2011 stuff

2010 stuff

2009 stuff

Lab materials

• EEID day 1 stuff (zip file)
• Webb evolution lab (zip file)

Data sets

• Commune measles
• Bombay plague

Papers

• Lekone and Finkenstadt 2006 (Ebola)
• Dubray et al 2006 (Niamey measles)

2008 stuff

Evolution section

• STRUCTURE exercise:
  • instructions (doc, PDF)
  • Roach et al 2001 paper
  • data files: Cynomys population study (xls), linear, drainage, road, drainage and road (?) distances (for MANTEL).
• Spatial autocorrelation exercise:
  • instructions (doc, PDF)
  • Bruno et al PLoS Biology 2007 paper
  • R code
  • data files: GBR_WS_data (csv), GBR_WS_data_reefs (csv)
• Rabies exercise (PAUP):
  • instructions (PDF)
  • data files: phylogeny (Nexus), locations (xls)
  • Wallace et al PNAS 2007
• Adaptive evolution modeling:
  • overview (PDF)
  • R code: AdaptiveDynamicsEcology, EcologySim, LandeEcology, AdaptiveDynamics, Lande
  • MATLAB code: AdaptiveDynamicsEcology, EcologySim, LandeEcology, AdaptiveDynamics, Lande, diseaseecology, disease

Ecology section

Lectures and R code

• R0 estimation basics (PDF, R code, Sweave)
• MLE basics (PDF)
• MLE basics 2 (PDF, Sweave )
• Niamey example (PDF, R code, Sweave)
• Simulations, spatial and otherwise (PDF, Sweave)
• Coupled-map lattice code (R)
• Geostats (PDF, Sweave,R code)
• Linear models with autocorrelation (PDF, Sweave, R code)
• Flu gravity model (R code, sample graph)

Data sets

• Niamey biweekly measles (CSV)
• Niamey weekly measles (CSV)
• Bombay weekly plague (CSV)
• yellow fever (dat)
• CML data (R data
• filipendula data (txt)
• prairie dogs (csv)
• habitat selection (txt)
• mouse (txt)
• flu counties data set (csv)

Material from CSU/PRIMES EEID workshop, May 16-18 2005

• misc R code (workaround for local library install without administrator privileges)
• Ben's material:
  • Intro to R: (pdf) (R code) (Sweave)
  • Continuous-time stochastic simulation (fancy): (pdf) (R code) (Sweave)
  • Continuous-time stochastic simulation (plain): (pdf) (R code) (Sweave)
• Ottar's material:
  • SIR/ode stuff: (pdf) (R code)
  • Measles time series: (data, CSV) (pdf) (R code)
• Karen Garrett's presentation (PPT):
  • intro and sampling
  • LTER example
  • Dur res ex
  • Questions
• Dave Smith's material:
  • Spatial models talk: (PDF) (R code)
  • spatial dispersal kernel estimation
  • spatial sim 1
  • spatial sim 2
  • spatial sim 3
  • y94.txt: incidence data for Filipendulum (spatial kernel estimation problem)