BIOL 4090 / 6090

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Last Updated September 21, 2017

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khyrenbach (at) hpu (dot) edu

 

Syllabus

(last updated: Aug 26)

     
   

Dr. David Hyrenbach


CTSA #1

Oceanic Institute

Office Hours:

Tu & Th; 10:45 - 12:00 (HLC, AC 249)

M & F; 11:15 - 12:00 (HLC, AC 249)

or by appointment at CTSA #1, OI

 

 

We will use two texts:

Discovering Statistics Using R, 2012, Andy Field, Jeremy Miles and Zoe Field. Sage Publications, Thousand Oaks (USA)

 

ISBN: 9781446200469

 

A Primer of Ecological Statistics, 2004, Nicholas Gotelli and Aaron Ellison, Sinauer Associates Inc., Sunderland

ISBN: 0878932690

(On Reserve, Atherton Library)

 

Course Readings

The PDFs posted on this page are for class use only.

Please do not distribute.

 

 

Week 1 - Course Introduction and Foundations

Task for this Week: Review The Scientific Method

 

Lecture 1: Tuesday Aug. 29

 

Introduction - Three Statistical Frameworks

 

 

Lecture 2: Thursday Aug. 31

 

 

The Scientific Method & Hypothesis Testing

 

 

Assigned Reading:

Platt J.R. (1964)

Strong inference. Science, 146: 347-353

Assigned Reading:

Quinn J.F., & Dunham A.E. (1983)

On hypothesis testing in ecology and evolution. The American Naturalist, 122(5): 602-617

 

(PDF, 2 Mb)

Extra Reading:

O'Donohue, W., & Buchanan, J.A. (2001)

The weaknesses of strong inference. Behavior & Philosophy, 29: 1-20

 

 

Week 2 - Simple and Conditional Probability

Task for this Week: Review Simple and Conditional Probability

 

 

Lecture 3: Tuesday Sept. 5

 

Sampling and Probability

 

 

Assigned Reading:

Diamond, J. (1988).
Why cats have nine lives.
Nature 332 (6165): 586–587.

Extra Reading:

Lewison, R.L., Soykan, C.U., & Franklin J. (2009).
Mapping the bycatch seascape: multispecies and
multi-scale spatial patterns of fisheries bycatch.
Ecological Applications 19(4): 920–930.

 

(543 Kb)

 

Lecture 4: Thursday Sept. 7

 


Conditional Probability (and Bayesian Statistics)

 

 

Assigned Reading:

Silver, N. (2012). Less and less and less wrong. Pp. 232 - 261.

In: The Signal and the Noise. Penguin Press, New York.

Assigned Reading:

Marcus, G., & Davis, E. (2013) What Nate Silver Gets Wrong.

The New Yorker.

 

(32 Kb)

Extra Reading:

Is God Bayesian ? Unwim VS. Wiggins

(88 Kb)

 

 

Week 3 - Statistical Inference

Task for this Week: Making Statistical Predictions

 

Lecture 5: Tuesday Sept. 12
 

 

Extra Reading:

Fairfield-Walsh, C. Garrison, L. 2007. Estimated Bycatch of Marine Mammals and Turtles in the U.S. Atlantic Pelagic Longline Fleet During 2006. NOAA Technical Memorandum NOAA NMFS-SEFSC-560: 54 p.

(883 Kb)

 

 

Lecture 6: Thursday Sept. 14

 

QUIZ#1 (Sampling and Probability)

 

 

Assigned Reading:

Silver, N. (2012). How to drown in 3 feet of water. Pp. 176 - 203.

In: The Signal and the Noise. Penguin Press, New York.

 

 

Week 4 - R & Probability Distributions

Task for this Week: Working with Probability Distributions

 

 

Lecture 7: Tuesday Sept. 19

 

Statistical Inference and Reliability

 

(Review of Homework #2)

 
 

Lecture 8: Thursday Sept. 21

 

QUIZ#2 (Estimation: Central Tendency / Variability)

 

Estimation and Statistical Modelling

 

Assigned Reading:

Silver, N. (2012). Desperately Seeking Signal. Pp. 142 - 175.

In: The Signal and the Noise. Penguin Press, New York.

 

 

 
 

Week 5 - Parametric Assumptions

Task for this Week: Assumptions and Data Transformations

 

Lecture 9: Tuesday Sept. 26

 

Probability Distributions

 

Introduction to Graphical Exploration in R

 

Assigned Reading:

Limbert, E., Stahel, W.A., & Abbt, M. (2001) Log-normal Distributions across the Sciences: Keys and Clues. Bioscience 51:5: 341-352.

 

(556 Kb)

 

 

Lecture 10: Thursday Sept. 28

 

QUIZ#3 (Z Scores and Confidence Intervals)

 

Statistical Assumptions

 

Week 6 - Assessing Normality

Task for this Week: Assessing Data Normality

 

 

Lecture 11: Tuesday Oct. 3

 


Descriptive Statistics in R- Graphical Exploration

 

 

Lecture 12: Thursday Oct. 5

 

QUIZ#4 (Assessing Normality: Assumptions & Approaches)

 

Data Transformations

 

Week 7 - Using Statistical Models to Test Hypotheses

Task for this Week: Start Exploring Statistical Models

 

 

Lecture 13: Tuesday Oct. 10

 

Dealing with the lack of Normality - Theory & Practice

 

 

 
 

Lecture 14: Thursday Oct. 12

 

QUIZ#5 (Assessing Normality - Descriptive Statistics)

 

Statistical Modelling - Introduction to Correlation

 

 

Week 8 - Correlation and Regression

Task for this Week: Explore Correlation and Regression

 

 

Lecture 15: Tuesday Oct. 17

 

Correlation: Parametric and Nonparametric Tests

 

 
 

Lecture 16: Thursday Oct. 19

 

Simple Linear Regression

 

 

Week 9 - Comparing Two (or more) Means

Task for this Week: Consider Multiple Variables

 

 

Lecture 17: Tuesday Oct. 24

 

Multiple Linear Regression

 

 
 

Lecture 18: Thursday Oct. 26

 

QUIZ#6 (Correlation and Linear Regression)

 

Comparing Two Means


 

 
Week 10 - Comparing Two (or more) Means


Task for this Week: Explore ANOVA

 

 

Lecture 19: Tuesday Oct. 30

 

Analysis of Variance -Theory & Implementation

 

 

Lecture 20: Thursday Nov. 2


Extensions of ANOVA

 

QUIZ#7 (Comparing Two Means)

 

Week 11 - Multi-way ANOVA

Task for this Week: Continue Exploring ANOVA

 

 

 

Lecture 21: Tuesday Nov. 7

 

Lecture 22: Thursday Nov. 9

 

Repeated Measures ANOVA

 

 

 

Week 12 - Other Statistical Applications

Task for this Week: Explore Other Statistical Tests

 

 

 

Lecture 23: Tuesday Nov. 14

 

Contingency Tests

 

 

Lecture 24: Thursday Nov. 16

 

Nonparametric Tests

 

QUIZ#8 (Analysis of Variance)

 

Week 13 - Other Applications

Task for this Week: Explore Other Statistical Concepts

 

 

Lecture 25: Tuesday Nov. 21

 

 

Statistical Power

 

Extra Reading:

Dayton, P.K. (1998) Reversal of the burden of proof in fisheries management. Science 279 (5352): 821-822.

(655 Kb)

Extra Reading:

Unreliable Research. trouble at the lab. The Economist, October 19th, 2013

(217 Kb)

 

 

Thursday Nov. 23

 

NO CLASS - Thanksgivings

 

 

Week 14 - Wrap-Up

Task for this Week: Wrap Up

 

 

Lecture 26: Tuesday Nov. 28

 

Wrap-up

 

QUIZ#9 (Contingency Tables and Nonparametric Tests)

 

 

 

Lecture 27 : Thursday Nov. 30

 

 

Final Exam Review: Jeopardy

 

 
Week 15 - Finals' Week

Thursday Dec. 7

 

(9.10 - 11.35)

 

Submit Take-home Final

 

Take In-Class Final

 

 

 

 

 

 

 

 

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