Hi all,

Todays' project involved modelling what happens if an infected flea
enters a burrow of gerbils. The biology is as follows: fleas feed
daily on gerbils, and drop off after every meal, only to climb on one
of the gerbils again. There is a small chance that a feeding flee
infects a gerbil with the plague. Once a gerbil is infected, it takes
3 days for it to become infectious, after which any flea feeding on it
will also become infected.

I needed to answer a few questions, two of which were: 1. Once there
are a few fleas infected in the burrow, does any influx of infected
fleas from the outside world still matter? 2. How long does it take
before a burrow is fully infected. Lacking a good intuition on how I
could approximate the within-burrow process in a larger meta-
population model, I decided to model what happens in the burrow.

The code is here, for whoever wants an example of a bit of modelling
with clojure. It is pretty neat (to me), as I modeled the timeline of
a burrow infection as a lazy seq, which could just be read out. I am
exploring what I can do model-wise with lazy seqs. They often don't
fit for modelling, but this time they did nicely. Warning: the code is
pretty ugly in the part where I shuffle the healthy (susceptible)
fleas and infected fleas (sfleas and ifleas) over the gerbils in the
burrow (I was out of concentration when I wrote that part).
http://dl.dropbox.com/u/150929/burrows.clj

It also features a nice example of an incanter graph.
http://dl.dropbox.com/u/150929/dist.png

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