BIOL 4090 / 6090

(Advanced)

Biometry

Last Updated November 10, 2018

Please report any problems here:

khyrenbach (at) hpu (dot) edu

 
Syllabi

(Last Updated: Aug 16)

   
     
     

 

Dr. David Hyrenbach


Office:

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:

Required:

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

ISBN: 9781446200469

Recommended:

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: www.openintro.org/stat/textbook.php

Recommended:


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

 

BeerGoggleDataset

 

 

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
 

 

 

 

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)

 

 

 

Wrap-Up

 

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)

 

 

 

 

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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