# Class used for stochastic epidemic simulations

I've developed a class used for some epidemic simulations I'm doing. Individuals are 'S' (susceptible), 'I' (infected), or 'R' (recovered). These are standard abbreviations in the research community. I assume some calculations are done in advance to determine who will be infected (and recover) when. There will be many different ways I do this calculation depending on the population studied.

Some questions I have:

1. Should I worry that I'm passing in some dicts that could later be edited by the user? What's the best way to prevent this?

2. Any advice on how to make this clean? I'm moderately familiar with Python, but it's self-taught, and this is the first time I'm seriously working with classes.

import scipy
import pylab as py
from collections import Counter

class SIREpidemic(object):
"""
This will have the basic commands we want for any variety of SIR epidemic.
When an epidemic is initialized, we will have already calculated the time of
infection and recovery for each individual.  These will be passed in as dicts.
Each individual, if infected will have individual.inftime as the time of infection
and individual.rectime as time of recovery.
"""

def __init__(self, infectionTime, recoveryTime, N):
'''Process the infectionTime and RecoveryTime to determine who is susceptible
when. infectionTime[individual] gives time of infection of individual.
recoveryTime[individual] gives recovery time of individual (the keys for both
lists must match).  N is the total population size (may include individuals
that are never infected.'''

statusTypes = ['S', 'I', 'R']
self._timeSeries = {status:scipy.array([]) for status in statusTypes}
self._timeSeries['t'] = scipy.array([])
self.N = N
self._infectionTime = infectionTime
self._recoveryTime = recoveryTime

infTimes = [infectionTime[individual] for individual in infectionTime.keys()]
recTimes = [recoveryTime[individual] for individual in infectionTime.keys()]

infTimeCounter = Counter(infTimes)
recTimeCounter = Counter(recTimes)

self._timeSeries['t'] = scipy.array(sorted(set(infTimes+recTimes)))
for status in statusTypes:
self._timeSeries[status] = 0*self._timeSeries['t']  #initializing to be the right size

datum = {'S':1, 'I':0, 'R': 0}
for index, time in enumerate(self._timeSeries['t']):
incidence = infTimeCounter[time]
recoveries = recTimeCounter[time]
datum['S'] -= float(incidence)/self.N
datum['I'] += float(incidence - recoveries)/self.N
datum['R'] += float(recoveries)/self.N
for status in statusTypes:
self._timeSeries[status][index]=datum[status]

def infTime(self, individual):
return self._infectionTime.get(individual,None)
def recTime(self, individual):
return self._recoveryTime.get(individual,None)

def t(self):
return self._timeSeries['t']
def S(self):
return self._timeSeries['S']
def I(self):
return self._timeSeries['I']
def R(self):
return self._timeSeries['R']

def size(self):
return self._timeSeries['R'][-1]
def initial_size(self):
return 1-self._timeseries['S'][0]

def plot(self,x=None, y=None, fid = None):  #x and y are either 'S', 'I', 'R', 'cumulative', or 't'.
'''if no arguments, plot S,I, and R vs t.  if just one argument, then plot that versus t.  if two arguments, plot second versus first.  Need to add a collection of arguments to pass to plot.'''
if y == None and x == None:
self.plot('t', 'S')
self.plot('t', 'I')
self.plot('t', 'R')
else:
if y == None:
y = x
x = 't'
elif x == None: #but y was something else
x = 't'
if fid != None:
py.figure(fid)
if x == 't':
py.plot(self._timeSeries[x],self._timeSeries[y], label = r'$'+y+'$')
else:
py.plot(self._timeSeries[x],self._timeSeries[y], label = r'$'+y+'$ versus $'+x+'$')


## Python coding conventions

There's a few places in the code where you have the following:

if y == None and x == None:


The Pythonic way to check against None is to use is:

if y is None and x is None:

if fid is not None:


Note that this works because None is always the same object.

There's a few other minor formatting issues that aren't considered idiomatic Python code style (for example no space after comma). The PEP8 document outlines some standard python coding conventions. I would recommend giving that a read.

## Constants

There's a few examples of unnamed constants floating around in the code, for example 't' is in a bunch of different places. Creating named variables for these is generally speaking a good thing for maintainability.

Also statusTypes = ['S', 'I', 'R'] isn't limited to one particular instance of the class so I would move that outside of the __init__.

## Generator expressions

If you don't need a list you don't have to create it:

infTimes = [infectionTime[individual] for individual in infectionTime.keys()]
recTimes = [recoveryTime[individual] for individual in infectionTime.keys()]

infTimeCounter = Counter(infTimes)
recTimeCounter = Counter(recTimes)


Here you have to make 2 lists in memory before you use the Counter. Given that you don't actually need the entire list to be generated here I would instead opt to use a generator expression:

infTimes = (infectionTime[individual] for individual in infectionTime.keys())
recTimes = (recoveryTime[individual] for individual in infectionTime.keys())

infTimeCounter = Counter(infTimes)
recTimeCounter = Counter(recTimes)


This allows you to count all the frequencies without having to maintain the whole list in memory at once. Given that you don't actually ever need that list this ends up saving you memory and is especially beneficial if those dictionaries are large.

Then you build a sorted list and remove duplicates.

self._timeSeries['t'] = scipy.array(sorted(set(infTimes+recTimes)))


This work was already done with the Counter though, you could do something like this instead:

combined_count = infTimeCounter + recTimeCounter
self._timeSeries['t'] = scipy.array(sorted(combined_count.elements()))


If you have a very large number of duplicated elements this optimization could save you quite a bit of processing.

## Documentation

There's a few parts in the code that are not immediately obvious and would benefit from a docstring. In particular it's not clear exactly what these are doing:

def size(self):
return self._timeSeries['R'][-1]
def initial_size(self):
return 1-self._timeseries['S'][0]


## plot method

The plot method could really do with an explanation of what x, y and fid are in the docstring. The docstring could also be better formatted as it's very wide.

def plot(self,x=None, y=None, fid=None):
if y == None and x == None:
self.plot('t', 'S')
self.plot('t', 'I')
self.plot('t', 'R')


First the indentation and formatting is off here, being that whitespace in python is significant having the 8 character wide space here is a bit odd, just make it all consistent. Adding an extra named variable might help readability here. Here's what it looks like with those changes:

def plot(self, x=None, y=None, fid=None):
if y is None and x is None:
for status in statusTypes:
self.plot('t', status)
elif y is None:
y_label = x
x_label = 't'
elif x is None:
y_label = y
x_label = 't'
else:
y_label = y
x_label = x

if fid is None:
py.figure(fid)

• What's the best way to handle the fact that the user will pass in "infectionTime", and possibly modify it later? I'd want it to stay the same in the class.
– Joel
Dec 16 '14 at 7:56
• @Joel You can take a copy using self._infectionTime = infectionTime.copy(). It is a shallow copy but that should be enough here when the dict contains simple values. Dec 16 '14 at 13:48