| Week | R packages | Topic | Readings |
|---|---|---|---|
| Jan 11 | dismo |
Overview, reproducible research | Elith and Leathwick (2009)R |
| Jan 18 | raster |
Data | Hijmans et al. (2005)R |
| Jan 25 | Niche and fitness | Kearney et al. (2010)R | |
| Hutchinson (1957)R | |||
| Leibold (1995)O | |||
| Feb 1 | Niche and distribution | Pulliam (2000)R | |
| Feb 8 | Machine learning | Breiman (2001)R | |
| Domingos (2016)O | |||
| Feb 15 | ROCR |
Evaluation | Fawcett (2006)R |
| Feb 22 | e1071 |
Presence-only: SVMs | Drake, Randin, and Guisan (2006)R |
| Drake (2014)R | |||
| Feb 29 | geometry |
Presence-only: Range bagging | Drake (2015)R |
| Mar 14 | dismo |
Presence-background: MaxEnt | S. J. Phillips, Dudik, and Shapire (2004)R |
| Elith et al. (2010)R | |||
| Mar 21 | ppmlasso |
Presence-background: Point processes | Renner and Warton (2013)R |
| Ward et al. (2008)O | |||
| Mar 28 | maxlike |
Presence-background: Probabilistic models | Royle et al. (2012)R |
| Apr 4 | inla |
Conditional autoregressive models | Beale et al. (2010)R |
| Beguin et al. (2012)O | |||
| Apr 11 | gbm |
Classification: Boosted regression trees | J. Elith, Leathwick, and Hastie (2008)R |
| Apr 18 | Special topics | Vel’asquez-Tibat’a, Graham, and Munch (2015)C | |
| S. J. Phillips et al. (2009)C | |||
| N. Barve et al. (2011)C | |||
| Apr 25 | Big data | Kelling et al. (2009)R |
R: Required reading; O: Optional reading; C: Choose one paper