Workshop: Hierarchical models for abundance, distribution
and species richness in spatially structured populations using
unmarked/R and WinBUGS
Instructors: Marc Kéry, Richard Chandler, Andy Royle;
USGS Patuxent Wildlife Research Center & Swiss Ornithological Institute
Date:
26–30 November 2012 (4.5 days)
Venue:
USGS Patuxent Wildlife Research Center, Laurel, Maryland
Computers: Bring your own laptop with latest R/unmarked and WinBUGS/OpenBUGS/JAGS
Course fee:
USD$700 (normal rate), USD$300 (student rate), 2 wild cards available.
The analysis of abundance, distribution, species richness, and of the dynamic rates governing their change, lies
at the core of ecology and its applications such as conservation and wildlife management. Metapopulation
designs, where repeated measurements of some quantity such as detection/nondetection or counts are made at a
collection of sites, underlie a vast number of studies in ecology and management. Inference about such data is
conveniently based on hierarchical models, where one submodel describes the underlying true state of the
process (e.g., presence or absence at a site) and another submodel describes the observation process that
connects the true state to the observations.
In recent years, much progress has been made in the development of methods and computer algorithms to fit
hierarchical models. In particular, Bayesian statistical analysis and the general-purpose Bayesian software
package WinBUGS have opened up entirely new possibilities for ecologists to conduct complex population
analyses. On the other hand, the new R package unmarked contains a wealth of functions to analyse
hierarchical models in a frequentist mode of inference.
This course introduces key hierarchical models used in the analysis of distribution, abundance and species
richness, as well as their spatial and temporal patterns, and provides both Bayesian and the frequentist methods
for their analysis. We use package unmarked in R as well as WinBUGS and JAGS to fit and understand some
of the most widely used models for the analysis of animal and plant populations. These include:
-
site-occupancy models (MacKenzie et al. 2002, 2003) for the analysis of species distributions,
CAR modeling of spatial autocorrelation in distribution or abundance
binomial (Royle 2004) and multinomial N-mixture models (e.g., removal, double-observer) for the
analysis of distribution and abundance,
hierarchical distance sampling models (e.g., Royle et al. 2004, Conn et al. 2012),
dynamic models of distribution (MacKenzie et al. 2003) and abundance (Royle & Dorazio 2008; Dail
& Madsen 2011)
multi-species site-occupancy models for inference about communities, e.g., species richness (Dorazio
& Royle 2005; Dorazio et al. 2006), and dynamic multi-species site-occupancy models for inference
about community dynamics (Dorazio et al. 2010)
This is an intermediate-level workshop with about 80% spent lecturing and 20% on solving exercises. A
working knowledge of modern regression methods (GLMs, mixed models) and preferentially of program R or
another programming language is required. No previous experience with program WinBUGS is assumed;
however, it is beneficial.
Please bring your own laptops and install a recent version of R, with the latest version of package unmarked,
plus WinBUGS 1.4., with the upgrade patch and the immortality key decoded (in this order). Alternatively,
OpenBUGS and JAGS work for most of what we do.
Send your application to Andy Royle (hmecology@gmail.com), describing your background and knowledge in
statistical modeling, R and WinBUGS/OpenBUGS/JAGS, by 31 October 2012 at the latest.