BIOL 4090 / 6090



Last Updated November 30, 2018

Please report any problems here:

khyrenbach (at) hpu (dot) edu


(Last Updated: Aug 16)



Dr. David Hyrenbach


CTSA # 1, Oceanic Institute

Office Hours:

(HLC, 2nd floor lanai)

Tu & Th; 10:45 - 12:00

or by appointment at CTSA #1, OI



We will use two texts and a free online resource:


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)


Download a free PDF andthe textbook’s source files at:


Updated: August 19th, 2017.
This textbook is available under a Creative Commons License.

(Available freely on line)



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. 28


Introduction - Three Statistical Frameworks



Lecture 2: Thursday Aug. 30



The Scientific Method & Hypothesis Testing



Assigned Reading:

Platt J.R. (1964)

Strong inference. Science, 146: 347-353


(61 Kb)

Assigned Reading:

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

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


(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. 4


Observations and Variables



Assigned Reading:

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

Extra Reading:

Chimowitz MI, et al. (2011). Stenting versus Aggressive Medical Therapy for Intracranial Arterial Stenosis. New England Journal of Medicine 365:993-1003.

(501 Kb)

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. 6


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.

Extra 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. 11


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. 13


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. 18


Statistical Inference and Reliability


Intro to Graphs in R


(Review of Homework #2)


Lecture 8: Thursday Sept. 20


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. 25


Probability Distributions



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. 27


QUIZ#3 (Z Scores and Confidence Intervals)


Statistical Assumptions


MusicFestival Dataset


Week 6 - Assessing Normality

Task for this Week: Assessing Data Normality



Lecture 11: Tuesday Oct. 2


Data Transformations


RExam Dataset



Lecture 12: Thursday Oct. 4


QUIZ#4 (Assessing Normality: Assumptions & Approaches)


Dealing with the lack of Normality - Theory & Practice


Week 7 - Using Statistical Models to Test Hypotheses

Task for this Week: Start Exploring Statistical Models



Lecture 13: Tuesday Oct. 9



From Data Exploration to Statistical Modelling



Lecture 14: Thursday Oct. 11


QUIZ#5 (Assessing Normality - Descriptive Statistics)


Introduction to Correlation



Week 8 - Correlation and Regression

Task for this Week: Explore Correlation and Regression



Lecture 16: Thursday Oct. 18


Simple Linear Regression


AlbumSales1 Dataset



Week 9 - Comparing Two (or more) Means

Task for this Week: Consider Multiple Variables



Lecture 17: Tuesday Oct. 23


Multiple Linear Regression


AlbumSales2 Dataset



Lecture 18: Thursday Oct. 25


QUIZ#6 (Correlation and Linear Regression)


Comparing Two Means


SpiderLong Dataset SpiderWide Dataset


Week 10 - Comparing Two (or more) Means

Task for this Week: Explore ANOVA



Week 11 - Multi-way ANOVA

Task for this Week: Continue Exploring ANOVA




Lecture 21: Tuesday Nov. 6


Lecture 22: Thursday Nov. 8


QUIZ#7 (Comparing Two Means)


Multifactor ANOVA: Factorial & Nested Designs





Week 12 - Other Statistical Applications

Task for this Week: Explore Other Statistical Tests



Lecture 23: Tuesday Nov. 13


Contingency Tests




Cats&Dogs Dataset



Lecture 24: Thursday Nov. 15


QUIZ#8 (Analysis of Variance)



Nonparametric Tests



DrugDataset SoyaDataset


Week 13 - Other Applications

Task for this Week: Explore Other Statistical Concepts



Lecture 25: Tuesday Nov. 20


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:

Benjamin, D.J. et al. (2017) Redefine Statistical Significance. PsyArXiv, 22 July 2017. Web.

(7.1 Mb)

Extra Reading:

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

(217 Kb)






Thursday Nov. 22


NO CLASS - Thanksgivings



Week 14 - Wrap-Up

Task for this Week: Wrap Up



Lecture 26: Tuesday Nov. 27


QUIZ#9 (Contingency Tables and Nonparametric Tests)









Lecture 27 : Thursday Nov. 29


Final Exam Review: Jeopardy


Week 15 - Finals' Week

Thursday Dec. 6


(9.10 - 11.35)


Submit Take-home Final


Take In-Class Final




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