Making your editor do statistics

All models are wrong, but some are useful.¹ ~George E. P. Box

Why is ESS useful?

ESS makes your command history searchable and modifiable. When you start doing statistics you think you will always remember what you did and instantly recall why you did it with that particular data. As you work on more projects you realize that is a hopeless task. But you will get questions on what you have done, especially if it was novel or well thought out. These questions may not start until months after your work is done. Having a command history is the bare minimum of what you will need to support your work. We will talk about creating replicable research later in these tutorials. Unbelievably, this is a topic almost never addressed in introductory courses.

ESS does other tasks for you as well that make interacting with your data easier. ESS gives you command line completion of both object (data) and file names which saves on both typing and mistakes. It creates so-called Hot Keys for quick performance of wrote tasks. It records a complete transcript of your R session. It provides an interface to the R help system. It allows you to edit your data. It provides highlighting and proper indentation which makes your code easier to read for you and others. It allows you to run either parts of files (called regions) or entire files.

ESS history

The project has been going since before the invention of R. It was around in 1989, when it was used to interact with R's proprietary antecedent Bell Lab's S-language built by Richard Chambers. I am a a geek about the history of scientific and mathematical ideas. If you are interested in the history, the wikipedia article is a good start. You can also check out the S-page at Bell Labs. For any academic work I strongly suggest citing the published paper on ESS which is available at this link.

Installing ESS

There are a number of ways to install ESS. I will create a separate series of posts on this. For many, this will be your first foray into FREE software and installing for the first time is not easy, particularly on a Mac. Here is a much to brief set of instructions:

Linux

Beginner

Install from the ELPA package manager. You should search for ESS (C-s, where C-s means press the Control and "s" keys at the same time). Refer to Xah Lee's tutorial on loading from the packackage manager.

Advanced

Download the package. If you do not have a hidden file called home/username.emacs create one and add the line:

(load "~/langs/emacs/elisp-ds/ess/lisp/ess-site")

Trap

Do not install Emacs and ESS from the Ubuntu or Debian repositories. They are usually hoplelessly out of date.

Windows

Download the emacs distribution for Windows from Vincent Goulet. Remember this is an executable file and you will have to allow it to work.

Mac OS X

Download the emacs distribution for Mac OS X Vincent Goulet. Remember this is an executable file and you will have to allow it to work. Also you have to drag the downloaded file to your apps file. I have never understood the point of this and I forget to how to do it every time. Here is a reference and explanation. It always makes me think of how Richard Stallman who founded the Free Software movement hated Steve Jobs:

Steve Jobs, the pioneer of the computer as a jail made cool, designed to sever fools from their freedom, has died.

As Chicago Mayor Harold Washington said of the corrupt former Mayor Daley, "I'm not glad he's dead, but I'm glad he's gone." Nobody deserves to have to die – not Jobs, not Mr. Bill, not even people guilty of bigger evils than theirs. But we all deserve the end of Jobs' malign influence on people's computing.

Unfortunately, that influence continues despite his absence. We can only hope his successors, as they attempt to carry on his legacy, will be less effective. ~Richard M Stallman

Testing your installation

You have to have installed R. The instructions are here. You have to have installed Emacs and ESS. For Windows and Mac Users, you get both Emacs and ESS when you download from Vincent Goulet. Now type M-x R. This will start an R process within a new buffer. These buffers are called inferior as they run a process under Emacs. The ESS manual calls them iESS buffers.

If something went wrong, note the error and search. If nothing happened try searching "Emacs can't find my R installation."

Editing R code

Indentation is automatic. If you want to do something special use the command M-x indent region. If you don't understand what that means please refer to my earlier tutorial on basic emacs. It also resets the underscore "_" to the assignment arrow "<-" which saves a keystroke many times. If not you can use the underscore by typing M-q _ or just "_" twice. You can tab complete objects (data) with C-c TAB in buffers that end with .R extension. It is by the file extension that Emacs knows what mode to use.²

Here are the key-bindings for moving around functions:

Viewing help files

You can view a help file two ways. If you are in the R console:

?pbinorm

If you are not:

C-c C-v RET pbinom RET

The R session

In the *R* buffer you can run any R command. R and statistics will be the next tutorial. You can recall your command history.

Transcripts

You can save an R buffer to create a transcript. You can clean up the transcript with M-x ess-transcript-clean-buffer. You can run multiple sessions of R.=M-x R= multiple times will generate multiple processes, e.g. *R*, *R:2*, …

Sending code from an R buffer to an R session

If you only have one R session (typical), it will automatically be associated with the R buffer. Otherwise you can associate the buffer with C-c C-s. Here are the bindings for sending code:

About 90% of the time I only use:

Next we are on to statistics!!