# Notes on Lab #6

## Part 1: Spread of Disease

Remember the
H1N1 (Swine Flu) outbreak of 2009
and the
SARS outbreak of 2003? These viruses have received some recent
media attention, and now would be an appropriate time
to experiment with a model of the spread
of disease. Read the beginning of the Spread of SARS material, stopping at the
SARS model itself (pp. 198-202). Because the full SARS model is so complicated
(see p. 204), we'll stick with the simpler SIR model.

When you're done reading, download
this model. Then skip ahead to p. 208 and do **Projects 1
and 2** on modeling the effect of vaccinations. The idea is that vaccination
represents another outflow from susceptibility -- if you're vaccinated or
already infected, you're no longer susceptible. If you start with a vaccination
rate of zero, you have the orginal model, which is a nice way of doing the
comparison specified in the projects. As usual, there is something slightly
different between the downloaded model and the specifications in the book;
in this case, you have to change the time units from months (the default)
to days, to make the plots sensible. Also, according to
this
reference, *vaccination* and *immunization* are the same thing,
which simplifies the task for Project 2. Don't fret over the
obi-wan error
on the interpretation of "after three days"; just make sure that there are two or
three initial days during which the vaccination rate is 0, after which it is
0.15. I'll leave it to you on how to implement this. A good model should make the parameters
(start time, vaccination rate) explicit, and not bury them in another variable.

Submit the final model (for Project 2). Your writeup should have five labeled
plots (no immunization, 15% per day starting immediately, 15% starting after three days,
25% starting immediately, 25% starting after three days),
along with a brief qualitiative description of the effects of the various
immunization schedules.
## Part 2: Predator/Prey

The
Lotka-Voltera model
of predator/prey dynamics is a classic that would be a
shame to skip. So along with the spread-of-disease model, I've picked it out of the
systems dynamics models in Chapter 6 as something for us to work on.

Read pp. 224 - 230. The four constants have somehwat confusing abbreviations, but
there's a nice summary of them at the bottom
of p. 227, which you might use to annotate the figure at the top of the page.
Then download
this model. Again, the model won't really work "out of the box"; you'll
have to change something to get it to run without errors or warnings.
(*Hint*: this is what we studied in Lab #5.)
Then do **Project 3bc** on p. 231. (The author's description suggests simplifying the
fishing component by using a single fishing rate for both predators and prey.) For extra credit, do parts a and/or d.
(If your calculus is as rusty as mine, you can find the equilbrium formula on
the Wikipedia page).
Submit the model and the writeup. Your writeup should include figures like
Figure 6.4.4 (p. 230) for various values of the fishing rate, as well as a
separate plots for predator (sharks) and prey (tuna) at the equilibrium value
for for the fishing rate.