This seminar for this semester will cover the background, development and
application of hierarchical Bayesian models in several areas, including species
distributions, geographical genetics, and spatio-temporal population analysis.
We will go through the book "Hierarchical Modelling for the Environmental
Sciences" by James Clark and Alan Gelfand (Oxford University Press, 2006). The
objective of the seminar is to provide both a conceptual foundation of the
probability and statistical ideas involved in these models, as well as cover
some of the mathematical details in Gibbs sampling and computational methods
such as Markov Chain Monte Carlo methods. The presumption is that the attendees
will have a mixture of levels of experience with statistical modeling, so we
will attempt to meet the diverse needs of participants by encouraging conceptual
understanding while also covering some details of the mathematics.
The seminar will be led jointly by Louis Gross (Professor of EEB and Mathematics)
and Brian Beckage (Associate Professor of Plant Biology at University of Vermont and
NIMBioS Sabbatical Fellow). Following a gentle introduction to the mathematics
which will require three to four meetings, participants will be expected to share
presentation of the various chapters based upon their own interest. We intend to
pair a more mathematically-oriented participant with a more biologically-oriented
one for each chapter to provide a mixture of perspectives. Participants
will be expected to present one section of the text along with more recent
publications related to the topic, as well as read through each week's
material before each meeting.
This seminar will meet once a week on Mondays from 11:15-12:05 in the
NIMBioS suite of rooms. Attendees should sign up for one credit hour (unless
prior arrangement is made with the Dr. Gross).
The first two hand-outs are:
Chapter 9 (The Confrontation: Bayesian Goodness of Fit) from Ray Hilborn and
Marc Mangel's book: "The Ecological Detective: Confronting Models with Data".
Princeton University Press, 1997.
Chapter 9 (Bayesian Inference and MCMC) from Darren J. Wilkinson's book
"Stochastic Modelling for Systems Biology". CRC Press, 2006.
Powerpoint Lecture files
Introduction to Bayesian Statistics (Powerpoint .ppt file)
Intro to Bayesian Modeling - background from Hilborn and Mangel Chapter 9 (Powerpoint .ppt file)
Overview of Markov Chain Monte Carlo - background from Wilkinson Chapter 9 (Powerpoint .ppt file)
Overview of Bayesian Estimation - background from Clark and Gelfand text (Powerpoint .ppt file)
Chapter 2 summary - models in geographical genetics (Powerpoint .ppt file)
Chapter 3 summary - synthesizing ecological experiments (Adobe .pdf file)