STT 464

Statistics for Biologists Section II

Interdepartmental with Animal Science/Crops and Soil Science (now Plant, Soil and Microbial Sciences)

Fall 2012

 

COURSE:      

            Statistics 464 - Statistics for Biologists

Section II

                                                                                                                                                                                          

INSTRUCTOR:

            Dr. Rob Tempelman

            Department of Animal Science

            1205J Anthony Hall

            Tel: 355-8445

            e-mail: tempelma@msu.edu

 

GRADER:

            Ms. Xiaoqing Zhu

            e-mail: zhuxiaoq@msu.edu

         

OFFICE HOURS FOR TEMPELMAN:      

            Monday afternoon (4:30-5:00)

            Wednesday afternoon (1:30-1:50 p.m.)

            Other times by appointment (through phone/email) please

            If you send an inquiry by email, I will almost always answer within 12 hours

 

OFFICE HOURS FOR MS. ZHU:

            Tuesday mornings (9:00-10:00) in the conference room of 1205 Anthony Hall.

 

TEXTS:

REQUIRED:

1. Course Notes:  available online through MSU Angel (www.angel.msu.edu )

2. Statistical Methods 3rd Edition (2010) by R.J. Freund, W.J. Wilson, and Donna L. Mohr. Academic Press, ISBN 0-12-267651-3.  This resource is FREELY available to anybody downloading materials from a campus computer through the MSU library link www.lib.msu.edu (or specifically: http://www.sciencedirect.com.proxy2.cl.msu.edu/science/book/9780123749703 )

 

 

RECOMMENDED:

3.  Introductory Statistics with R. 2nd Edition (2008) by Peter Dalgaard, Springer, ISBN 978-0-12-374970-3

This resource is also FREELY available to anybody downloading materials from a campus computer through the MSU library link www.lib.msu.edu (or specifically: http://www.springerlink.com.proxy1.cl.msu.edu/content/m17578/?MUD=MP )

 

Please note that the following electronic textbooks pertaining to the use of R in statistical analyses are freely available to the MSU community and may be useful for the course.

 

General Introduction to R references

http://www.springerlink.com.proxy1.cl.msu.edu/content/ht5453/#section=1024950&page=1  (R by example: Concepts to Code  by Jim Albert and Maria Rizzo)

http://www.springerlink.com.proxy1.cl.msu.edu/content/m00470/#section=872625&page=1 (Tiny Handbook of R, by Mike Allerhand)

http://www.springerlink.com.proxy1.cl.msu.edu/content/w26370/#section=79195&page=1 (A Beginner’s Guide to R by Alain F. Zuur, Elena N. Ieno and Erik Meesters)

 

 

General statistics and R references

http://www.crcnetbase.com/isbn/978-1-4398-2755-0  (Using R for Data Management, Statistical Analysis, and Graphics by Nicholas J. Horton and Ken Kleinman)

http://www.crcnetbase.com/isbn/978-1-4200-7933-3 (Handbook of Statistical Analyses Using R, Second Edition by Torsten Hothorn and Brian S. Everitt)

http://www.crcnetbase.com.proxy1.cl.msu.edu/ISBN/9781584885740 (Multiple comparisons using R by Frank Bretz, Torston Hothorn, and Peter Westfall).

http://onlinelibrary.wiley.com.proxy1.cl.msu.edu/book/10.1002/9781444319620 (Biostatistical Design and Analysis Using R by Murray Logan)

http://www.springerlink.com.proxy1.cl.msu.edu/content/j50262/#section=1003214&page=1 (Biostatistics with R: An Introduction to Statistics through Biological Data by Babak Shahbaba)

http://onlinelibrary.wiley.com.proxy1.cl.msu.edu/book/10.1002/9780470721896  (Statistics and Data with R: An applied approach through examples by Yosef Cohen and Jeremiah Y. Cohen)

http://site.ebrary.com.proxy1.cl.msu.edu/lib/michstate/docDetail.action?docID=10435404 (Statistical Analysis with R by John M. Quick)

 

Statistics and R references with specific biological application areas:

http://www.crcnetbase.com/isbn/978-1-4200-8826-7  (Introduction to Data Analysis with R for Forensic Scientists by James Michael Curran)

http://www.springerlink.com.proxy1.cl.msu.edu/content/p415n2/#section=641583&page=1 (Advances in Social Science Research Using R by H.D. Vinod)

http://www.springerlink.com.proxy1.cl.msu.edu/content/x36228/#section=808528&page=1 (Forest Analytics with R by Andrew P. Robinson and Jeff D. Harnann)

http://onlinelibrary.wiley.com.proxy1.cl.msu.edu/book/10.1002/9780470987605 (Statistical Data Analysis Explained: Applied Environmental Statistics with R by Clemens Reimann, Peter Filzmoser, Robert G. Garrett, and Rudolf Dutter)

http://www.springerlink.com.proxy1.cl.msu.edu/content/p70228/#section=982568&page=1  (Analysis of Phylogenetics and Evolution by R Emmanuel Paradis)

http://www.springerlink.com.proxy1.cl.msu.edu/content/l48073/#section=64710&page=1 (A Primer of Ecology with R by M. Henry H. Stevens)

http://www.springerlink.com.proxy1.cl.msu.edu/content/uw07v1/#section=147788&page=1 (Applied Spatial Analysis with R by Roger S. Bivand, Edzer J. Pebesma and Virgilio Gómez-Rubio)

 

I would also draw your attention to the fact that there are other electronic textbooks on statistics available to the MSU community via http://www.crcnetbase.com/page/statistics_ebooks

 

 

GRADING PROCEDURE:

           

MATERIAL

Contribution to GradePoint

First Hourly Test (~ September 28, 2012)

15%

Second Hourly Test (~ October 19, 2012)

15%

Third Test (~ November 19, 2012)

20%

Homework

25%

Final Examination (FRIDAY  December 14, 2012 @ 10:00 a.m.)

25%

 

·        The first and second test will be held in class, the third test will be scheduled for two hours in the early evening (i.e. 6:30-8:30 p.m.).  These dates are tentative; however, final test-dates will be announced at least 9 days in advance.

 

·        If you have a 4.0 GradePoint within 7 days of the final examination, you are not required to write the final.  Your GradePoint will then be based on all other materials and reweighted accordingly (i.e., divide the above percentages by 75), including homework due during the last week of classes.  However, please note that if you qualify and your last homework is not graded 7 days prior to the final examination, you do run the risk of having a GradePoint < 4.0 if your last homework was done poorly.

 

Gradepoints on homeworks and tests/final are assigned as follows:

 >90%            -> GradePoint = 4.0

80-89%         -> GradePoint = 3.5

70-79%         -> GradePoint = 3.0

60-69%         -> GradePoint = 2.5

50-59%         -> GradePoint = 2.0

35-49%         -> GradePoint = 1.5

20-34%         -> GradePoint = 1.0

10-19%         -> GradePoint = 0.5

 <10%            -> GradePoint = 0.0          

 

OBJECTIVE:

Provide the student with the fundamental statistical knowledge and toolbase to perform exploratory and statistical analyses on experimental and observational research data.  Provide the student the tools to read the scientific literature critically on basic statistical design and analysis issues.

 

 

COURSE OUTLINE (very approximate timeline)

Week

Topic

1

Introduction, Notation and Definitions, Exploratory Data Analysis, R statistical software

2

Descriptive measures, Probability

3

Distributions, Sampling distributions of statistics

4

Estimation/Confidence Intervals and Hypothesis testing

5

Power, Variance testing

6

Experimental Design, Multi-population (treatment) inference

7

Analysis of Variance (ANOVA), Linear Model, and Distributional Assumptions

8

Preplanned Contrasts, Multiple comparisons

9

Two-way factorials, interaction

10

Correlation and Linear Regression

11

Linear Regression/Residual and Influence Diagnostics

12

Categorical Data Analysis

 

Other notes:

The public domain software R will be used extensively throughout the course. You can download this software freely on your own laptop/desktop from http://www.r-project.org/.  If you wish to get some practice with R, go through the introductory materials available at http://cran.r-project.org/doc/manuals/R-intro.pdf or the recommended text by Dalgaard.  This software is also freely available on all MSU computer labs.  For locations of these labs, check  http://computerlabs.msu.edu/general.html 

 

Datasets required for homeworks will be periodically available on ANGEL. 

 

Special note for the first week: 

 

·        Two computer lab orientations for STT 464 Section II students have been scheduled, one for each half of the class.   Your attendance at any one of the following two sessions is highly encouraged. Please sign up for one session via ANGEL. 

 

1.     Tuesday September 4, 2012             10:00 – 11:30 a.m.

 

2.     Tuesday September 4, 2012             1:00 – 2:30 p.m.

 

 

·        Both lab sessions will be held in Room 1210 Anthony Hall.

 

 

Please be aware of the following MSU policies:

 

1.    Academic Honesty: Article 2.3.3 of the Academic Freedom Report states that "The student shares with the faculty the responsibility for maintaining the integrity of scholarship, grades, and professional standards." In addition, the (insert name of unit offering course) adheres to the policies on academic honesty as specified in General Student Regulations 1.0, Protection of Scholarship and Grades; the all-University Policy on Integrity of Scholarship and Grades; and Ordinance 17.00, Examinations. (See Spartan Life: Student Handbook and Resource Guide and/or the MSU Web site:www.msu.edu.)
Therefore, unless authorized by your instructor, you are expected to complete all course assignments, including homework, lab work, quizzes, tests and exams, without assistance from any source. You are expected to develop original work for this course; therefore, you may not submit course work you completed for another course to satisfy the requirements for this course. Also, you are not authorized to use the www.allmsu.com Web site to complete any course work in this course. Students who violate MSU academic integrity rules may receive a penalty grade, including a failing grade on the assignment or in the course. Contact your instructor if you are unsure about the appropriateness of your course work. (See alsohttp://www.msu.edu/unit/ombud/dishonestyFAQ.html )

2.    Accommodations for Students with Disabilities (from the Resource Center for Persons with Disabilities (RCPD): Michigan State University is committed to providing equal opportunity for participation in all programs, services and activities. Requests for accommodations by persons with disabilities may be made by contacting the Resource Center for Persons with Disabilities at 517-884-RCPD or on the web at rcpd.msu.edu. Once your eligibility for an accommodation has been determined, you will be issued a Verified Individual Services Accommodation ("VISA") form. Please present this form to me at the start of the term and/or two weeks prior to the accommodation date (test, project, etc.). Requests received after this date may not be honored.

3.    Commercialized Lecture Notes: Commercialization of lecture notes and university-provided course materials is [permitted] [not permitted] in this course.*

4.    Disruptive Behavior: Article 2.III.B.4 of the Academic Freedom Report (AFR) for students at Michigan State University states: "The student's behavior in the classroom shall be conducive to the teaching and learning process for all concerned." Article 2.III.B.10 of the AFR states that "The student has a right to scholarly relationships with faculty based on mutual trust and civility." General Student Regulation 5.02 states: "No student shall . . . interfere with the functions and services of the University (for example, but not limited to, classes . . .) such that the function or service is obstructed or disrupted. Students whose conduct adversely affects the learning environment in this classroom may be subject to disciplinary action through the Student Judicial Affairs office.