Spring 2008 schedule, Data for Exercises, PDF docs.
Instructors: Al M. Best, PhD, Associate Professor of Biostatistics and
Jessica McKinney Ketchum, PhD, Assistant Professor of Biostatistics

Course Description

Prerequisites
The graduate catalog says that you must have: "Prerequisite: STAT/BIOS 541 or STAT/BIOS 543, or equivalent." Although mathematics will be minimized, at least one course in college level algebra is assumed. We will assume that you have encountered the material in these prerequisite courses. You may wish to see my BIOS 543 web pages to see the material we cover.

The main focus of the course will be on using data to make informed judgments. The course will be looking at a lot of actual journal articles with real data. Students in the course will be doing a lot of data analysis. (This is not a "statistical literacy" course where we'll just touch the surface of concepts.)

Reality is this: The class is taught as though it is in a computer lab so; We assume that everyone will be able to see a computer. Students should bring their own laptop to class. All students are expected to 'work along' with the instructor in class. That is, this class is taught as a lab-class; we presume that you have ready access to the hardware and software tools necessary to "learn by doing".

However, officially we have to say the following: The course assumes that you have access to a computer and know how to use it. You are NOT required to own your own hardware, but if you want to Online@VCU can help you with purchases. Whether you use your own machine, a machine owned by the University in your office, or one of the publicly available machines, familiarity with modern computer operating systems and software is assumed. To receive instruction in these areas you may want to look into the short courses offered by the University.

The instructor and TAs can NOT provide any "tech support" on anything other than the stat-software used in this course. This course does NOT assume you have familiarity with any statistical software. You'll learn about stat software here; we will not answer questions regarding hardware, windows, or any other software.

Topics

Specifically, this means that students should already know how to do* the following:

For all of the above, we use p-values for decision making, and confidence intervals for description. We will assume you are completely comfortable the fundamentals of hypothesis testing.

*By "do the following" we mean: that student should be able to take real data, go thru the steps of statistical decision making, and write up their understanding of the conclusions. Most calculation should be done by the software but students must demonstrate their mastery of the process by writing clear explanations of the methods and conclusions, including a consideration of the assumptions made.

However, We will review these topic areas before beginning the new material for BIOS 544.

These methods will be extended to repeated-measures ANOVA, where the response of interest is measured over multiple time points.
Use continuous covariates and regression analysis to extend the ANOVA model to the analysis of continuous effects.
We will do an introduction to Equivalence testing, making "Just as good as" claims (rather than "difference" claims).
We will do an introduction to logistic regression, which is a way to do ANOVA-like analyses on a binary response variable.
We will do an introduction to survival analysis, which is a way to analyze time-to-event data.

Classes

Monday and Wednesday, 3:30-4:50pm in Sanger Hall 6-032 Section 001 (#11157)
Tuesday and Thursday 4:00-520pm in Sanger Hall 6-032 Section 003 (#17901)
The topics to be discussed each day are on the web.

Attendance: 100% in-class attendance is expected. There will be concepts and approaches discussed in-class that can not be gleaned from the book(s). You are expected to be prepared for class (read the assigned material) and come with questions. You are expected to participate in class.
If you miss class: Get the handout from your fellow students (or the TA). See the web-page for that class. You are responsible for all the information you missed.

If any questions or issues arise in class that are outside the scope of what we need to discuss in class, then the instructor will defer the question until later or ask that the student see the instructor after class. Of course, your participation in class is expected to be courteous and considerate. Accordingly, please refrain from side conversations. Sleeping in class is disruptive, so you'll be asked to leave. If you arrive late, sit in the back of the class. If you know you need to leave early, sit in the back of the class. We will all appreciate it if you could minimize noise and disruption due to lateness or early departure. Students will abide by the University Statement on "Student Conduct in the Classroom."

"Snow days" or other weather disruptions: If the University is open, class will meet.

Instructors

Al Best, Ph.D is the course director for BIOS 544. His office is Theater Row 3024. Office Hours are between 3:00-5:00 on Tuesday and Thursday. Or, catch me after class on Monday and Wednesday or by appointment. It's best to call 827-2045 or eMail: AlBest@VCU.edu. It's possible that you can drop by, but I may be involved in other things. If so, we'll set up an appointment.

Jessica McKinney Ketchum, PhD is the is instructor for BIOS 544. Her office is Theater Row 3085. Her eMail is McKinneyJL@vcu.edu and phone is 827-2057. Office hours are Tuesday and Thursday between 10:00-noon or by appointment.

Office Hours are in Theater Row Room 3049. The Teaching Assistants are:
Bob Carrico (carricorj@vcu.edu) office hours are between 3:00-5:00 on Monday and 3:00-4:00 on Wednesday,
Allison Dunning (amdunning@vcu.edu) office hours are between 9:00-10:30 on Monday,
Tobi Guennel (tguennel@vcu.edu) office hours are between 12:30-3:30 on Thursday,
Omar Ibrahim (ibrahimom@vcu.edu) office hours are between 1:00-3:00 on Tuesdays and 1:00-2:00 Monday,
Sarah Reese (reesese@vcu.edu) office hours are between 10:30-noon on Monday and 1:00-2:30 on Wednesday,
Emily Sheldon (sheldoneh@vcu.edu) office hours are between 8:30-11:30 on Wednesday,
Mercer Thorp (thorpjm@vcu.edu) office hours are between 3:30-5:00 on Tuesday.
Here is a summary of all the office hours.

Come to Room 3049 Theater Row for TA office hours. Do not "walk in" to the TAs offices outside of the regularly scheduled office hours; they have other responsibilities beyond this course and are not available 24-7. Other office hours are by appointment (eMail is preferred).

Textbook and Software

The required textbook is:
Wayne W. Daniel (2005) Biostatistics: Foundations for Analysis in the Health Sciences, 8th Edition. John Wiley & Sons. ISBN 0471456543. (Note that you may find 7th Editions out there but we would not buy then because all homework will be out of the 8th edition and they are different.) Feel free to purchase this book from the MCV/VCU bookstore ($80-120) or from BarnesAndNoble.com (new $96, used $73).

1 - Download the software from: http://www.ts.vcu.edu/faq/stats/jmp.html. Note that this link will allow you to download a CD "image". You then use that to make your own installation CD. Note that you MUST have the ability to write a CD (not just read). If you can not write a CD then come by the BIOS offices and check out a CD for installation.

2 - Students who downloaded JMP in the Fall will have a way to update the license. We are working on exactly how this will be done--stay tuned. If you can not write a CD then come by the BIOS offices and check out a CD for installation.

You may ask, "But I already know/use ____ for statistics, do I need to get JMP?" Yes.
If ___ in the question is "Excel," the answers it gives are often wrong; don't use it.
If ___ in the question is SPSS, SAS, or Minitab the results they give are often incomplete--specifically they are short on graphics--and you'll find JMP much easier to use too. It's slightly possible that you could get by with some other software but the course (and the grading) will assume that you can produce every table and figure that JMP can produce and will not accommodate differences that arise because of your choice to use other software.

What about SAS? Some of you need to be able to do statistical calculations and data management with SAS software. We've prepared a supplemental document for this purpose. See the SAS Companion if you want to use SAS to do everything we cover in class. But know that for BIOS 544 all homework and inclass work will be done ONLY using JMP.

Grades

Note: This is graduate school. Do not expect and "A". A grade of "B" is a "just-do-what's required" grade. A grade of "A" reflects the superior understanding that is the result of:
1-asking questions in class,
2-doing all homework completely,
3-making sure you understand how to fix all errors made in the homework, and
4-being able to write a defendable summary of your answer to all questions.

A = 90 and above (over 95 = A+)
B = 80 and above (over 85 = B+)
C = 70 and above (over 75 = C+)
D = 60 and above
F = below 60.
Grading disputes (or questions) should first be addressed to the TA. Then to the Instructor.

Homework = 70% -- And there is A LOT of homework. Each homework is equally weighted
Mid term exam = 10%
Cumulative Final exam = 15%
In-class participation, discussion, attendance, extra credit = 5%.
There will be extra-credit opportunities.

Plagiarism

The course lecture notes have a copyright but this is NOT intended to keep students from using the "sample write-up" text. That is, YES, you can copy the paragraph/sentences in the course notes and use them in your homework and exams. Yes, you have permission to use my wording (after all, there is only so many ways to say "The groups were not significantly different").

All of your homework and exams are expected to be the product of your own effort. Yes, in graduate school, students collaborate--that is OK. But what you turn in should be yours. This is an important component of the learning process--writing up your own work. Turning in someone else's work with your name on it IS plagiarism.

Homework and Exams

Homework: Homework should be done on a word processor (because the graders can't always read hand writing). Print out your homework (on paper); do not submit the document electronically. Handwritten homework will be returned and subject to the late penalties (below). No homework grades will be "dropped." All homework will count towards your grade.

"Pledged" versus "Unpledged" work: At the option of the instructor, work assigned for classes, clinics, internships, and all other types of instruction offered at the University may be accomplished in either of two ways: (1) as “Pledged” work, for which the student will sign a pledge statement indicating that the work was completed independently, without giving or receiving assistance from another; or (2) as “Unpledged” work, which may be completed in collaboration with others as directed by the instructor and for which no pledge statement is required. For all “Pledged” work, the instructor shall encourage all students to sign the official Honor Pledge of the VCU Honor System. However, neither the presence nor the absence of a signed pledge statement shall prevent a student from being charged under the VCU Honor System.

The University honor pledge is
“On my honor, I have neither given nor received aid on this assignment.”
Student’s Signature:

All work is considered to be pledged work unless the instructor specifies otherwise.

All work is considered pledged with the following specific understanding with regards to "aid":

The following are resources always available to you for homework and exams*:

*That is, the above is permitted "aid" not subject to the honor pledge exclusion.
**Note that the advice given by other members of the faculty may be different than the advice given by Dr. Best.

Homework resources: In addition, the following resources are available to you for homework only:

Note: viewing copies of previous years homework assignments or grade sheets is not a permitted resource and is a VCU honor system violation.

Exams: All Exams (including mid-term exams) are "pledged" and the product of your individual effort. If the Instructor feels that the VCU Honor System will be followed, exams will be take home, open book, open notes. If he receives the slightest hint that there might be the slimmest possibility that students are colluding on exams, then exams will be in class.

Access to any of the above resources is a VCU honor system violation.
Caution: If you do an exam on a public or "lab" computer, note that you must take steps to protect the security of your work. That is, say student XX does an exam and saves the MSWord document on a computer available to the public. Then student YY finds the document on the computer, changes the name on it and turns it in. BOTH student XX and student YY will be turned in to the Honor Council. The usual penalty for a first-time honor code violation is an F in the class.

Collaboration: Yes, you may work together on homework but turn in a document that reflects your own personal understanding and effort. No, you may not work together on the mid-terms or final exam.

Lateness: You should turn in every homework assignment on time. "On time" means that the assignment is in the Instructor's hand by the end of class on the assignment due-date.

"Re-Do"s: Occasionally, a student will make a computational (or other "minor") mistake on "step 1" of a homework problem and, as a result, they loose credit on most of the subsequent steps. That is, it's roughly clear that the student "gets it" but, because of the minor mistake, the grade is very low. In such a case, the homework will be graded and marked as a "Please REDO"; The student should re-do the homework with the mistakes fixed and turn it in (again) to be regraded. Usually, the most that can be expected from such a regrade is a 90%=A minus.
Occasionally, a student will make a major blunder and, as a results, the grade is a C or below. In such a case, the homework will be returned with the (low) grade. The student is free to re-do the homework with the mistake(s) fixed and turn it in (again) to be regraded. Usually, the most that can be expected from such a regrade is 80%=B minus.
If you turn in a homework for a "Re-Do", include: 1) the full original homework, 2) the original grade-sheet, 3) your corrected homework, and mark the packet of material as "Please Regrade". After your original homework is returned to you, you have 7-10 days to turn in a "Re-Do".

Other

There are a number of policies that students should be aware of. Some are listed at http://www.students.vcu.edu/rg/policies/. There are, for instance, expectations regarding student (and faculty) conduct in the classroom. Please turn off cell phones an beepers during class. Other specific items we draw your attention to are as follows:

Americans With Disabilities Act:

Section 504 of the Rehabilitation Act of 1973 and the Americans with Disabilities Act of 1990 require Virginia Commonwealth University to provide academic adjustments or accommodations for students with documented disabilities. Students seeking academic adjustments or accommodations must self-identify with the Coordinator of Services for Students With Disabilities on the appropriate campus. After meeting with the Coordinator, students are encouraged to meet with their instructors to discuss their needs, and if applicable, any lab safety concerns related to their disabilities.

BIOS 544 Biostatistical Methods II