ESSM 689 Quantitative Methods in Ecology, Evolution, and Biogeography [Online Syllabus]
SPRING 2015

All Lectures meet in HSFB 126

Date Topic Notes
Jan 20 Introduction to course [pres]
Planning
Try R - Complete chapters 1 through 6 at http://tryr.codeschool.com/
Jan 27 Data management [pres]
Introduction to R [pres]
Intro to R Tutorial [PDF | Web]
Feb 3 The Data Frame and Graphing [pres]

Regression and correlation
Linear models and GLM
Jess G., Hannah B., Sam S. [RC pres | GLM pres]
Jess G., Hannah B., Connie W., Whitney P., Cynthia W. [dis]
Jessica R., Shannon H., Jess G., Hannah B. [RC demo | GLM demo code | GLM demo pres | RC tutorial | RC tutorial with code | GLM tutorial]
Feb 10 Graphing and Importing [pres]

Probability and Distributions
Cynthia W., Jane M., Shishir B. [pres]
Jane M., Shishir B. [demo | tutorial]

extra LM tutorial [web] or GLM tutorial [web]
Feb 17 Programming in R [pres]

Bootstrapping and Model selection
Andrew E., Rosaleen M. [pres]
Luiza A. [MS demo | MS tutorial]
Eric P. [B demo | B tutorial | B code]
Feb 24 Multivariate ordination Tony R., Luke B., David S., Edwin L. [pres | demo]
[vegan | pca ]
March 3 Apply [pres]
Proposal Guidelines [pdf]

Mixed fixed and random effects models
Shannon H., Jessica R. [pres]
Connie W., Sam S. [pdf | demo | anova]
Whitney P., Sam S. [tutorial]
March 10 Data In (rOpenSci) & Out [pres]

Phylogenetics
Adrian C., Michelle C., Oona T, Pedro L. [pres | tree structure demo | tutorial 1 - phylo demo | tutorial 2 - parsimony demo - primates dna - vertebrates phylo ]
March 24 Grammar of Graphics [pres | code]

Survival analysis

Danielle W., Cyrenea P., Thomas H. [pres | references]
Danielle W., Cyrenea P. [estimating survival | right whale demo | mark bunting - capture bunting | killer whale tutorial]

March 31 GIS basics, experimental design, and getting your data into shape [pres | code]

GIS in R & Contingency analysis
Connie W., Eric P. pres
Andy E., Cynthia W., Thomas H. demo and tutorial

[pres | demo | tutorial | code | data]

April 7 Planning and more data extraction from online [pres | code]

Meta-analysis
Tony R., Luke B., David S., Edwin L. [pres | demo | tutorial]
April 14

Intro to Niche Theory [pres]

Species Distribution Modeling

Whitney P. [pres]
Oona T., Whitney [demo]
Rosaleen M., Oona T., Thomas H. [tutorial]
April 21 Reproducible Research [pres | html | code]

End to end reproducibility
Meshal A., Luiza A. [pres]
Meshal A., Rosaleen M. [demo pres | demo code | demo data]
Meshal A., Connie W. [tutorial | tutorial data]
April 28 Geometric morphometrics [pres] Adrian C., Michelle C., Pedro L.

[pres | demo | tutorial | Geomorph Guide]
May 5 No Class. Redefined Day.
May 12 Final Project Due Tuesday, May 12, 2015 at 5:00 PM CST