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

### afternoon

## 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

## 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 (
**Mu**lti-**m**odel**In**ference). 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)

page revision: 91, last edited: 11 Jul 2009 02:02