Version 1.0

Author: wcota

README.md

@@ -1,4 +1,6 @@
-# Optimized Gillespie algorithms for the efficient simulation of Markovian epidemic processes on large and heterogeneous networks: SIS-OGA
+# Optimized Gillespie algorithms for the simulation of Markovian epidemic processes on large and heterogeneous networks: SIS-OGA
+
+This code is part of the article "[Optimized Gillespie algorithms for the simulation of Markovian epidemic processes on large and heterogeneous networks](http://wesleycota.com/)"
 
 ### [NetworkX](https://networkx.github.io/) implementation
 
@@ -10,9 +12,11 @@
 
 (this) [NetworkX Python implementation - range of options](https://github.com/wcota/dynSIS-networkx)
 
+[GA Fortran implementation - Statistically exact, but NOT optimized](https://github.com/wcota/dynSIS-GA)
+
 ## Synopsis
 
-This code is a implementation of the SIS-OGA algorithm, as detailed in our paper (to be cited). It receives as input a NetworkX graph object and the dynamical parameters.
+This code is a implementation of the SIS-OGA algorithm, as detailed in our [paper](http://wesleycota.com/). It receives as input a NetworkX graph object and the dynamical parameters.
 
 For performance, see https://github.com/wcota/dynSIS (Fortran implementation)
 

dynSIS.py

@@ -4,11 +4,12 @@
 # ! ## See README.md for more information and use
 # !-----------------------------------------------------------------------------
 # ! SIS epidemic model algorithm based on the article 
-# !           "Optimized Gillespie algorithms for the efficient simulation of 
-# !            Markovian epidemic processes on large and heterogeneous networks"
+# !           "Optimized Gillespie algorithms for the simulation of Markovian
+# !            epidemic processes on large and heterogeneous networks"
 # ! Copyright (C) 2017 Wesley Cota, Silvio C. Ferreira
 # ! 
-# ! Please cite the above cited paper as reference to our code.
+# ! Please cite the above cited paper (available at <http://wesleycota.com/ ) as reference
+# ! to our code.
 # ! 
 # !    This program is free software: you can redistribute it and/or modify
 # !    it under the terms of the GNU General Public License as published by
@@ -25,8 +26,8 @@
 # !-----------------------------------------------------------------------------
 # ! Author    : Wesley Cota
 # ! Email     : [email protected]
-# ! Date      : 10 Mar 2017
-# ! Version   : 0.2
+# ! Date      : 27 Mar 2017
+# ! Version   : 1.0
 # !-----------------------------------------------------------------------------
 # ! See README.md for more details
 # ! This code is available at <https://github.com/wcota/dynSIS-networkx>
@@ -37,10 +38,11 @@
 from math import log
 
 print(  '################################################################################',
-        '### Optimized Gillespie algorithms for the efficient simulation of Markovian ###',
+        '######### Optimized Gillespie algorithms for the simulation of Markovian  ######',
         '####### epidemic processes on large and heterogeneous networks: SIS-OGA. #######',
         '##============ Copyright (C) 2017 Wesley Cota, Silvio C. Ferreira ============##',
-        '##======= This code is available at <https://github.com/wcota/dynSIS>. =======##',
+        '##================ Paper available at <http://wesleycota.com/ ================##',
+        '##======= The codes are available at <https://github.com/wcota/dynSIS> =======##',
         '##======== Please cite the above cited paper as reference to our code ========##',
         '##=== This code is under GNU General Public License. Please see README.md. ===##',
         '################################################################################',
@@ -142,7 +144,8 @@ def dyn_run(nw, fnOutput, dynp_sam, dynp_lb, dynp_tmax, dynp_pINI):
 
         # Write output file
         flOutput = open(fnOutput, 'wt')
-        print(  '#@ Number of nodes: '+str(net_N),
+        print(  '## ***** Algorithm used: Optimized Gillespie Algorithm for SIS (SIS-OGA, NetworkX) *****',
+                '#@ Number of nodes: '+str(net_N),
                 '#@ Number of edges: '+str(2*nw.number_of_edges()),
                 '#@ Samples: '+str(dynp_sam),
                 '#! Infection rate (lambda): '+str(dynp_lb),

example_karate.py

@@ -4,11 +4,12 @@
 # ! ## See README.md for more information and use
 # !-----------------------------------------------------------------------------
 # ! SIS epidemic model algorithm based on the article 
-# !           "Optimized Gillespie algorithms for the efficient simulation of 
-# !            Markovian epidemic processes on large and heterogeneous networks"
+# !           "Optimized Gillespie algorithms for the simulation of Markovian
+# !            epidemic processes on large and heterogeneous networks"
 # ! Copyright (C) 2017 Wesley Cota, Silvio C. Ferreira
 # ! 
-# ! Please cite the above cited paper as reference to our code.
+# ! Please cite the above cited paper (available at <http://wesleycota.com/ ) as reference
+# ! to our code.
 # ! 
 # !    This program is free software: you can redistribute it and/or modify
 # !    it under the terms of the GNU General Public License as published by
@@ -25,8 +26,8 @@
 # !-----------------------------------------------------------------------------
 # ! Author    : Wesley Cota
 # ! Email     : [email protected]
-# ! Date      : 10 Mar 2017
-# ! Version   : 0.2
+# ! Date      : 27 Mar 2017
+# ! Version   : 1.0
 # !-----------------------------------------------------------------------------
 # ! See README.md for more details
 # ! This code is available at <https://github.com/wcota/dynSIS-networkx>

example_read.py

@@ -4,11 +4,12 @@
 # ! ## See README.md for more information and use
 # !-----------------------------------------------------------------------------
 # ! SIS epidemic model algorithm based on the article 
-# !           "Optimized Gillespie algorithms for the efficient simulation of 
-# !            Markovian epidemic processes on large and heterogeneous networks"
+# !           "Optimized Gillespie algorithms for the simulation of Markovian
+# !            epidemic processes on large and heterogeneous networks"
 # ! Copyright (C) 2017 Wesley Cota, Silvio C. Ferreira
 # ! 
-# ! Please cite the above cited paper as reference to our code.
+# ! Please cite the above cited paper (available at <http://wesleycota.com/ ) as reference
+# ! to our code.
 # ! 
 # !    This program is free software: you can redistribute it and/or modify
 # !    it under the terms of the GNU General Public License as published by
@@ -25,8 +26,8 @@
 # !-----------------------------------------------------------------------------
 # ! Author    : Wesley Cota
 # ! Email     : [email protected]
-# ! Date      : 10 Mar 2017
-# ! Version   : 0.2
+# ! Date      : 27 Mar 2017
+# ! Version   : 1.0
 # !-----------------------------------------------------------------------------
 # ! See README.md for more details
 # ! This code is available at <https://github.com/wcota/dynSIS-networkx>
@@ -60,3 +61,11 @@
 
 # Run dynamics
 dynSIS.dyn_run(G, fnOutput, dynp_sam, dynp_lb, dynp_tmax, dynp_pINI)
+        
+print('')
+print('Everything ok!',True)
+print('Input file (edges list): '+ fnInput)
+print('Output file: '+ fnOutput)
+print('')
+print('*****Algorithm used: Optimized Gillespie Algorithm for SIS (SIS-OGA, NetworkX)*****')
+print('Codes available at <https://github.com/wcota/dynSIS>.')