Mendoza

Materials for Mendoza course, 29 June - 10 July

Monday

morning

• outline (pdf, html)
• overview (pdf, html, R, Rnw)
• incantation for making Tinn-R copy and paste blocks correctly:

.trPaths <- paste(paste(Sys.getenv('APPDATA'),
      '\\Tinn-R\\tmp\\', sep=''),
        c('', 'search.txt', 'objects.txt','file.r',
       'selection.r','block.r','lines.r'), sep='')

• readings: Platt 1964, Crome 1997, Gerber and Malhotra 2006 ("p-value" paper: Gerber, A., and N. Malhotra. “Can political science literatures be believed? A study of publication bias in the APSR and the AJPS.” Annual Meeting of the Midwest Political Science Association (2006): 12-15)

afternoon

• lab 1 (pdf, html, R, Rnw)
• data and scripts for lab 1: ChlorellaGrowth.txt, Intro1.R, Intro2.R
• incantation for switching times and dates to English so you can read the month abbreviations:

Sys.setlocale("LC_TIME","English")

I think this should revert to normal (Spanish) when you start R the next time, but if not try

Sys.setlocale("LC_TIME","Spanish")

to switch back.

Tuesday

morning

• deterministic models (pdf, Rnw)
• lab (pdf)

afternoon

• data entry and exploratory analysis (pdf, Rnw)

Wednesday

morning

• lab (pdf)
• data files for lab: duncan_10m.csv, duncan_25m.csv

afternoon

• stochastic models (pdf)

projects

Thursday

• likelihood etc. (pdf)
• data files: simtham.txt, DamselRecruitment.csv
• readings: Yang 2005, Ludwig and Walters 1985

Friday

• very sketchy notes

Monday

• basic Bayesian stuff (pdf, R, Rnw, WinBUGS model)
• references: Crome et al 1996, Dennis 1996, Gelman 2008

Tuesday

• dynamic/state-space models (pdf)

Miscellaneous

• Page 79 and following of Harrell, F. Regression Modeling Strategies. Springer, 2001 give some ideas for thinking about modeling with many predictors

• Richards 2008, "Dealing with overdispersed count data in applied ecology" (J. Appl. Ecol. 218-227) gives a good description of QAIC etc.

Presentations

• solitary bees
• spines/fruit tradeoff
• small mammal distribution
• guanaco and ganado
• shark diet analysis)
• Trichloris germination curves

Miscellaneous

• Page 79 and following of Harrell, F. Regression Modeling Strategies. Springer, 2001 give some ideas for thinking about modeling with many predictors
• Richards 2008, "Dealing with overdispersed count data in applied ecology" (J. Appl. Ecol. 218-227) gives a good description of QAIC etc.
• "the package formerly known as dRedging", by Kamil Bartón, is now MuMIn (Multi-model Inference). This package allows you to fit a model and all of its submodels (respecting marginality conditions, i.e. not fitting models where some interactions are present but their respective main effects or lower-order interactions are absent) and calculate AIC tables, do model averaging, etc.. This is a powerful, but potentially dangerous, tool: think before using! It was formerly available from his web page, now it is on R-forge; you can install it by saying

install.packages("MuMIn",repos="http://r-forge.r-project.org")

The web page says it is "pre-alpha" (i.e., experimental) but I think it should be fairly robust.

Spatial stuff

I never wrote down notes in any great detail: does anyone have some they'd like to volunteer?

References:

• Bolker et al 2009 (GLMMs)
• Dormann et al 2007, Ecography (spatial analysis)
• Betts et al 2009 (a response to Dormann et al)