Tag: Reproducible Research

Edit a source block with its name shown in org

My preference is to rely upon heading property inheritance to define source block
names. That way, you can just do your work knowing “where” you are working and
keep it simple by not having to name everything. That was just fine until I
wrote a document where I needed to name each source block.
It gets easy to forget the source block’s name. Not the end of the world, but very nice to know. 

(defun gcr/org-edit-src-code-plus-name ()
  "Edit the well-described source code block.
Attribution: URL `https://lists.gnu.org/archive/html/emacs-orgmode/2014-09/msg00778.html'"
  (interactive)
  (let* ((eop  (org-element-at-point))
         (name (or (org-element-property :name (org-element-context eop))
                  "ॐ"))
         (lang (org-element-property :language eop))
         (buff-name (concat "*Org Src " name "[" lang "]*")))
    (org-edit-src-code nil nil buff-name)))

R Markdown

R Markdown is an authoring format that enables easy creation of dynamic documents, presentations, and reports from R. It combines the core syntax of markdown (an easy-to-write plain text format) with embedded R code chunks that are run so their output can be included in the final document. R Markdown documents are fully reproducible (they can be automatically regenerated whenever underlying R code or data changes).

Package management in R

Once you start using different versions of packages for different projects
then you will probably want a package-management solution for R. Or perhaps
you are coming from another language that had a package-management solution
that you were already happy with. Curious about the offerings I searched
and found two options, rbundler and Packrat. Having read the literature for both,
they seem to be more than adequate providing everything that one would expect.

Package Github CRAN PDF
rbundler here here here
Packrat here NA NA

My current approach is to install all packages into my user directory so as not
to spoil the global package cache. Most likely that approach won’t scale for
larger projects, so when the need arises I will migrate to one of these
solutions.

If you’ve never used something like this before, then you will be well-served to
first becomes comfortable and masterful managing it yourself before automating
it.

Whatever your approach, it is a real treat to know that both solutions are
available for when you embrace reproducible research.

A progress indicator for code blocks in org-mode

A progress indicator for code blocks in org-mode courtesy
of John Kitchin: 

;; give us some hint we are running
(defadvice org-babel-execute-src-block (around progress nil activate)
  (set-face-attribute
   'org-block-background nil :background "LightSteelBlue")
  (message "Running your code block")
  ad-do-it
  (set-face-attribute 'org-block-background nil :background "gray")
  (message "Done with code block"))

What all of those org-babel functions do

For the lazy org users like myself who want to know what the functions
listed here do, just evaluate the one you want: 

(describe-function 'org-babel-execute-src-block)
(describe-function 'org-babel-open-src-block-result)
(describe-function 'org-babel-load-in-session)
(describe-function 'org-babel-pop-to-session)
(describe-function 'org-babel-previous-src-block)
(describe-function 'org-babel-next-src-block)
(describe-function 'org-babel-execute-maybe)
(describe-function 'org-babel-open-src-block-result)
(describe-function 'org-babel-expand-src-block)
(describe-function 'org-babel-goto-src-block-head)
(describe-function 'org-babel-goto-named-src-block)
(describe-function 'org-babel-goto-named-result)
(describe-function 'org-babel-execute-buffer)
(describe-function 'org-babel-execute-subtree)
(describe-function 'org-babel-demarcate-block)
(describe-function 'org-babel-tangle)
(describe-function 'org-babel-tangle-file)
(describe-function 'org-babel-check-src-block)
(describe-function 'org-babel-insert-header-arg)
(describe-function 'org-babel-load-in-session)
(describe-function 'org-babel-lob-ingest)
(describe-function 'org-babel-view-src-block-info)
(describe-function 'org-babel-switch-to-session-with-code)
(describe-function 'org-babel-sha1-hash)
(describe-function 'org-babel-describe-bindings)
(describe-function 'org-babel-do-key-sequence-in-edit-buffer)

There are some very special functions in there!