[Swarm-Modelling] short reading list for IBMs/ABMs in ecology?

[Alex Lancaster]

Hi folks,

A question to all you agent-based [ABM] (aka individual-based [IBM])
ecological modellers out there.

I am taking my PhD qualifying exam in less than 2 months and I have a
committee member who is a theoretical ecologist, who, while interested
in individual-based modelling (Swarm-style), isn't an active
practitioner (not counting "individual-oriented" stochastic models).

Even though I am not an ecologist, I have chosen this person because:

(1) I have worked with ecologists developing IBM/ABM models in the
past so am familiar with many of the issues in IBM/ABM modelling (but
not so much the "classical" theory); (2) although this faculty member
does field work, is mainly a theory person, which is hard to find in
biology departments, since I am completely a theory/data analysis
person (although I have helped others on field trips!); (3) this
ecologist seems receptive to the idea of IBMs/ABMs in ecology; (4)
I've worked with ABMs for long enough to know I know many of the
advantages as well as some of the standard criticisms and limitations;
(5) I know and Swarm (and ABM tools) pretty well... ;-)

My own work thus far in grad school and most of my knowledge of
"classical", non-ABM modelling is largely in population and
evolutionary genetics (both modelling and data analysis).  My other
committee members consist of: a population geneticist; an evolutionary
biologist and morphologist, and a computational cell biologist.

Since it's outside of my main research focus, it's understood that I
wouldn't be expected to know as much ecology as an ecology grad
student, but I do need to be able intelligently address and discuss
issues of ABM in biology, with some reference to ecology (since that's
the speciality of this particular professor).

I know that there have been various discussions and lists of papers on
ABM/IBM in ecology on this very list (and all in the archives), but I
have a very specific request.

I am looking to put together a short (say 3 or 4 papers) reading list
which is focused (so the questions in the exam will also be focused)
with this committee member, given the following constraints:

1. I only know a smattering of ecology.
2. I have less than 2 months for reading and discussing (and I also
   have 3 other committee members to study for)
3. I'd like to put my experience of Swarm and ABM in general to good
   use (that part I know pretty well).
4. The papers should specifically address the usual objections raised
   as to the need for agent-based or individual-based modelling in the
   first place (i.e. they shouldn't assume that they are preaching to
   the converted).

I am familiar with the work of Steve Railsback, Steve Jackson, Glen
Ropella and their colleagues at Humboldt State, and Steve has already
kindly pointed me at some relevant papers.  I also know the work of
Doug Donalson, in particular Donalson & Nisbet in Ecology 80:2492
(1999).  (Incidentally, does anybody know whether Donalson's HADES
predated Swarm, or did it use Swarm internally. Is Doug still lurking
on this list?)

Also, I know from SwarmFest's past, of Jim Anderson's work at CBR at
U. Washington on modelling salmon, but don't which paper would be a
good one to read in this context.

I'm looking for papers that compare and constrast ABM/IBM to classical
models (ecological or otherwise) such as Lotka-Volterra predator-prey
dynamics, or otherwise help provide a bridge from classical
equation-based models to ABM/IBM (e.g. setting up an ABM/IBM in a
"special case" mode to reproduce known classical dynamics).

If there's anybody out there who can recommend papers on ABM/IBM that
would be general enough to digest, but with reference to ecology,
please let me know.

Phew, that's a long question!  Many thanks,

Alex