Methods in Experimental Ecology II (PCB 6468)

Course Information

Time: Wednesdays & Fridays (2:30-3:20pm)
Room: Bio 305
Instructors: Pedro F. Quintana-Ascencio & Michelle Bardales Cruz

Description

This course will assist graduate students to design, analyze and interpret their own experiments and observations and establish a research program in ecology and other biological fields. This course reviews basic analytical tools needed to collect, organize and interpret ecological data in a critical way. It is based on the revision of case studies illustrating frequent research problems and the discussion of potential solutions. As much as possible, several alternative approaches are evaluated and compared. This class complements courses on basic statistics and is directed to beginning graduate and senior undergraduate researchers. The course confronts concepts in experimental design, execution and analysis as a tool to improve ecological research.

Syllabus 2024

Materials

Installing rstan and rethinking

Old Methods 2 (Frequentist and JAGS)
Extra Material (from Old Methods 1)

Session	Topic	PDFs	Scripts and Data	Excercises
I	Class Presentation	Gigerenzer 2004	Exercise 0 (in class)	Extra Credit EC excel file Exercise 1 EX 1 excel file
II	Assumptions	Assumptions Demo Dushoff et al. 2019	Assumptions Script Hypericum Data	Exercise 2 EX2 data
III	Analysis Frameworks	Frameworks Demo	Frameworks Script Frameworks Data	Exercise 3 EX3 data
Extra	Probability, likelihood, and MCMC		Likelihood script MCMC script Poisson – Comparison
IV	Analysis of Averages	Averages Demo	Averages Script Hypericum Data pop mean data	Exercise 4
V	Logistic Regressions	Regression Demo Low-Decarie et al.	Logistic Regression Script Hypericum Survival Data	Exercise 5 EX5 data
VI	Non-Linear Relationships	Non-Linear Relationships Demo Ellison 2004 Gordon et al. 1998 Morris et al. 2015	wg_priors (script) wire grass (script) wg_priors (data) wg_data	Exercise 6 McCarthy and Masters 2005 Choy et al. 2009
VII	Count Data	Count Data Demo OHanlon et al. 2014	Mantis R (script) Mantis (data)	Exercise 7 EX7 data
VIII	Linear Mixed Models	Linear Mixed Models Demo	LMM (script) Hypericum Data	Exercise 8 EX8 data
IX	Model Selection of Mixed Models	Mixed Model Selection Demo	Mixed Model Selection (script) Coordinates Balds (script) Distance Matrix (script) ——————- Hypericum Data Bald Coordinates Bald Dist and Area Bald distance matrix Relative Elevation	Exercise 9 Aho et al. 2014 Aho_et_al. 2017 Bolker et al. 2009
X	Model Selection of Mixed Models Binary	Mixed Model Selection Binary Demo	Mixed GLM (script) Hypericum Data Chaos(EXTRA)	Exercise 10 EX10 data
XI	Zero Inflated Models	Zero Inflated Models Demo	Zero Inflated (script) Data for Demo Martin et al.	Exercise 11 EX11 Data
XII	Non-linear Count Data	Non Linear Counts Demo	Non Linear Counts (script) Non Linear Counts – updated (script)Data for Demo	Exercise 12
XIII	TBD			Exercise 13

** = file in .docx format due to incompatibility with host – copy paste into R!