BIOS 543 Biostatistical Methods I

Fall 2008 schedule, Data for Exercises, PDFs

Professors: Jessica Ketchum, PhD and Roy Sabo, PhD
Course Director: Al M. Best, PhD

Note that we have given the PDF to the bookstore -- they will be printing up course notes.

Registration

Monday and Wednesday, 3:30-4:50pm in Sanger Hall 6-032. The two MCV campus sections are identical.
Tuesday and Thursday 4:00-520pm in Sanger Hall 6-032
Note that section 902 does not meet on the MCV Campus--and it is not taught using the material here.

Preregistration should be open to all who have the prerequisites.

Course Syllabus

Prerequisites
The graduate catalog says that you must have: "Graduate standing, or one course in statistics and permission of instructor." Although mathematics will be minimized, at least one course in college level algebra is assumed. 

The main focus of the course will be on using data to make informed judgments. The course will be looking at 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.) 

Hardware and software

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 http://g2g.vcu.edu/ 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 software this course assumes (requires):

• Microsoft Windows or MacOS. The University recommends WinXP Pro or Mac OSX10.3 or higher (not VISTA). See http://g2g.vcu.edu/specs.html.
  • NOTE: Do NOT purchase hardware with the "home" edition of the Microsoft operating systems. Do NOT buy Windows Vista Home. Do NOT buy Windows Vista Home Premium. (really.) These operating systems do NOT have the security features required in our university environment and they do not allow you  to access the shared network services you'll need.
  • NOTE: DO buy Windows Vista Business or Windows Vista Premium.
• A word processor (such as Microsoft Word). No "written" (pencil or pen) homework allowed, however feel free to write in the few equations that may be necessary.
• An eMail program (such as Mozilla Thunderbird, Netscape Messenger or Microsoft Outlook)
  Students must have a valid eMail account (and one is available for free from VCU, if you don't already have one).
  Your @VCU.edu email is the one you must monitor for all course-related information.
• A hypertext browser (such as Netscape Communicator or Jaguar or Microsoft Explorer).
• JMP statistical software (see below).
• Plus, if you want to view the PDF files, you'll need the (free) Adobe Acrobat Reader.
• Plus, a few "homework-calculator workbooks" are provided in Microsoft Excel format. These may make homework calculations easier.

The instructor and TAs can NOT provide any "tech support" on anything other than the stat-software used in this course. See VCU Technology Services. and the 2008-09 Technology Guide. 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

The Graduate Catalog says:

• Basic concepts and techniques of statistical methods, including:
  the collection and display of information,
  data analysis, and
  statistical measures;
• Variation, 
  sampling, and 
  sampling distributions;
• Point estimation, 
  confidence intervals, and 
  tests of hypotheses for one and two sample problems;
• principles of one-factor experimental design, 
  one-way analysis of variance, and 
  multiple comparisons;
• correlation and 
  simple linear regression analysis;
• contingency tables and 
  tests for goodness of fit.

Specifically, this means that students will do* the following:

Using categorical data (proportions), consider:

• A single population average
• Differences between two populations
• Association between two responses

Using continuous data (numerical measures), consider:

• A single population average
• Differences between two independent populations
• Differences between two paired measures
• Differences between more than two populations
• Association (correlation, curve fitting) between two responses
• Nonparametric alternatives

For all of the above, we will use all of the following approaches: hypothesis testing, p-values, and confidence intervals. We will also consider study design including sample size and power.

*By "do the following" we mean: that student will take real data, go thru the steps of statistical decision making, and write up their understanding of the conclusions. Most calculation will 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.

Classes

Monday and Wednesday, 3:30-4:50pm in in Sanger Hall 6-032.
Tuesday and Thursday 4:00-5:20pm in Sanger Hall 6-032. The topics to be discussed each day are on the web.

Promptness: The class will start promptly on time according to the "correct time" at www.time.gov. The wall clock and/or your watch may show a different time; we start at the "correct time". If you come in late, use the left-hand door (as you enter from the hall). Since the Monday/Wednesday class has every seat filled, please fill every seat from audience-left. That is, leave the right-row seats empty for the late comers.

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. 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

Roy Sabo, PhD is the is instructor for BIOS 543. His office is  Theater Row 3032.  His eMail is RSabo@vcu.edu and phone is 828-3047. Office hours are 10-11:30 Monday and Wednesday or by appointment.

Jessica Ketchum, PhD is the is instructor for BIOS 543. Her office is  Theater Row 3085.  Her eMail is McKinneyJL@vcu.edu and phone is 827-2057. Office hours are Monday 11:00 to 12:30, and Wednesday between 1:00-2:30, or by appointment.

Al Best, Ph.D is the course director for BIOS 543. His office is Theater Row 3024. Office Hours are between 3:00-5:00 on Tuesday and Thursday 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.

Office Hours are in Theater Row Room 3049. The Teaching Assistants are:
Caroline Carr, (carrck@vcu.edu) office hours are between 8:30-11:30 on Friday,
Allison Dunning (amdunning@vcu.edu) office hours are between 10:00-noon on Tuesday and 11-noon on Thursday,
Parinaz Ghaswalla (ghaswallapk@vcu.edu) office hours are between 1:00-2:30 on Tuesday and 12:30-2:00 on Thursday,
Jiayi Hou (houj2@vcu.edu) office hours are Friday 1:30-4:30,
Adam Sima (simaa@vcu.edu) office hours are Monday 12:15-1:25, 3:15-5:15,
Mercer Thorp (thorpjm@vcu.edu) office hours are between 11:00-12:30 on Monday,
Amber Wilk (wilkar@vcu.edu) office hours are between 9:00-noon on Thursday.
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 recommended 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 do 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).

The required software is: JMP statistical analysis software.

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.

You may ask, "But I already know/use ____ for statistics, do I need to buy 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 543 all homework and inclass work will be done ONLY using JMP.

Grades

Letter grades will be determined by:

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.

The weight of assignments and examinations are as follows:

Homework (nine of them) = 70%
Mid term exam (two) = 10%
Cumulative Final exam = 15%
TBL, in-class participation, discussion, attendance = 5%.
Note: extra credit is possible.

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.

VCU Honor System: To quote from the VCU Honor System document:

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*:

• Published books (especially the Daniel text),
• Course notes provided by the instructor or TAs,
• All online BIOS543 course materials,
• All of the notes you've written during the course,
• Statistical software (especially JMP), and
• Discussion with the instructors (Drs. Ketchum, Sabo, or Best) or any other member of the VCU graduate faculty**.

*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:

• Discussion with the BIOS 543 TAs,
• Discussions with other students enrolled in the course this semester.

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. All examinations will be turned in electronically.

Non permitted resources for exams:

• You may not discuss the exams with the BIOS 543 TAs
• You may not discuss the exams with any other student or individual except Dr. Sabo, Dr Ketchum or Dr. Best
• You may not have any access to previous years exams or grade sheets.

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.

• 5 points will be taken off (out of 100) per day for each day late. After one week past the due date, the assignment will be graded as 0 (zero).
• If you know (ahead of time) you are going to miss an assignment due date, then you must see (or phone) the Instructor (before the due date) and request a new due date. If you are out of town to present a paper at a conference, or you have a scheduled medical procedure, then you will receive a new due date. Other exceptions are at the sole discretion of the Instructor.
• If you are sick (or whatever) then you can once write "SICK, one day late" on your homework assignment and turn it in for full credit.
  If you are sick for a longer period, you should phone the Instructor and request a new due date. Note, the Instructor is under no obligation to change due dates unless there is documentation of an illness or an established handicapping condition.

"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 three things: 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, 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.provost.vcu.edu/policies/.

Student Conduct:
Everyone has a responsibility to foster an environment where learning can occur. So, the University has clarified  expectations regarding student (and faculty) conduct in the classroom (see http://www.provost.vcu.edu/pdfs/FacultyGuideToStudentConductInInstructionalSettings.pdf). In particular:

• If you arrive late or leave early, do so by the door "away" from the instructor's podium and do so in a manner that does not disturb the class.
• It is inappropriate to have side conversations during the class. If course material is unclear, please raise your hand and ask a question.
• It is inappropriate to use text messaging systems during class. Only receipt of university emergency alert text is permitted.
• Please turn off cell phones and beepers during class or set them to vibrate.
  If you must answer these devices, do so in a manner that does not disturb the class.
• There is a wireless connection in the classroom. If you use a laptop during class to view the BIOS 543 course material, that is appropriate. It is inappropriate to use the wireless connection during class for non-class related activities.

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.

Honor System

For more info on the VCU honor system, see http://www.medschool.vcu.edu/graduate/student_res/honor_system.html.

The correct URL for this page is: http://www.people.vcu.edu/~albest/BIOS543/ .
Last modified: Friday October 10, 2008