

  **************************************************************
  *                                                            *
  * NEXCADE 2.1    (release date: 2012/01/05)                  *
  *                                                            *
  * A Program For Analysis of Perturbations On Complex Networks*
  *                                                            *
  *                                                            *
  *                                                            *
  *  (c) Gitanjali Yadav (gy@nipgr.res.in)                     *
  *                                                            *
  **************************************************************


This package implements a collection of algorithms for analysing
complex systems that can be conceptualized by networks, and rep-
resented as interconnected matrices of interactions. It includes
programs for generating various kinds of perturbations on the 
networks such as single, multiple or sequential extinctions. It 
focuses on the changes in topology and connectivity of the network 
as a function of the perturbation. Perturbations may be induced in
a user-defined manner followed by analysis of the resulting sub-
networks.

Please see the file README for instructions on USAGE of NEXCADE. 

An online version of the program can be found at NIPGR WWW server
http:/nipgr.res.in/nexcade.html.

Please read the licence terms in file LICENSE, as per GNU GPL.
 
For problems please contact gy@nipgr.res.in (Gitanjali Yadav).

FEATURES :
---------

 o Portability. The programs should run on any linux based computer
   with R installed in /usr/local/bin along with the package IGRAPH

 o Simulations. The programs can be run in four steps, of which the
   the first is necessary in order to run any of the other optional
   simulations:
   1. Network Analysis         (Script "run_nexcade") 
   2. Single Perturbation      (Script "run_single_extinction")
   3. Grouped Perturbation     (Script "run_group_extinction")
   4. Sequential Perturbation  (Script "run_cascades")

 o Parameters. In each case of perturbation induction, the user can 
   alter parameters about the number and type of network entity to 
   be perturbed. These parameters can be set by proper usage of each
   script as described in README

 o Analysis & Outcome. A number of files are generated after each run.
   These include regular text files that show the results of the runs 
   as well as low resultion (.jpg) and high resolution ( .pdf) images 
   for the respective networks plotting the changes before and after 
   perturbations. Details can be found in the README.

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EXAMPLES:
---------

TEST.ncol is an example network file in the 'example' directory.

To test the program on this network, do as follows:
	1. In the main dir, type:
		'./Make_Nexcade'
	2. Go to the newest directory in RUNS and type:
	  	 './run_nexcade TEST'

A new directory gets generated inside RUNS with every instance of 
the script 'Make_Nexcade' in the main directory.

-- 
Gitanjali Yadav (gy@nipgr.res.in) 2012/01/05
