Map analysis code
=================

This directory contains the code for Willshaw &al. (2013) "Analysis of
local and global topographic order in mouse retinocollicular maps".

Each directory contains the following:

* lib: The core code. 

* cang: Code specific to analysis of the data of Cang &al (2008). To
  generate figures, type "figures" at Matlab prompt.  To generate a
  CSV file of statistics ("summary_stats.csv"), type
  "get_summary_stats([])". 

* misc: An R script to extract statistics presented in the paper from
  the "summary_stats.csv" file generated as explained above. To run
  the script, start R and type 'source("analyse-summary-stats.R")'.

* old: Redundant code - much can probably be dispensed with.


Git tags
========

adrianna-may-2011      - The files as handed over by Adrianna

adrianna-final-cleaned - The files minus all the derived (pdf, xls,
                         eps) files

adrianna-dw-changes    - David Willshaw's changes to Adrianna's
                         existing files

pre-directory-reorg    - The state of code just before reorganisation
                         into lib and cang directories


Git branches (only master has been pushed to GitHub)
====================================================

master            - the main branch

adrianna-final    - files as Adrianna left them, complete wtith figures

dw-figs-for-paper - Import of all M-files in David's
                    Computing/Matlab/MapPrecision11/Adriannas_legacy/Figs_for_paper
                    directory  

dw-figs-for-paper-clean 
                  - Cleaned up version of above

merge-sim-exp     - Branch in which work on merging experiment- and
                    simulation-specific code was carried out