rabbits3


Modeling and Simulation in Python

Rabbit example

Copyright 2017 Allen Downey

License: Creative Commons Attribution 4.0 International


In [1]:
%matplotlib inline

from modsim import *

Rabbit is Rich

This notebook starts with a version of the rabbit population growth model. You will modify it using some of the tools in Chapter 5. Before you attempt this diagnostic, you should have a good understanding of State objects, as presented in Section 5.4. And you should understand the version of run_simulation in Section 5.7.

Separating the State from the System

Here's the System object from the previous diagnostic. Notice that it includes system parameters, which don't change while the simulation is running, and population variables, which do. We're going to improve that by pulling the population variables into a State object.


In [2]:
system = System(t0 = 0, 
                t_end = 20,
                juvenile_pop0 = 0,
                adult_pop0 = 10,
                birth_rate = 0.9,
                mature_rate = 0.33,
                death_rate = 0.5)

system


Out[2]:
value
t0 0.00
t_end 20.00
juvenile_pop0 0.00
adult_pop0 10.00
birth_rate 0.90
mature_rate 0.33
death_rate 0.50

In the following cells, define a State object named init that contains two state variables, juveniles and adults, with initial values 0 and 10. Make a version of the System object that does NOT contain juvenile_pop0 and adult_pop0, but DOES contain init.


In [3]:
# Solution goes here

In [4]:
# Solution goes here

Updating run_simulation

Here's the version of run_simulation from last time:


In [5]:
def run_simulation(system):
    """Runs a proportional growth model.
    
    Adds TimeSeries to `system` as `results`.
    
    system: System object
    """
    juveniles = TimeSeries()
    juveniles[system.t0] = system.juvenile_pop0
    
    adults = TimeSeries()
    adults[system.t0] = system.adult_pop0
    
    for t in linrange(system.t0, system.t_end):
        maturations = system.mature_rate * juveniles[t]
        births = system.birth_rate * adults[t]
        deaths = system.death_rate * adults[t]
        
        if adults[t] > 30:
            market = adults[t] - 30
        else:
            market = 0
            
        juveniles[t+1] = juveniles[t] + births - maturations
        adults[t+1] = adults[t] + maturations - deaths - market
        
    system.adults = adults
    system.juveniles = juveniles

In the cell below, write a version of run_simulation that works with the new System object (the one that contains a State object named init).

Hint: you only have to change two lines.


In [6]:
# Solution goes here

Test your changes in run_simulation:


In [7]:
run_simulation(system)
system.adults


Out[7]:
value
0 10.000000
1 5.000000
2 5.470000
3 6.209900
4 7.057723
5 8.021560
6 9.117031
7 10.362107
8 11.777219
9 13.385586
10 15.213601
11 17.291261
12 19.652658
13 22.336542
14 25.386953
15 28.853947
16 32.794414
17 34.478600
18 36.487431
19 37.893339
20 39.401924
21 40.546917

Plotting the results

Here's a version of plot_results that plots both the adult and juvenile TimeSeries.


In [8]:
def plot_results(system, title=None):
    """Plot the estimates and the model.
    
    system: System object with `results`
    """
    newfig()
    plot(system.adults, 'bo-', label='adults')
    plot(system.juveniles, 'gs-', label='juveniles')
    decorate(xlabel='Season', 
             ylabel='Rabbit population',
             title=title)

If your changes in the previous section were successful, you should be able to run this new version of plot_results.


In [9]:
plot_results(system, title='Proportional growth model')


That's the end of the diagnostic. If you were able to get it done quickly, and you would like a challenge, here are two bonus questions:

Bonus question #1

Write a version of run_simulation that puts the results into a single TimeFrame named results, rather than two TimeSeries objects.

Write a version of plot_results that can plot the results in this form.

WARNING: This question is substantially harder, and requires you to have a good understanding of everything in Chapter 5. We don't expect most people to be able to do this exercise at this point.


In [10]:
# Solution goes here

In [11]:
run_simulation(system)

In [12]:
# Solution goes here

In [13]:
plot_results(system)


Bonus question #2

Factor out the update function.

  1. Write a function called update that takes a State object and a System object and returns a new State object that represents the state of the system after one time step.

  2. Write a version of run_simulation that takes an update function as a parameter and uses it to compute the update.

  3. Run your new version of run_simulation and plot the results.

WARNING: This question is substantially harder, and requires you to have a good understanding of everything in Chapter 5. We don't expect most people to be able to do this exercise at this point.


In [14]:
# Solution goes here

In [15]:
run_simulation(system, update)


---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-15-5d0666d579e1> in <module>()
----> 1 run_simulation(system, update)

NameError: name 'update' is not defined

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plot_results(system)

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