Reproducible Research & Code

Amazon Mechanical Turk Bonus Script

Python script to programmatically pay bonuses to workers on Amazon Mechanical Turk. Requires Amazon Command Line Tools.

Qualtrics to R Integration

R function to programmatically download survey data from Qualtrics directly into your R environment.

Continuous Inclusion of Other in Self (IOS) Scale

JavaScript implementation of a continuous IOS scale using Raphael.js for online experiments.

One-line redaction of identifiable information in R

Simple one liner to replace identifiable information (e.g. mTurk workerids). (Has some cons, but it's fast.)
d0$workerid_random <- match(d0$workerid, unique(sort(d0$workerid)))

If you want to be even cooler and use a one-way hash function, here's a one-liner using the digest() function (from the digest package):

library(digest); d0$workerid_hash <- substr(sapply(as.character(d0$workerid), digest, algo="md5", serialize=F), 1, 6)

(the code above: (1) converts workerid into a character string, (2) uses sapply() to apply digest() vectorially, (3) takes the first 6 characters of the resulting string.)

(Painlessly) updating R

A neat and simple trick to update R and re-install all your packages here.

Data Munging: Concatenate many (e.g. .csv) files in Terminal.

Sometimes you just want to concatenate all the data files in a directory into one big file. If it's in a format like .csv, and you want to skip the first header, you can use the following command in Terminal:
awk 'FNR > 1' *.csv > combined_file.csv

Destructively crop pdfs (useful for LaTeX-ing)

If you crop a pdf file in Preview, it doesn't destructively crop it. The parts you cropped out are still hidden in the file (i.e. so you can undo cropping). I've found that this gives trouble with LaTeX when it doesn't recognize the bounding boxes. If you need to destructively crop the file, one way to do it is using Ghostscript. Let's say you want to crop "in.pdf" to "out.pdf" (note that you can't use the same filename, because of the way gs works), at the command line, type:
gs -sDEVICE=pdfwrite -dUseCropBox -sOutputFile=out.pdf - < in.pdf

Convert Files to EPS (useful for LaTeX-ing)

Reference: http://electron.mit.edu/~gsteele/pdf/

[Postscript] Level 1 uses only ascii-coded RGB values, and is very wasteful, producing very large files. Level 2 includes support for JPEG encoded images, which produces much smaller files. Level 3 includes support for Zlib compression, making it well suited for making EPS files from png files.

In general, level 3 will produce the smallest files. Level 2 provides the best compatibility, and works well with jpeg images.

If you decide to use level 2 postscript, I recommend converting first to a jpg file. The "convert" program included Imagemagick uses a quality factor in "percent" that ranges from 0 to 100:

convert -quality 80 fig.png fig.jpg

I find a quality factor of 80 on high resolution images gives good compresssion without too much loss in quality. You can then to convert the image to eps using "convert" with the eps2 settings:

convert fig.jpg eps2:fig.eps

If you can use level 3 postscript, you can convert directly from png to eps:

convert fig.png eps3:fig.eps

Using level 3 postscript from a png image file for scientific figures will often produce a very small eps file. Ghostscript is compatible with these level 3 eps files, so this is often a good way to go.

Set Default Zoom in MS Word

Here's a simple Macro that you can use so that everytime Microsoft Word opens a new document, it does so at a specific zoom level. (Personally, I like 100% on my Retina Pro.).
1) In Word, Go to Tools->Macro->Macros.
2) On the dropbox after "Macros in", click Normal (Global Template)
3) Create a new Macro called AutoOpen [This particular name seems to be required for it to be run upon opening].
4) Paste the following macro in, where 100 is the desired zoom percentage.
Sub AutoOpen()
ActiveWindow.ActivePane.View.Zoom.Percentage = 100
End Sub
(refs: various places like this and this.)

Increase Mouse Sensitivity on Mac OS X

I love having really high sensitivity on my mouse/trackpad. Unfortunately, the maximum that you can go in System Preferences isn't high enough for me. There is a way to increase this sensitivity further. In Terminal, typing:
defaults read -g com.apple.mouse.scaling
will give you the current value of your mouse scaling. You can modify it by changing read to write. For example, if you want to set your mouse scaling to 3.0 (the maximum in System Preferences), type:
defaults write -g com.apple.mouse.scaling 3.0
In addition, to change the trackpad, use com.apple.trackpad.scaling. You can also use .scrolling to change scrolling speed.