Bio Z620 - Biostatistics

Section: 22384
Class Day and Times: MWF 10:10-11:00
Class Location: SW 221
Text: Lecture Notes accessible from this WEB page
WEB Page: http://elizabethhousworth.com/Fall2012/BioZ620
Instructor: Elizabeth Housworth
Office and Office Hours: 371 Rawles Hall, 1-2:30 MW, and by appointment
Important dates: Last day for automatic withdrawals is Wednesday, October 17. Our Final Exam period is 10:15am-12:15pm on Friday, December 14.

Grading Procedure and class policies: Regular homework assignments with routine, pre-determined analyses will be given weekly. More involved mini-projects where you completely analyze a data set and turn in a written report about your results will be assigned periodically. The lowest two homework assignment scores and the lowest mini-project score will be discarded from your calculated grade. The assignments can be found through their links which are located on their due dates on the syllabus given below. In addition, you have one individual data analysis project of a data set of your choosing. Your data and research proposal are due on Friday, November 2, a progress report is due Wednesday, November 28, and your final report due by Friday, December 14 at 12:15pm. The grading rubric can be found through the following link: Grading Rubric

A sample mini-project write-up can be found at: Sample Mini-Project Write Up

Minitab can be purchased or rented through

R can and RStudio can be downloaded from
 
                           
Points
Homeworks  150
Mini-Projects  150
Attendance and Participation  100
Individual Project  100
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Total  500

Cheating Policy: You can work together on the homeworks and on the mini-projects. The write-up on the mini-projects should be in your own words but the analysis can be discusse freely with your classmates. Individual projects should be your individual work only. If I have determined that you have cheated, I will give you an F* in the course.

Religious Holiday Policy: If you will miss class, especially a class during which there will be an exam or other required work, for a religious holiday, you must inform me during the first two weeks of the semester.  

 
Tentative Syllabus
Date Topics Supplementary Material and Work Due
Monday, August 20 L01: Developing your common sense John McDonald's Free Online Text: Handbook of Biological Statistics
Standard references: Biometry by Sokal and Rohlf; Biostatistical Analysis by Zar
Wednesday, August 22 L02: Intuitive p-values Data and Code for Lecture 2
Friday, August 24 L03: Various versions of the t-test. --
Saturday, August 25 Computer Lab BLBH 118 Lab 1: Introduction to R (and Minitab and...)
Monday, August 27 L04: Assumptions --
Wednesday, August 29 L05: Log Transformations Homework 01
Data for Lecture 5
Friday, August 31 L06: Nonparametric procedures for comparing two distributions Data and Code for Lecture 6
Monday, September 3 LABOR DAY
Wednesday, September 5 L07: Bootstrapping and Permutation tests Data and Code for Lecture 7
Friday, September 7 L08: Paired Samples Mini-project 1
Data for Lecture 8
Saturday, September 8 Computer Lab BLWY 125 Lab 2:
Monday, September 10 L09: Guide to comparing two samples --
Wednesday, September 12 L10: One-way ANOVA theory Homework 02
Friday, September 14 L11: One-way ANOVA examples Data for Lecture 11
Monday, September 17 Class cancelled: I am at a conference out of the country. Alternative instruction: lab Saturday, August 25, 10:10 am and/or lecture notes about the analysis of ratios
Supplemental 1: Analysis of Ratios 		--
Wednesday, September 19 Class cancelled: I am at a conference out of the country. Alternative instruction: lab Saturday, September 8, 10:10 am and/or lecture matrial about Bayes's Theorem.
Supplemental 2: Bayes's Theorem and the Existence of God 		--
Friday, September 21 Class cancelled: I am at a conference out of the country. Alternative instruction: lab Saturday, September 29, 10:10 am.
Better Explained: Bayes's Theorem
Drug Testing Example at the bottom of the Wikipedia entry
 --
Monday, September 24 L12: ANOVA alternatives Welch's ANOVA Macro
Wednesday, September 26 L13: Making Comparisons after ANOVA Homework 03
Friday, September 28 Class cancelled: The administration asked me to represent IU at a statewide meeting about quantitative reasoning. Alternative instruction: lab Saturday, November 10, 10:10 am. --
Saturday, September 28 Computer Lab BLBH 118 Lab 3:
Monday, October 1 L14: Multiple comparisons Data for Lecture 14
Wednesday, October 3 L15: Simple linear regression I Mini-project 2
Data for Lecture 15
Friday, October 5 L16: Simple linear regression II Pearson's Data on Father and Son heights
Monday, October 8 L17: Outliers and leverage points --
Wednesday, October 10 L18 Regression diagnostics Homework 04
Friday, October 12 FALL RECESS --
Monday, October 15 L19: Transformations and regression
A cautionary note on the statistical analysis of allometric relationships. 		Bird heart rate and egg mass data from Tazawa et al. 2001
Wednesday, October 17 L20: Serial correlation To compute the significance of the serial correlation you need the table in Durbin's and Watson's paper: Tables for assessing the significance of the Durbin and Watson Statistic Mini-project 3
Consumption of Spirits in the United Kingdom
Friday, October 19 L21: Weighted regression Data for Lecture 21
Monday, October 22 L22: Multiple linear regression I - Theory --
Wednesday, October 24 L23: Multiple linear regression II - Beginning Diagnostics Data for Lecture 23
Friday, October 26 L24: Multiple linear regression III - More Diagnostic Tools --
Monday, October 29 L25: Regression and ANOVA --
Wednesday, October 31 L26: Interactions in Regression Data for Lecture 26
Friday, November 2 L27: General Linear Models Research proposal and data due
Monday, November 5 L28: Model selection I --
Wednesday, November 7 L29: Model Selection II Homework 05
Data for Lecture 29
Friday, November 9 L30: 2(+)-way ANOVA Data for Lecture 30
Saturday, November 10 Computer Lab BLBH 118 Lab 4: Discrete data analysis in R
Monday, November 12 L31: 2(+)-way ANOVA without replication Data for Lecture 31
Wednesday, November 14 L32: Random effects and experimental design Mini-project 4
Friday, November 16 L34: Categorical responses: test for equal proportions and odds ratios --
Thanksgiving Recess November 19-23
Monday, November 26 L35: Categorical responses: Chi-square tests and Fisher's exact test --
Wednesday, November 28 L36: Mantel-Haenszel test
L36: Beamer 		Progress report due
Friday, November 30 L37: Logistic regression - theory
L37: Beamer 		--
Monday, December 3 L38: Logistic regression - examples Data for Lecture 38
Wednesday, December 6 L39: Logistic regression - diagnostics Homework 06
Friday, December 9 L40: Logistic regression with binomial counts
Notes Not Available 		Data for Lecture 40
Written Project due Friday, December 14 by 12:15 pm