Methods 2 – Old

Methods in Experimental Ecology II (PCB 6468)

Course Information
  • Time: Mondays and Wednesdays (11:30-12:20) & Thursdays (9:00-11:50)
  • Room: Bio 305
  • Instructor: Pedro 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 2018


Extra Material (from Old Methods 1)


Session Topic PDFs Scripts and Data Excercises
I Class Presentation Exercise 0
Ex0 Chart
Extra Credit
II Assumptions Assumptions Demo Assumptions Script

Hypericum Data

Exercise 1

EX1 data

III Analysis Frameworks Frameworks Demo Frameworks Script
Frameworks Data
Exercise 2

EX2 data

IV Analysis
of Averages
Averages Demo Averages Script (jags)

mean model Inform

mean model diffused

Hypericum Data

pop mean data


Exercise 3


V Logistic Regressions Regression Demo
Low-Decarie et al.
Logistic Regression Script
Hypericum Survival Data
Exercise 4


VI Non-Linear
Non-Linear Relationships Demo


Ellison 2004

Gordon et al. 1998

Morris et al. 2015

wg_priors (script) **




wg_priors (data)


Exercise 5
VII Count Data Count Data Demo

OHanlon et al. 2014

Mantis R (script) **

Mantis Jags – Poisson (script) **

Mantis jags -Neg Binom (script) **

Mantis (data) **

Exercise 6

Exercise 6 Data

VIII Linear Mixed Models Linear Mixed Models Demo LMM (script)

LMM  intercept (script)

LMM intercept and slope (script)

Hypericum Data

Exercise 7

Exercise 7 Data


IX Model Selection of
Mixed Models
Mixed Model Selection Demo Mixed Model Selection (script)

Model_w_year (script)

Comparison Bayesian/Frequentist

Hypericum Data

Exercise 8
Nuzzo 2014 Wasserstein & Lazar 2016
X Model Selection of
Mixed Models Binary
Mixed Model Selection Binary Demo Mixed GLM vR (script)

Mixed GLM vR Bayes (script)

Model_w_year binary (script)

Model_w_year binary intercept (script)

Hypericum Data


Exercise 9
Exercise 9 Data
XI Zero Inflated Models Zero Inflated Models Demo Zero Inflated (script)

Data for Demo

Martin et al.
Zero Inflated (with Bayesian)
bayesian zero inflated poisson
bayesian zero inflated neg binom

Exercise 10

Data for Exercise 10


XII General Additive Models GAMs Demo GAMs (script)

Data for Demo

Exercise 11
Data for EX11
ISIT file
Gillibrand et al. 2007
XIII Non-linear Count Data Non Linear Counts Demo Non Linear Counts (script)

Data for Demo

Exercise 12 
** File is in .doc format and has to be copied into an R script