# Agenda

Workshop agenda

DRAFT

Begin: Monday, January 10 at 8:30 AM

End: Friday, January 14 at 4:30 PM

Wed 10am Tea Time with Postdocs**Introduction**

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)

Other

-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**

Report

Manuscripts

Example code and data for each application

Simulated data sets for each application

Evaluation of simulated data

Web-based guide