jt14den/workshops-1

IQSS RTC workshop materials

Statistical Software Workshops From The RTC Team at IQSS

Looking for the workshops index page? Go to http://tutorials/iq/harvard/edu.

Most of the notes for these workshops were written in http://orgmode.org markup and should be viewed in the http://www.gnu.org/software/emacs/ text editor >= version 24.3 with orgmode >= 8.0. If you use a version of emacs >= 24.3 the required emacs packages can be installed by opening the StartHere.el file in the “Classes” folder. While I have made an effort to make these materials usable by someone new to emacs and org-mode, working with these materials will be much more pleasant if you have at least some experience with emacs and the org-mode emacs package.

These files includes literate code blocks that can be executed in emacs by typing the command ‘M-x org-babel-execute-src-block’, which is usually bound to ‘C-c C-c’ (See http://oreilly.com/openbook/mh/conv.htm if you are unfamiliar with emacs key conventions). You can execute all the example code in this document using the command ‘M-x org-babel-execute-buffer’. You must have R installed on your system, and you must have the emacs package ‘ess’ installed (ess can be auto-installed by opening the “StartHere.el” file in the “Classes” folder).

The contents of these documents can be exported to a variety of formats, including pdf slides (requires a LaTeX distribution, preferably TeXlive or MacTex), html, or text. To access the export menu run the command ‘M-x org-export-dispatch’, usually bound to ‘C-c C-e’ (choose “Beamer” for pdf slide export). Export to pdf requires python and the python module ‘Pygments’ (you must install this manually).

For pdf/beamer I like to set ‘exports results’. For html set either ‘exports results’ or ‘exports both’. For script/text export set ‘exports code’. In this later case my system is not fully automated; export to text, open the .txt file and save it with a .R extension. Coment out everything (C-x h M-x comment-region) and then use find and replace to uncomment to the code sections (M-x replace-string). Available export tags include ‘prototype’ (exercise solutions) ‘labsetup’ (instructions specific to IQSS lab machine setup), ‘setup’ (generic setup instructions) and ‘mitsetup’ (instructions specific to MIT Athena computing cluster setup).