资源说明：Add ons for orgmode

* orgmode-accessories

_Add ons for orgmode_

This is the =org-9-plus= branch. Use this with *Release 9.0* or higher. It utilizes
the new versions of `org-babel-get-src-block-info' and `org-babel-lob-get-info'.

If you are running on the `master' branch this commit of Org mode is
this first with new versions of those functions:

#+BEGIN_QUOTE
 commit 9738da473277712804e0d004899388ad71c6b791
  Author: Nicolas Goaziou 
  Date:   Wed Feb 10 00:22:09 2016 +0100
#+END_QUOTE


* The other files here:

- ox-ravel.org :: description and definition of backends to create
               ~Sweave~, ~brew~, ~Rmd~, and ~html~ style files.

- demos.org :: demonstrations of various ravel features and use cases.

- test.org :: ERT unit tests of ravel features.

- example-1-Rnw.org :: includes an orgmode translation of example-1 from the
     Sweave user's manual. Exporting with ~ravel-latex~ produces a
     file very similar to the =*.Rnw= code.

- knitr-minimal-rhtml.org :: includes an orgmode translation of
     =knitr-minimal.Rhtml= from the [[http://yihui.name/knitr/demos][the knitr demos page]].

- test-cases.org :: this sets up to allow parallel exports using
                    ~latex~ and two derived backends ~ravel-latex~
                    and ~ravel-brew~ and inspect the =diffs= between
                    them.

- autodep.org :: orgmode translation of 017-auto-dependson.Rnw from
     [[https://github.com/yihui/knitr-examples][knitr examples page]] illustrates dependency aware caching of
     computed objects.

- slidify-example.org :: how to use the ~slidify~ package to make
     slides.

- markdown.org :: describes features of the ~ravel-markdown~ backend.

* Bugs?

Bugs happen. Please let me know if you encounter a bug or if
something seems to break that once worked as that might indicate a
change in the exporter or Babel that I need to keep up with.

The example ~*.org~ files should always work! 


* Why Bother ?

  
** orgmode

[[http://orgmode.org/index.html][Orgmode]] is /for keeping notes, maintaining TODO lists, doing project planning, and authoring with a fast and effective plain-text system./ The same org document can be used to create LaTeX, HTML, plain ASCII, and various other formats upon export.

[[http://orgmode.org/worg/org-contrib/babel/index.html][Babel]] is /Org-mode's ability to/ /execute source code/ /within Org-mode documents/. It is powerful and flexible and a useful tool for generating reproducible research reports as outlined in [[http://www.jstatsoft.org/v46/i03][the report :]] Eric Schulte, Dan Davison, Thomas Dye, and Carsten Dominik. A Multi-Language Computing Environment for Literate Programming and Reproducible Research. Journal of Statistical Software. 46(3) Jan 2012. Source code blocks can be editted in place or in a language major-mode edit buffer containing the body of the code block. And for R blocks, ~ESS~ is fully functional.

** R document/report Generators 

There are many markup and report and document generating packages and
functions for R. A useful overview of them is at [[http://cran.r-project.org/web/views/ReproducibleResearch.html][CRAN Task View for
Reproducible Research]]

Several to which this software is aimed are 

   - Sweave
   - brew 
   - knitr

** Putting orgmode and Sweave together

Each approach (orgmode as report generator vs Sweave-like report
generators) has its own strengths and weaknesses.

orgmode makes it really easy to track things and to build code
incrementally.

Sweave has several /dependency aware/ caching systems in R that are
simple and powerful. Also, there are some nice formatting tools
available and more coming into use. And many of them are hard (or
maybe impossible) to use when Babel is doing the final report
generation. There are terrific possibilities presented by R packages
like [[http://yihui.name/knitr/][=knitr=]] and [[https://github.com/daroczig/pander][=pander=]].

** The Org export engine

The Org export engine (see the Org manual [[http://orgmode.org/org.html#Exporting][Exporting]] section or the [[http://orgmode.org/worg/dev/org-export-reference.html][Org
Export Reference Documentation]]) offers the possibility to have a
workstyle in which an orgmode master document contains a /subtree/
with text and code blocks that when exported becomes an Sweave or brew
style document that when run produces LaTeX, HTML, and/or some other
markup language. By including caching options in those documents the
development process becomes easy to organize, restarting work after a
break is just a matter of rerunning the document to load the cached
objects and libraries, then switching to the orgmode master to try out
some new code, reorganize the presentation, and so on.

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