# Instructions for use #
This component contains the analysis and plotting scripts for Experiment 2c. The scripts are organized into two folders (AnalysisScripts and AnalysisScripts_EyePos). Under the heading for each folder there are brief descriptions of what each script does (roughly listed in the order you'd want to run them).
## AnalysisScripts ##
This folder contains all the scripts to run the main analyses reported in the paper.
**SubList.mat:** a .mat file that contains the list of subjects with usable data.
**compileBehavior_JJF_17_5:** compiles relevant variables from raw behavior files (one file for each block of the task) into a single file for each participant. Note: the compiled behavior files are already available in the 'Compiled Data' component.
**fitModel:** fit mixture model to response errors using MemToolbox (http://visionlab.github.io/MemToolbox/).
**summarizeParamEsts:** summarize the parameter estimates (for all subjects) obtained using fitSwapModel in a single matrix.
**SpatialEM_v3:** runs the spatial encoding model on alpha-band (8-12 Hz) activity.
**SpatialEM_Permute_v3:** runs the relevant spatial encoding model routine 1000 times, each time with the location bin labels permuted within each train/test set. The output of these scripts is the basis for the permutation tests that we report in the paper.
**calculateSlopes_Alpha_v3:** cacluate CTF slope matrix for both the unpermuted (output of SpatialEM_v3) and permuted (output SpatialEM_Permute_v3) data.
**PermTest_Alpha:** uses the output of the calculateSlopes scripts to run the permuation test using the CTF slope metric.
**bootstrapSlopes_v3:** bootstrap standard error bars across time.
**baselinedEOG:** baseline the EOG data.
### Plotting functions ###
**plotHEOGBias:** plot the average baselined HEOG as a function of position bin. Uses output from baselinedEOG.m
**plotSlopes:** plot the time-resolved slope of target- and non-target-CTFs (Fig 3c').
### Sub-functions called by other scripts ###
**eegfilt:** EEGLAB’s filtering function (http://sccn.ucsd.edu/eeglab/; Delorme & Makeig, 2004). Called by the SpatialEM scripts for filtering data.
**shadedErrorBar:** used for generating shaded error bars (retrieved from: https://www.mathworks.com/matlabcentral/fileexchange/49382-pict--particle-image-characterization-tool/content/PICT/shadedErrorBar/shadedErrorBar.m)
## AnalysisScripts_EyePos ##
This folder contains the scripts used to analyzed the eye tracking data reported in Figure S4 in the Supplemental Information.
**EyeTrackSubList:** a .mat file that contains the list of subjects with usable eye tracking data.
**shadedErrorBar** and **eegfilt** are described above.
**EyeTrack_processData:** read in eye tracking data, mark trials with bad eye tracking data (i.e., eye tracker lost the pupil), drift correct the data, save to a file.
**EyeTrack_AveByBin:** average eye data for each position bin.
**plot_SuppEyeFig:** plot data as in Figure S4 in Supplemental Information.
**sortEyePosition:** create a trial-by-trial gaze position values (in polar coordinates) for each subject. Used to generate the gaze-position-based CTFs in Figure S4.
**SpatialEM_v3_EyeControl:** run the spatial encoding model using either the target position or the gaze position.
**summarizeBinCounts:** check how many trials per bin we have for each subject for this analysis.
**bootstrapSlope_EyeControl:** bootstrap error bars for the target- and gaze-related CTFs.
**plotSlopes_EyeControl:** plot time-resolved slope for the eye movement control (see Figure S4).
