Spike Train Analysis Toolkit Documentation  Spike Train Analysis Toolkit Function Reference  Contents

Spike Train Analysis Toolkit

Contents

 Spike Train Analysis Toolkit table of contents.

 General functions and utilities.
   make                      - Compile functions in the Spike Train Analysis Toolkit.
   entropy1d                 - Entropy from a 1-D histogram.
   entropy1dvec              - Entropy from a vector of 1-D histograms.
   info2d                    - Information and entropies from a 2-D histogram.
   infocond                  - Information and entropies from conditional and total histograms.
   matrix2hist2d             - Converts a 2-D matrix of counts to a 2-D histogram.
   staread                   - Read STAD and STAM files into an input data structure.  
   stawrite                  - Write STAD and STAM files from an input data structure. 
   staraster                 - Raster plot of an input data structure.
   multisitearray            - Convert a multi-site input data structure
   multisitesubset           - Extract a subset of sites from a multi-site
   staversion                - Return the version and revision number of the Spike Train Analysis Toolkit.

 Demonstrations and verification.
   demo/demo_all             - Run all directcat, binless, and metric information demos on the 'synth' and 'taste' datasets.
   demo/demo_binless         - Run binless information demo on the 'synth', 'taste', or 'drift' datasets.
   demo/demo_ctwmcmc         - Run CTWMCMC formal information demo on the 'inforate' datasets.
   demo/demo_directcat       - Run directcat information demo on the 'synth', 'taste', or 'drift' datasets.
   demo/demo_directformal    - Run directformal information demo on the 'inforate' datasets.
   demo/demo_entropy         - Compare entropy estimates on sythentic data (not NSB).
   demo/demo_metric          - Run metric information demo on the 'synth', 'taste', or 'drift' datasets.
   demo/demo_metric_multi    - Run metric information demo on a multineuron dataset.
   demo/demo_nsb             - Compare entropy estimates with NSB on reduced synthetic data.
   demo/scalefig             - Scale a given figure window by a given factor.
   demo/staverify            - Verify successful installation of the toolkit.

 Direct method.
   directcat                 - Direct method analysis to determine category-specific information.
   directcat_jack            - Direct method analysis to determine category-specific information with leave-one-out jackknife.
   directcat_shuf            - Direct method analysis to determine category-specific information with shuffled inputs.
   directformal              - Direct method analysis to determine formal information.
   directbin                 - Bin spike trains for direct method analysis.
   directcondcat             - Condition data on category.
   directcondformal          - Condition data on both category and time slice.
   directcondtime            - Condition data on time slice.
   directcountclass          - Count spike train words in each class.
   directcountcond           - Count spike train words in each class and disregarding class.
   directcounttotal          - Count spike train words disregarding class.
 
 Metric space method.
   metric                    - Metric space analysis
   metric_jack               - Metric space analysis with leave-one-out jackknife.
   metric_shuf               - Metric space analysis with shuffled inputs.
   metricopen                - Prepare input data structure for metric space analysis.
   metricdist                - Compute distances between sets of spike train pairs.
   metricclust               - Cluster spike trains based on distance matrix.

 Binless method.
   binless                   - Binless method analysis.
   binless_jack              - Binless method analysis with leave-one-out jackknife.
   binless_shuf              - Binless method analysis with shuffled inputs.
   binlessopen               - Extract useful information for binless method.
   binlesswarp               - Warp spike times.
   binlessembed              - Embed the spike trains.
   binlessinfo               - Compute information components using binless method. 

 CTWMCMC method.
   ctwmcmc                   - CTWMCMC method analysis.
   ctwmcmctree               - Build CTW tree graph(s).
   ctwmcmcsample             - Do MCMC sampling of entropy on CTW tree graph(s).
   ctwmcmcbridge             - Build and sample CTW tree graph(s) without outputing tree(s) (to conserve memory).
   ctwmcmcinfo               - Compute information from CTW entropy estimates.

Cross-reference information

This function calls:

This function is called by:


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