Methods in Experimental Ecology II (PCB 6468)

Course Information
  • Time: Mondays and Wednesdays (11:30-12:20)
  • Instructor: Pedro F. Quintana-Ascencio
  • TA: Federico Lopez Borghesi

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 2020
Syllabus Amendment – In response to COVID-19 pandemic.


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 Exercise 0 (in class) Extra Credit
Exercise 1
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
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
Non-Linear Relationships Demo


Ellison 2004

Gordon et al. 1998
Morris et al. 2015

wg_priors (script)
wire grass (script)
wg_priors (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
Nuzzo 2014 Wasserstein & Lazar 2016
X Model Selection of
Mixed Models Binary
Mixed Model Selection Binary Demo Mixed GLM (script)

Hypericum Data


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 
Aho et al. 2014
Aho_et_al. 2017
Bolker et al. 2009
XIII General Additive Models GAMs Demo GAMs (script)

Data for Demo

Exercise 13
Data for EX 13 Data
ISIT file
Gillibrand et al. 2007
** = file in .docx format due to incompatibility with host – copy paste into R!