Lecture information

Navigating slide decks in .html format:

• Use the arrow keys (←/→) on your keyboard to go forward or backward

• Press the “o” key on any slide to show you an overview of the slide deck

• In overview mode, click on a slide or press “esc” to zoom in on it

Date	Topic(s)	Slides	Source	Background info
30 March	Course overview	html	Rmd
1 April	Required software R / RStudio R Markdown GitHub	html	Rmd	R software RStudio Intro to R Markdown Video intro to GitHub
3 April	Ecological data & distributions Detections Counts Survival	html	Rmd	Understanding data Statistical distributions Distribution relationships
6 April	Linear models Non-linear approximations Regression, ANOVA, ANCOVA	html	Rmd	Farraway (2015) Chap 2
8 April	Linear models Models in matrix form Least squares Identifiability	html	Rmd	Farraway (2015) Chap 2
10 April	Inference Variance partitioning F-tests for nested models Confidence intervals	html	Rmd	Farraway (2015) Chap 3 Farraway (2015) Chap 4 Wasserstein et al. (2019)
13 April	Model diagnostics Assumptions about errors Leverage Outliers	html	Rmd	Farraway (2015) Chap 6
15 April	Problems with model errors Generalized least squares Weighted least squares Robust regression	html	Rmd	Farraway (2015) Chap 8
17 April	Data transformations Box-Cox Powers/roots Logarithms	html	Rmd	Farraway (2015) Chap 9 O’Hara & Kotze (2010) Xiao et al. (2011)
20 April	Design matrices Models in matrix form Regression ANOVA / ANCOVA	html	Rmd	Venables (2018)
22 April	Review session All topics to date
24 April	Maximum likelihood estimation Relationship to probability Estimation Characteristics of MLE	html	Rmd	Faraway (2016) Appendix A
27 April	Model selection Bias-Variance trade-offs In-sample selection AIC	html	Rmd	Burnham & Anderson (2002) Hobbs & Hilborn (2006)
29 April	Model selection Out-of-sample selection Cross-validation Multi-model inference	html	Rmd	Aho et al (2014) Banner & Higgs (2017) Burnham & Anderson (2002) Cade (2015) Hooten & Hobbs (2015) Link & Barber (2006)
1 May	Mixed effects models Fixed vs Random effects Shrinkage Costs/benefits	html	Rmd	Freeman’s visualization Harrison et al (2018) Zuur et al (2009) Chap 5
4 May	Mixed effects models Inference Diagnostics Model selection	html	Rmd	Gurka (2006) Harrison et al (2018)
6 May	Guest lecture: Dr. Staci Amburgey Using quantitative ecology for species conservation in the face of anthropogenic change	html		Amburgey et al (2017) Amburgey et al (2019) Amburgey et al (2020)
8 May	Introduction to GLMs Data distributions Link functions Linear predictors	html	Rmd	Nelder & Wedderburn (1972) Faraway (2016) Chap 8
11 May	Modeling binary data Logistic regression Model selection Diagnostics Project plan due	html	Rmd	Faraway (2016) Chap 2
13 May	Overdispersion in binary data Variance inflation Beta-binomial modes Quasi-likelihood	html	Rmd	Faraway (2016) Chap 2 & 3
15 May	Modeling count data Poisson regression Leverage and influence Diagnostics	html	Rmd	Faraway (2016) Chap 5 St-Pierre et al. (2017)
18 May	Overdispersion in count data Variance inflation Quasi-likelihood Negative-binomial distribution	html	Rmd	Faraway (2016) Chap 5 Ver Hoef & Boveng (2007)
20 May	Zero-truncated & zero-inflated models Zero truncation Zero inflation Hurdle models Mixture models	html	Rmd	Faraway (2016) Chap 5 Zuur et al (2009) Chap 11 Blasco-Moreno (2019)
22 May	Working with GLMMs Computing likelihoods Diagnostics Goodness-of-fit	html	Rmd	Faraway (2016) Chap 13 Zuur et al (2009) Chap 13 Bolker et al (2009)
25 May	Memorial Day - No class
27 May	Review of materials
29 May	Course synthesis What did we learn? Where do we go from here?	html	Rmd
1 June	Presentations of class projects	html
3 June	Presentations of class projects	html
5 June	Presentations of class projects	html