BIOL 6090

(Advanced)

Biometry

Last Updated September 19, 2019

Please report any problems here:

khyrenbach (at) hpu (dot) edu

 
Syllabus

(Last Updated: Aug 16)

   
     
     

Dr. David Hyrenbach

Offices:

AC 249, HLC

EMSB, Oceanic Institute

Phone:

(808) 236-3563

Office Hours:

HLC: Tu & Th; 10:45 - 12:00

OI: Tu & Th; 12:00 - 13:00

 

or by appointment at EMSB, 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. 27

 

Introduction - Three Statistical Frameworks

 

Lecture 2: Thursday Aug. 29

 

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. 3

 

Observations and Variables

 

 

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. 5

 

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. 10
 

 

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. 12

 

 

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. 17

 

QUIZ#1 (Hypotheses, Sampling and Probability)

 

Statistical Inference and Reliability

 

Intro to Graphs in Rcmdr

 

 

 
 

Lecture 8: Thursday Sept. 19

 

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. 24

 

Probability Distributions

 

Intro to Advanced Graphs 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. 26

 

Statistical Assumptions

 

MusicFestival Dataset

 

Week 6 - Assessing Normality

Task for this Week: Assessing Data Normality

 

Lecture 11: Tuesday Oct. 1

 


Data Transformations

 

RExam Dataset

 

 

Lecture 12: Thursday Oct. 3

 

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. 8

 

QUIZ#2 (Estimation: Central Tendency / Variability and Probability Distributions)

 

From Data Exploration to Statistical Modelling

 

 
 

Lecture 14: Thursday Oct. 10

 

Introduction to Correlation

 

 

Week 8 - Correlation and Regression

Task for this Week: Explore Correlation and Regression

 

 
 

Lecture 16: Thursday Oct. 17

 

Simple Linear Regression

 

AlbumSales1 Dataset

 

 

Week 9 - Comparing Two (or more) Means

Task for this Week: Consider Multiple Variables

 

 

Lecture 17: Tuesday Oct. 22

 

Multiple Linear Regression

 

AlbumSales2 Dataset

 

 
 

Lecture 18: Thursday Oct. 24

 

 

Information Theory


 

 
Week 10 - Comparing Two (or more) Means


Task for this Week: Explore ANOVA

 

 

Lecture 19: Tuesday Oct. 29

 

Comparing Two (or more) Means

 

 

SpiderLong Dataset SpiderWide Dataset

More Ways to Compare Two Means

SpiderRegression Dataset

 

Lecture 20: Thursday Oct 31


QUIZ#3 (Assessing Normality and Descriptive Statistics)

Analysis of Variance: Theory & Implementation

 

ViagraDataset

 

Week 11 - ANOVA Extensions

Task for this Week: Continue Exploring ANOVA

 

 

 

Lecture 21: Tuesday Nov. 5

 

Lecture 22: Thursday Nov. 7

 

Two-Way ANOVA

 

BeerGoggleDataset

 

 

Week 12 - Other Statistical Applications

Task for this Week: Explore Other Statistical Tests

 

 

Lecture 23: Tuesday Nov. 12

 

QUIZ#4 (Correlation and Regression)

 

Nested and Factorial ANOVA

 

 

Lecture 24: Thursday Nov. 14

 
 

Contingency Tests

 

 

Cats&Dogs Dataset

 

Week 13 - Other Applications

Task for this Week: Explore Other Statistical Concepts

 

 

Lecture 25: Tuesday Nov. 19

 

Nonparametric Tests

 

DrugDataset SoyaDataset

 

 

Thursday 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:

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)

 

 
Week 14 - Wrap-Up

Task for this Week: Wrap Up

 

 

Lecture 26: Tuesday Nov. 26

 

QUIZ#5 (ANOVA)

 

 

Review & Wrap-Up

 

 

 

Lecture 27 : Thursday Nov. 28

 

NO CLASS - Thanksgivings

 

 
Week 15 - Finals' Week

Tuesday Dec. 3

 

(9.10 - 11.30)

 

Project Presentations

 
 

 

Tuesday Dec. 5

 

(9.10 - 11.30)

 

Submit Project Write-up via Email

 
 

 

 

 

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