repository for code and data from Wallis, Dorr & Bex (2015).
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figs
funs
output
analysis_master.R
gcd_contrast_final_manuscript.bbl
gcd_contrast_final_manuscript.tex
license.txt
readme.md

readme.md

Detection of gaze-contingent contrast increments in natural image movies

DOI

These are R scripts to reproduce the analyses in Wallis, Dorr & Bex (in press).

These files are released under the GPL-3 License. I don't offer any support. You are welcome to send me an email but I make no claim that I will (be able to) help, particularly if you are attempting to use a different platform or setup than mine (I'm running on OSX 10.9 with RStudio; the MCMC sampling was conducted on a Debian distribution).

IMPORTANT: If you adapt any part of these scripts for your own academic work, please help keep me employed by citing the following paper:

Wallis, T. S. A., Dorr, M., & Bex, P. J. (2015). Sensitivity to gaze-contingent contrast increments in naturalistic movies: An exploratory report and model comparison. Journal of Vision, 15(8), 3. http://doi.org/10.1167/15.8.3

Subdirectories in this repository

The main file is analysis_master.R in the parent directory. Use this as a guide to follow all the analyses.

Other directories are:

  • /output/ contains data used for analysis. These are currently distributed as R binaries to reduce file size, but if you want .csv files let me know.
  • /funs/ contains all scripts and functions to produce the analysis and figures. There are also a bunch of legacy functions included for completeness that were not used in the final paper, and may no longer run.

Very raw data

We have chosen not to provide the raw-est of raw data or MCMC samples here due to size limitations (these files are very large). If you need them, please contact me. They may go up on a different venue at some time; if so I will provide a link here.

Reproducing the analysis

The analyses in the paper were performed in R using various libraries. By looking through the analysis_master.R file you can determine which scripts in the /funs/ directory to run in which order (or just source analysis_master.R. There may be problems with paths, particularly if you're running a windows system (this code uses hard-coded / characters for directory separation; sorry).

Dependencies

I've tried to compile a list of dependencies for these scripts here. These packages are required to run all the scripts to reproduce the analysis. If I've left something off please let me know.

  • Rstan (available from www.mc-stan.org)
  • wutils (available from my github here)
  • psybayes (available from my github here)

Everything else is on CRAN:

  • plyr
  • dplyr
  • xtable
  • ggplot2
  • reshape2
  • scales
  • grid
  • gridExtra
  • ROCR
  • mgcv
  • ggmcmc

Stan version for the sampling in the paper

The MCMC samples reported in the paper were all performed using Stan version 2.2.0.

License

Copyright 2013, Thomas Wallis.

This is free, open source software released under the GPL-3 License. See LICENSE.txt for details.

Use this software at your own risk.