jzelner

#a simple network-based SIR model written in Python
#Jon Zelner
#University of Michigan
#August 11, 2009
import sys, getopt
from igraph2Sonia import igraph2sonia

#for networks
def main():
    def usage():

jzelner

#a simple network-based SIR model written in Python
#Jon Zelner
#University of Michigan
#August 11, 2009
import sys, getopt
from igraph2Sonia import igraph2sonia

#for networks
def main():
    def usage():

jzelner

#a simple network-based SIR model written in Python
#Jon Zelner
#University of Michigan
#August 11, 2009
import sys, getopt
from igraph2Sonia import igraph2sonia

#for networks
def main():
    def usage():

jzelner

#a simple SIR model written in Python
#Jon Zelner
#University of Michigan
#October 8, 2009

#import random number and plotting libraries
import random
import pylab as pl

#set quantities of individuals in each state

jzelner

#A simple SIR model written in Python
#Jon Zelner
#University of Michigan
#October 8, 2009

#Ok, so first we're going to import our random number and plotting libraries

# this is Python's standard random number library. 
#For heavy-duty applications you'll want to use something else 
#(like Scipy) but for this example, this will be more than adequate.

jzelner

#A simple SIR model written in Python
#Jon Zelner
#University of Michigan
#October 8, 2009

#Ok, so first we're going to import our random number and plotting libraries

# this is Python's standard random number library. 
#For heavy-duty applications you'll want to use something else 
#(like Scipy) but for this example, this will be more than adequate.

jzelner

#a simple object-based SIR model written in Python
#Jon Zelner
#University of Michigan
#October 20, 2009

#import 'sirWithClasses' to use the components of this model as you wish
#or just run this script as 'python sirWithClasses.py' to do a sample model run

import random
import heapq

jzelner

#a simple network-based SIR model written in Python
#Jon Zelner
#University of Michigan
#October 20, 2009

#import this file (networkSIRWithClasses) to use the model components
#or run as 'python networkSIRWithClasses.py' to do sample runs

import igraph
import random

jzelner

import random
import scipy
import pylab as pl

pl.figure()
for i in range(30):

	S = 99999
	I = 1
	R = 0

jzelner

#Forward-backward algorithm implementation in Theano, 
#with example taken from Wikipedia: 
#http://en.wikipedia.org/wiki/Forward%E2%80%93backward_algorithm

import theano
import theano.tensor as T
import numpy as np

#Set up vectors, etc to represent 
#observations, indexes into the observation