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

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 2017


Extra Material (from Old Methods 1)


Session Topic PDFs Scripts and Data Excercises
I Class Presentation
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 Logistic Regression Script

Hypericum Survival Data

Exercise 4

Ex4_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 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


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

Nuzzo 2014 

Wasserstein & Lazar 2016

XI Zero Inflated Models Zero Inflated Models Demo Zero Inflated (script)

Data for Demo

Martin et al.

Exercise 10

Data for Exercise 10


XII General Additive Models GAMs Demo GAMs (script)

Data for Demo

Exercise 11
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