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Workshop agenda


Begin: Monday, January 10 at 8:30 AM
End: Friday, January 14 at 4:30 PM

Wed 10am Tea Time with Postdocs

Workshop introduction/welcome
Participant introductions
NCEAS introductions/welcome

Register with the WIKI!

Discussion of Agenda

Overview of BUGS (Beth Gardner)
Overview of ADMB (Mark Maunder)
Overview of R (Ben Bolker)

Initial evaluation of the benefits of each package and what types of applications they have been applied to

Description of proposed applications
Simple models
-e.g. simple nonlinear model - growth curve, add temporal or individual random effects
Population dynamics
-Multistage state-space lifecycle model with application to delta smelt (Mark Maunder - ADMB)
-Pella-Tomlinson fisheries model (Arni Magnusson - ADMB)
-Comparison of inference using the theta logistic model for population dynamics using AD Model Builder and BUGS (Casper Berg - ADMB/BUGS).
Mark recapture
-Random effects mark-recapture model (Mark Maunder - ADMB)
-Mark-recapture state-space formulated to incorporate an individual covariate with a random effect (Olivier Gimenez - BUGS)
-Modificied Arnason-­‐Schwarz? (AS) multistate model where a climatic covariate is thought to influence a transition probability (Olivier Gimenez - BUGS)

-Spatial capture-recapture model (Beth Gardner - WinBUGS)
Occupancy models
-Dynamic site-occupancy model in the hierarchical formulation fit to 9 years of crossbill data from the Swiss breeding bird survey MHB (Marc Kery - BUGS)
-Occupancy models using ADMB and comparison with BUGS (Hans Skaug - ADMB/BUGS)
ANOVA and linear regression
-Zero inflated models (See Chapter 11 in Zuur et al.2009) (Cleridy Lennert - R)
-Poisson random effects model (See Chapter 23 in Zuur et al.2009) (Cleridy Lennert/Maunder - BUGS/ADMB/R)

-Poisson spatial random effects model (Beth Gardner - WinBUGS)

Spatial temporal species distribution
A spatial model for soil calcium content is developed using the geostatstical approach of kriging with an external trend (Cleridy Lennert - R)
-Mineralization of terbuthylazine; a small ODE problem  (Anders Nielsen - ADMB)

-Other commonly used ecological models - habitat selecvtion models

Discussion of applications and choice of applications to analyze

Discussion of format for describing and presenting models

Development of models in each software

Further evaluation of the benefits of each package and what types of applications they have been applied to

Discussion of evaluation criteria

Development of simulators

Development of work plan, time table, and assignment of tasks
Example code and data for each application
Simulated data sets for each application
Evaluation of simulated data
Web-based guide

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