New tutorials

June 20, 2018

I am working on two new series of tutorials, one using R and the other using Stata. The focus will be on biostatistical computing or computational statistics at a glance but this is just the beginning and I have no definitive idea how this will turn out. The projects can be watched on GitHub (rstats-sk and stata-sk) or they are rendered online on this site.

Of note, the rstats-sk project has been abandoned.

When I think about it I can’t help but smile at the idea that my business has resumed on GitHub even though Microsoft has taken the lead. Anyway, I hope to be able to write enough material by the end of the Summer.

Regarding the format, this time I choose to use Org instead of Markdown (not much standards, too few exporting options without having to resort on inserting plain HTML code) or $\LaTeX$ (managing to find good HTML rendering has always been a pain and the language is definitely too much for these kind of projects). It works quite nicely with ox-bibtex and standard html-export. I know I could use the Pandoc backend (ox-pandoc) but I prefer a simple solution where I can manage my own CSS and focus on the content. After all, isn’t it also the purpose of markup languages like $\LaTeX$ or Markdown? (Unless you have very poor standards you are likely to spend a lot of time customizing your $\LaTeX$ template or YAML header, assuming you are using Pandoc as you should.) But prettu much like John D. Cook said, with time we come back to appreciate just plain text:

Then comes the Makefile, because I don’t want to have to export all Org files one at a time and keep them in sync with my static blogging engine. Currently, I am using a very basic Makefile grabbed from StackOverflow. There are further refinements to add, especially regarding the cleaning of intermediate files, but overall it is quite working. There are little subtleties with using org-babel for Stata code: besides the minor annoyance of replicating the input commands in the output block, it is not possible to generate PNG files and a default font family is chosen because the Terminal exec file says this is how it should be. Rob Hicks has some tricks to customize ob-stata.el but I don’t want to spend too much time in updating my packages repository. (BTW, I did try his workaround at some point and it works really great.)

One nice thing about Emacs is that you can use it without any shebang: Right now, I am just asking to run Emacs in batch mode and load a custom init file with default setting for R or Stata. So basically, you just need to have org-mode, which comes with Emacs in almost all system-wide install, ESS and ox-bibtex. Here is the magic invocation:

emacs --batch -l setup.el $< -f org-html-export-to-html --kill

And here is what I have in setup.el in the case of Stata:

;; FIXME Find a way to make the following independant of ELPA versioning
(add-to-list 'load-path "~/.emacs.d/elpa/27.0/develop/org-plus-contrib-20180514")
(add-to-list 'load-path "~/.emacs.d/elpa/27.0/develop/htmlize-20180412.1244")
(add-to-list 'load-path "~/.emacs.d/elpa/27.0/develop/ess-20180610.800/lisp")

;; Required stuff
(require 'ess-stata-mode)
(require 'org)
(load "ox-bibtex.el")

;; Setup default settings
(setq inferior-STA-program-name "/usr/local/bin/stata"
      org-confirm-babel-evaluate nil
      org-src-fontify-natively nil
      org-html-htmlize-output-type nil
      ess-ask-for-ess-directory nil)
(org-babel-do-load-languages 'org-babel-load-languages '((stata . t)))

;; Add-ons
(org-add-link-type "span" #'ignore
                   #'(lambda (class desc format)
                       (pcase format
                         (`html (format "<span class=\"%s\">%s</span>"
                                        (or desc "")))
                         (_ (or desc "")))))
(org-add-link-type "stata" #'ignore #'my/export-stata-link)
(defun my/export-stata-link (path desc format)
  "Export org stata links to html."
  (cl-case format
    (html (format "<a href=\"\" class=\"stata\">%s</a>" path (or desc "")))
    (latex (format "\"%s\")" path))))

The “Add-ons” part is just a custom org-link that allows to auto-link Stata commands to their online documentation on

♪ Timber Timbre • Cedar Shakes

See Also

» Automated ML interpretation » Minor update on SAS2R » Spacemacs June 2018 » Setting Up Mu4e 1.0 C » Org and Bibtex