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 3^{rd} 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. 2^{nd}
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.