SciRNotebook: A CSS repository from kriemo

title

author

date

output

html_document

SciRNotebook

Kent Riemondy

12/16/2015

theme	highlight
cosmo	tango

An electronic Scientfic notebook format based on RMarkdown

Key Features
- lunr.js search feature
- RMarkdown integration with local html web interface

Requirements

indexing the lunr.js database requires node.js
RMarkdown and Knitr
R
R packages tm jsonlite wordcloud pacman
imageMagick (convert function)
Only tested on Mac OS 10.10 as of now

Included packages

Usage

Example notebook entry

cd SciRNotebook/Entries

Take a look at the Example.Rmd and Example.html files to see how to use markdown syntax to link html documents together and how to reference local data files.

To add a new entry

cd SciRNotebook/

add your first entry to the Notebook_toc.Rmd document using the new_notebook_entry.sh script

scripts/new_notebook_entry.sh "my first entry"

render the .Rmd documents Notebook_toc.Rmd and Search.Rmd to .html using knitr and the provided script render_Rmarkdown_to_html.sh

for file in Entries/*.Rmd
do echo $file
scripts/render_Rmarkdown_to_html.sh $file
done

Open up the Notebook_toc.html to navigate the notebook. Check out the coding links in the navbar to navigate to an example document.

Themes

To customize the outlook you can change the bootstrap theme. The current default is cosmo but you can change it to other themes.

Available themes are default, cerulean, journal, flatly, readable, spacelab, united, cosmo
Also can edit the text highlight scheme for syntax highlighting in the _output.yaml file

To change the theme edit Entries/_output.yaml theme type to desired bootstrap theme in the following manner.

Default _output.yaml with cosmo theme

 html_document:
  self_contained: false
  theme: cosmo
  highlight: textmate
  lib_dir: libs
  includes:
    in_header: include/in_header.html
    before_body: include/before_body.html

_output.yaml with united theme

 html_document:  
  self_contained: false  
  theme: united  
  highlight: textmate  
 lib_dir: libs  
  includes: 
    in_header: include/in_header.html  
    before_body: include/before_body.html

Customizing header navbar links

The html that controls the links in the navbar is located in the Entries/include/before_header.html file. Edit the "dummy links" included to link to .html files of interest.

Wordcloud

A wordcloud is displayed on the Notebook_toc.html page. This wordcloud is derived from the database.json file used for indexing the lunr.js search. Words can be removed from the wordcloud by editing the wordcloud_generator.R script and adding words to the badwords variable. If you want to disable the wordcloud, remove the html code in lines 12-15 of the Entries/Notebook_toc.Rmd file.

Credits

This format was mostly inspired by the RMarkdown documentation website.

kriemo/SciRNotebook