
-rw-r--r--. 1 root root  164 Oct  8 20:45 Rd.rds

/usr/lib64/R/library/knitrBootstrap/R:
total 16
-rw-r--r--. 1 root root 1056 Oct  8 20:45 knitrBootstrap
-rw-r--r--. 1 root root 7354 Oct  8 20:45 knitrBootstrap.rdb
-rw-r--r--. 1 root root  523 Oct  8 20:45 knitrBootstrap.rdx

/usr/lib64/R/library/knitrBootstrap/rmarkdown:
total 8
drwxr-xr-x. 5 root root 4096 Oct  8 20:45 rmd
drwxr-xr-x. 4 root root 4096 Oct  8 20:45 templates

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd:
total 16
drwxr-xr-x. 5 root root 4096 Oct  8 20:45 bootstrap3
-rw-r--r--. 1 root root 2690 Oct  8 20:45 default.html
drwxr-xr-x. 3 root root 4096 Oct  8 20:45 highlightjs
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 magnific_popup

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3:
total 12
drwxr-xr-x. 3 root root 4096 Oct  8 20:45 css
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 fonts
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 js

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css:
total 112
-rw-r--r--.  1 root root 109518 Oct  8 20:45 bootstrap.min.css
drwxr-xr-x. 19 root root   4096 Oct  8 20:45 themes

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css/themes:
total 68
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 amelia
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 cerulean
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 cosmo
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 cyborg
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 darkly
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 flatly
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 journal
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 lumen
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 paper
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 readable
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 sandstone
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 simplex
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 slate
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 spacelab
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 superhero
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 united
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 yeti

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css/themes/amelia:
total 112
-rw-r--r--. 1 root root 111576 Oct  8 20:45 bootstrap.min.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css/themes/cerulean:
total 112
-rw-r--r--. 1 root root 114267 Oct  8 20:45 bootstrap.min.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css/themes/cosmo:
total 112
-rw-r--r--. 1 root root 111733 Oct  8 20:45 bootstrap.min.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css/themes/cyborg:
total 112
-rw-r--r--. 1 root root 111555 Oct  8 20:45 bootstrap.min.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css/themes/darkly:
total 112
-rw-r--r--. 1 root root 113576 Oct  8 20:45 bootstrap.min.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css/themes/flatly:
total 112
-rw-r--r--. 1 root root 113285 Oct  8 20:45 bootstrap.min.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css/themes/journal:
total 112
-rw-r--r--. 1 root root 111171 Oct  8 20:45 bootstrap.min.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css/themes/lumen:
total 116
-rw-r--r--. 1 root root 116301 Oct  8 20:45 bootstrap.min.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css/themes/paper:
total 116
-rw-r--r--. 1 root root 116578 Oct  8 20:45 bootstrap.min.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css/themes/readable:
total 112
-rw-r--r--. 1 root root 112177 Oct  8 20:45 bootstrap.min.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css/themes/sandstone:
total 112
-rw-r--r--. 1 root root 112036 Oct  8 20:45 bootstrap.min.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css/themes/simplex:
total 112
-rw-r--r--. 1 root root 113254 Oct  8 20:45 bootstrap.min.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css/themes/slate:
total 124
-rw-r--r--. 1 root root 123889 Oct  8 20:45 bootstrap.min.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css/themes/spacelab:
total 116
-rw-r--r--. 1 root root 116538 Oct  8 20:45 bootstrap.min.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css/themes/superhero:
total 112
-rw-r--r--. 1 root root 112381 Oct  8 20:45 bootstrap.min.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css/themes/united:
total 108
-rw-r--r--. 1 root root 110052 Oct  8 20:45 bootstrap.min.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/css/themes/yeti:
total 116
-rw-r--r--. 1 root root 114962 Oct  8 20:45 bootstrap.min.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/fonts:
total 152
-rw-r--r--. 1 root root 20335 Oct  8 20:45 glyphicons-halflings-regular.eot
-rw-r--r--. 1 root root 62927 Oct  8 20:45 glyphicons-halflings-regular.svg
-rw-r--r--. 1 root root 41280 Oct  8 20:45 glyphicons-halflings-regular.ttf
-rw-r--r--. 1 root root 23320 Oct  8 20:45 glyphicons-halflings-regular.woff

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/bootstrap3/js:
total 32
-rw-r--r--. 1 root root 31819 Oct  8 20:45 bootstrap.min.js

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/highlightjs:
total 44
drwxr-xr-x. 2 root root  4096 Oct  8 20:45 highlight
-rw-r--r--. 1 root root 37977 Oct  8 20:45 highlight.pack.js

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/highlightjs/highlight:
total 196
-rw-r--r--. 1 root root 2235 Oct  8 20:45 arta.css
-rw-r--r--. 1 root root  830 Oct  8 20:45 ascetic.css
-rw-r--r--. 1 root root 1738 Oct  8 20:45 atelier-dune.dark.css
-rw-r--r--. 1 root root 1752 Oct  8 20:45 atelier-dune.light.css
-rw-r--r--. 1 root root 1763 Oct  8 20:45 atelier-forest.dark.css
-rw-r--r--. 1 root root 1772 Oct  8 20:45 atelier-forest.light.css
-rw-r--r--. 1 root root 1753 Oct  8 20:45 atelier-heath.dark.css
-rw-r--r--. 1 root root 1762 Oct  8 20:45 atelier-heath.light.css
-rw-r--r--. 1 root root 1784 Oct  8 20:45 atelier-lakeside.dark.css
-rw-r--r--. 1 root root 1793 Oct  8 20:45 atelier-lakeside.light.css
-rw-r--r--. 1 root root 1774 Oct  8 20:45 atelier-seaside.dark.css
-rw-r--r--. 1 root root 1783 Oct  8 20:45 atelier-seaside.light.css
-rw-r--r--. 1 root root 1769 Oct  8 20:45 brown_paper.css
-rw-r--r--. 1 root root 1520 Oct  8 20:45 codepen-embed.css
-rw-r--r--. 1 root root 2809 Oct  8 20:45 color-brewer.css
-rw-r--r--. 1 root root 1740 Oct  8 20:45 dark.css
-rw-r--r--. 1 root root 2602 Oct  8 20:45 default.css
-rw-r--r--. 1 root root 1814 Oct  8 20:45 docco.css
-rw-r--r--. 1 root root 1849 Oct  8 20:45 far.css
-rw-r--r--. 1 root root 1604 Oct  8 20:45 foundation.css
-rw-r--r--. 1 root root 1723 Oct  8 20:45 github.css
-rw-r--r--. 1 root root 2138 Oct  8 20:45 googlecode.css
-rw-r--r--. 1 root root 2674 Oct  8 20:45 hybrid.css
-rw-r--r--. 1 root root 1775 Oct  8 20:45 idea.css
-rw-r--r--. 1 root root 1486 Oct  8 20:45 ir_black.css
-rw-r--r--. 1 root root 1547 Oct  8 20:45 kimbie.dark.css
-rw-r--r--. 1 root root 1547 Oct  8 20:45 kimbie.light.css
-rw-r--r--. 1 root root 1878 Oct  8 20:45 magula.css
-rw-r--r--. 1 root root  923 Oct  8 20:45 mono-blue.css
-rw-r--r--. 1 root root 1992 Oct  8 20:45 monokai.css
-rw-r--r--. 1 root root 2334 Oct  8 20:45 monokai_sublime.css
-rw-r--r--. 1 root root 2256 Oct  8 20:45 obsidian.css
-rw-r--r--. 1 root root 1513 Oct  8 20:45 paraiso.dark.css
-rw-r--r--. 1 root root 1514 Oct  8 20:45 paraiso.light.css
-rw-r--r--. 1 root root 1663 Oct  8 20:45 pojoaque.css
-rw-r--r--. 1 root root 2574 Oct  8 20:45 railscasts.css
-rw-r--r--. 1 root root 1619 Oct  8 20:45 rainbow.css
-rw-r--r--. 1 root root 1961 Oct  8 20:45 school_book.css
-rw-r--r--. 1 root root 1622 Oct  8 20:45 solarized_dark.css
-rw-r--r--. 1 root root 1622 Oct  8 20:45 solarized_light.css
-rw-r--r--. 1 root root 2262 Oct  8 20:45 sunburst.css
-rw-r--r--. 1 root root 1449 Oct  8 20:45 tomorrow.css
-rw-r--r--. 1 root root 1623 Oct  8 20:45 tomorrow-night-blue.css
-rw-r--r--. 1 root root 1553 Oct  8 20:45 tomorrow-night-bright.css
-rw-r--r--. 1 root root 1620 Oct  8 20:45 tomorrow-night.css
-rw-r--r--. 1 root root 1557 Oct  8 20:45 tomorrow-night-eighties.css
-rw-r--r--. 1 root root 1534 Oct  8 20:45 vs.css
-rw-r--r--. 1 root root 2270 Oct  8 20:45 xcode.css
-rw-r--r--. 1 root root 1854 Oct  8 20:45 zenburn.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/rmd/magnific_popup:
total 24
-rw-r--r--. 1 root root  7782 Oct  8 20:45 magnific-popup.css
-rw-r--r--. 1 root root 14630 Oct  8 20:45 magnific-popup.js

/usr/lib64/R/library/knitrBootstrap/rmarkdown/templates:
total 8
drwxr-xr-x. 3 root root 4096 Oct  8 20:45 knitrBootstrap
drwxr-xr-x. 3 root root 4096 Oct  8 20:45 simple

/usr/lib64/R/library/knitrBootstrap/rmarkdown/templates/knitrBootstrap:
total 8
drwxr-xr-x. 4 root root 4096 Oct  8 20:45 skeleton
-rw-r--r--. 1 root root   59 Oct  8 20:45 template.yaml

/usr/lib64/R/library/knitrBootstrap/rmarkdown/templates/knitrBootstrap/skeleton:
total 12
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 css
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 js
-rw-r--r--. 1 root root  124 Oct  8 20:45 skeleton.Rmd

/usr/lib64/R/library/knitrBootstrap/rmarkdown/templates/knitrBootstrap/skeleton/css:
total 12
-rw-r--r--. 1 root root 11706 Oct  8 20:45 knitrBootstrap.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/templates/knitrBootstrap/skeleton/js:
total 4
-rw-r--r--. 1 root root 1252 Oct  8 20:45 knitrBootstrap.js

/usr/lib64/R/library/knitrBootstrap/rmarkdown/templates/simple:
total 8
drwxr-xr-x. 4 root root 4096 Oct  8 20:45 skeleton
-rw-r--r--. 1 root root   74 Oct  8 20:45 template.yaml

/usr/lib64/R/library/knitrBootstrap/rmarkdown/templates/simple/skeleton:
total 12
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 css
drwxr-xr-x. 2 root root 4096 Oct  8 20:45 js
-rw-r--r--. 1 root root  107 Oct  8 20:45 skeleton.Rmd

/usr/lib64/R/library/knitrBootstrap/rmarkdown/templates/simple/skeleton/css:
total 8
-rw-r--r--. 1 root root 5017 Oct  8 20:45 simple.css

/usr/lib64/R/library/knitrBootstrap/rmarkdown/templates/simple/skeleton/js:
total 4
-rw-r--r--. 1 root root 894 Oct  8 20:45 simple.js

/usr/lib64/R/library/knitrBootstrap/templates:
total 44
-rw-r--r--. 1 root root  2742 Oct  8 20:45 default.html
-rw-r--r--. 1 root root  7297 Oct  8 20:45 knitr_bootstrap_code_style_toggle.html
-rw-r--r--. 1 root root 11730 Oct  8 20:45 knitr_bootstrap.css
-rw-r--r--. 1 root root  1947 Oct  8 20:45 knitr_bootstrap_includes.html
-rw-r--r--. 1 root root  5391 Oct  8 20:45 knitr_bootstrap.js
-rw-r--r--. 1 root root  4110 Oct  8 20:45 knitr_bootstrap_style_toggle.html

jimhester · 2014-10-09T12:22:56Z

Sorry you ran into difficulties, I split a few functions into their own file but neglected to add it to the repository. If you reinstall the latest version from the branch it should now work.

znmeb · 2014-10-09T19:01:18Z

Yep - working now! Notes:

MathJax doesn't seem to be enabled by default - I'll dig into that a bit later
The toggles for displaying R code and results seem to be there by default. I don't remember seeing in the documentation how to get rid of those in the YAML front matter.
It is using Bootstrap 3.2.0 - I haven't cycled through the themes yet.

I don't know if I've posted this before, but the target for all of this activity is my new blog, znmeb.bitbucket.org. That's built with Nikola and I can either post HTML out of knitrBootstrap or raw Markdown there. Actually I can post anything Pandoc can handle; Nikola has the option to call out to Pandoc as a compiler. Nikola's "native" language is Restructured Text, which is big amongst the Pythonistas.

jimhester · 2014-10-10T13:57:42Z

@znmeb Mathjax should be working now. As far as the toggles go there is no way to get rid of them completely. You may want to try using simple_document which uses only a small toggle on the side of each block instead of the buttons or panels used in bootstrap_document.

I could also make a version which does not have a toggle at all and only has a thin panel outline based on the code type if that is what you are looking for.

znmeb · 2014-10-10T18:38:43Z

I'm going for "mobile first" here - the toggles (and the old navbar and theme magic) work on a mobile small screen but they distract from the content. If you've got a recent version of Firefox handy, go into the 'Developer' menu, select 'Responsive Design View' and look at a rendered page with resolution 320x480. Bootstrap 3 itself works that way, although I've had some issues with a few of the themes. I ended up with 'Cosmo' on http://znmeb.bitbucket.org/stories/mosaic-fancy-test-document.html because of the theme issues.

znmeb · 2014-10-10T18:45:06Z

Incidentally, the workflow for that test page used RStudio knit .Rmd -> Pandoc Markdown followed by Nikola Pandoc compilation of the Markdown to HTML. Migrating to knitrBootstrap will replace all the rendering in Nikola with HTML made in RStudio.

lcolladotor · 2014-10-14T02:17:09Z

Hi,

I just noticed all of these changes. Is there somewhere I should look for some minor docs? Or should I wait a bit longer before testing?

I am hoping that it won't be too hard to switch to this version from the previous github one as I'm using knitrBootstrap for my recently accepted packages in Bioconductor.

derfinder BioC version (has to use knitrBootstrap's CRAN version) vignettes: basic and advanced versus GitHub hosted versions basic and advanced
derfinderHelper Vignette in Bioconductor has link to GitHub hosted version.
derfinderPlot (same as above)
regionReport (same as above)

I'm using a makefile for creating the vignettes and specifying the appropriate call depending on the knitrBoostrap version as seen here.

Thank you again for making knitrBootstrap!

znmeb · 2014-10-14T06:08:22Z

I've updated my workflow for http://znmeb.bitbucket.org; see http://znmeb.bitbucket.org/stories/blogging-with-rstudio-and-nikola.html for the details. I'm generating un-themed HTML using the standard RStudio knitr-pandoc chain. I then pass the un-themed HTML to Nikola for theming and the rest of the site building. I'll be migrating to knitrBootstrap once the next release is out and turning off most of the Nikola theming for RStudio-authored documents.

jimhester · 2014-10-15T13:11:54Z

@lcolladotor Please try out the new version, I would like as much user input as possible before switching. If you miss something let me know and I can add it. I am also thinking of making the simple format the default one, so I feedback on how everyone likes that would be great.

In terms of creating vignettes with the new version it should be easier than previously, you can just use the following YAML header. I will make a template with this header in it, so it will be very easy to do in the future.

---
title: "Vignette Title"
author: "Vignette Author"
date: "`r Sys.Date()`"
output: 
  knitrBootstrap::simple_document
    toc: true
vignette: >
  %\VignetteIndexEntry{Vignette Title}
  %\VignetteEngine{knitr::rmarkdown}
  \usepackage[utf8]{inputenc}
---

Align chunks with text

Support Rmarkdown's tabbed navigation

This allows referencing a chunk with label `chunkLabel` in the text with something like [this code](#chunkLabel).

into tag-chunks

jimhester · 2016-03-21T13:55:03Z

Just an FYI to anyone watching this thread the newest version of Rmarkdown has support for code folding (http://blog.rstudio.org/2016/03/21/rmarkdown-v0-9-5/) which was one of the few remaining features knitrBootstrap had that regular rmarkdown did not.

lcolladotor · 2016-03-21T14:39:26Z

Thanks for the note @jimhester. It looks very promising.

I'm guessing that you were involved in this now that you are at RStudio.

Cheers,
Leo

With rmarkdown v0.9.5 released today and described at http://blog.rstudio.org/2016/03/21/rmarkdown-v0-9-5/ it doesn't look like knitrBootstrap adds much anymore as commented by Jim Hester himself at jimhester/knitrBootstrap#68 (comment) With this in mind, I'm switching the default to rmarkdown instead of using knitrBootstrap. Specially because the version of knitrBootstrap I like to use is only available via GitHub and will probably never make it to CRAN. It might even make sense to completely drop the knitrBootstrap dependency, although I'll leave it for now since there is no immediate need to drop it. I'm also testing using the DT package for the datatables features instead of the JS code that was included before. This might not work on this commit but I'll get it to work soon anyway.

Tag chunks

lcolladotor · 2016-03-22T02:24:50Z

I had a lot of unread notifications from knitrBootstrap and until I went through them did I realize that @humburg has been doing a lot of great work on this package. I did switch my regionReport to use rmarkdown v0.9.5 by default as documented at leekgroup/regionReport@e9d8aeb. One feature from knitrBootstrap that I think is missing in rmarkdown is the thumbnails for the figures.

Anyhow, I don't know if you plan on pushing this branch to CRAN or not and it's probably too early to tell. For now, I'll leave the option to use knitrBootstrap on regionReport.

* Place 'include after' block after body * Add scrollbar to long TOC * Replace deprecated '--no-wrap' option * Allow wrapping option to be set in yaml header

With rmarkdown v0.9.5 released today and described at http://blog.rstudio.org/2016/03/21/rmarkdown-v0-9-5/ it doesn't look like knitrBootstrap adds much anymore as commented by Jim Hester himself at jimhester/knitrBootstrap#68 (comment) With this in mind, I'm switching the default to rmarkdown instead of using knitrBootstrap. Specially because the version of knitrBootstrap I like to use is only available via GitHub and will probably never make it to CRAN. It might even make sense to completely drop the knitrBootstrap dependency, although I'll leave it for now since there is no immediate need to drop it. I'm also testing using the DT package for the datatables features instead of the JS code that was included before. This might not work on this commit but I'll get it to work soon anyway. git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/regionReport@115061 bc3139a8-67e5-0310-9ffc-ced21a209358

jimhester added 3 commits October 7, 2014 14:20

Simple document format

d2f2c67

Fix calc_offset function

801314c

Update readme and remove more functionality

41c840f

jimhester added 2 commits October 8, 2014 09:07

Some tweaks to get things displaying properly

bb5a8e5

Update examples

25924a2

Add missing utils files

a662950

jimhester mentioned this pull request Oct 9, 2014

incompatibility with pandoc citations #53

Open

jimhester added 3 commits October 10, 2014 09:34

Fix mathjax

19f8e4a

Add missing default bootstrap style

7368eaf

Get TOC working for both simple_document and bootstrap_document

30b2cc1

jimhester added 2 commits October 15, 2014 08:40

Add well back to the TOC

2af9d0b

Move default.html, remove old unused code

8881044

jimhester added 2 commits October 16, 2014 09:35

Add table styles to simple

120ae15

add newlines after tags

a7615dc

lcolladotor mentioned this pull request Oct 16, 2014

Pandoc step hanging with knitrBoostrap 1.0.0 (jimhester/knitrBootstrap@76c41f0) #72

Closed

humburg added 14 commits February 26, 2016 16:16

Merge pull request #186 from jimhester/chunk-alignment

c03b82a

Align chunks with text

Support Rmarkdown's tabbed navigation

0d05a57

Update dependencies

b368ed5

Merge pull request #187 from jimhester/tabbed-navigation

c2771fb

Support Rmarkdown's tabbed navigation

Add anchor to named chunks.

6ca25ac

This allows referencing a chunk with label `chunkLabel` in the text with something like [this code](#chunkLabel).

Factor out code to add anchors.

9020099

Add anchor to figure captions.

3885ba3

Update README

498a1a5

Update NEWS

af5e55b

Fix formatting issues

708407c

Update TOC

10ecba6

Use id attribute for internal links

26c2fd1

Merge branch 'tag-chunks' of https://github.com/jimhester/knitrBootstrap

746c445

into tag-chunks

Use knitr's 'fig.lp' option

d8a12c8

lcolladotor mentioned this pull request Mar 21, 2016

Add code folding Bioconductor/BiocStyle#1

Closed

Merge pull request #188 from jimhester/tag-chunks

8b87eb2

Tag chunks

Update chunk reference documentation

f971572

lcolladotor mentioned this pull request Mar 22, 2016

long TOC which doesn't scroll #34

Open

humburg added 2 commits March 24, 2016 11:35

Add missing semicolons

463cde8

Minor improvements and bug fixes (#191)

2138644

* Place 'include after' block after body * Add scrollbar to long TOC * Replace deprecated '--no-wrap' option * Allow wrapping option to be set in yaml header

This was referenced Jul 10, 2016

Improving documentation about using package options #166

Open

rpivotTable is not getting drawn with this #192

Closed

humburg added 2 commits July 14, 2016 22:09

Update to rmarkdown 1.0

b8c569e

Styling for TOC scroll bar (webkit only)

7a9b8c7

humburg mentioned this pull request Feb 13, 2017

Update to bootstrap v3.3.7 & highlight.js v9.9.0 #193

Closed

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Simple document format #68

Are you sure you want to change the base?

Simple document format #68

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