Introduction to Biostatistical Methods II: Syllabus
BIOS 544 – Spring 2012

Registration

Important: Register for BIOS 544; either sections 001 (#11157) or 901 (#17901).  Do not register for the cross-listed sections for STAT 544; either section 001 (#16053) or section 901 (#17902).
Also, please note that the sections taught on the MCV campus do not use the same materiel as those taught on the Monroe Park campus.

General Course Description

This course (BIOS 544) is the second part of a two-semester series (BIOS 543/544) providing an introduction to biostatistical methods. The main focus of the series is on using data to make informed decisions/judgments with statistical tools. The courses are targeted for non-statisticians and do not require background beyond algebra; but BIOS 543 (or similar) is required (the sections taught on the MCV campus are preferred). These are not math classes and students do not need to be “good at math” to understand and master the material presented here. The courses will use real data from actual biomedical studies; we do not create data to make problems more simple or difficult; we keep it real. While the emphasis on the types of research presented in these courses is biomedical, students not in the medical field can still apply the concepts and tools to other types of research studies and are encouraged to enroll. The courses are taught with an emphasis on understanding the entire research process – from a scientist’s perspective. This includes determining the research question, planning the study, data collection and management, summarizing the data with descriptive statistics, determining and performing the appropriate statistical analysis using the JMP statistical software, and communicating the results in a clear and concise manner using the IMRaD format (Introduction, Methods, Results, and Discussion). All concepts will be presented using a problem based learning strategy (i.e. centered on specific real life examples) and mastered through the use of homework assignments, examinations, the critical reading and discussion of journal articles, and team based learning activities (i.e. group learning opportunities).

Prerequisites

The only prerequisites for BIOS 544 are BIOS 543 (or similar) and at least one course in college level algebra. If you have not taken BIOS 543 with Professors Sabo or Sima (Fall 2010) or Professors Best or Ketchum (Fall 2009) you should pay particular attention to the list below to determine if you are prepared to join this class. In general, you should already know how to perform the standard statistical methods and tests when presented with a single variable or when presented with two variables (a single predictor/independent variable (X) and a single outcome/dependent variable (Y)). More specifically, you are expected to know how to do the following descriptive, univariate, and bivariate analyses:

• summarizing categorical data;
• chi-square tests for one proportion compared to a fixed (hypothesized) proportion;
• chi-square tests for comparing two proportions from (two) independent samples;
• chi-square tests for comparing many proportions from (many) independent samples;
• chi square tests for assessing the relationship between two nominal/categorical variables;
• summarizing continuous data;
• t-tests (and z-test) for one mean compared to a fixed (hypothesized) mean ;
• t-tests (and z-test) for comparing two means from (two) independent samples2;
• t-tests (and z-test) for comparing two paired means from a single sample2;
• ANOVA (F-test) for comparing many means from (many) independent samples2; and
• correlation & simple linear regression methods for assessing the relationship between two continuous variables2.

If you are not sure if you have the background knowledge for this course, please speak with the professor immediately to determine if your enrollment status is appropriate.

Specific Learning Objectives

In this course we are going to take things a step beyond one predictor variable and consider multivariable analyses. More specifically, the statistical methods presented in this course will focus on many predictor/independent variables (X’s) and a single outcome/dependent variable (Y). Multivariate analyses, when there are many outcome variables will not be presented in this course. Some concepts from BIOS 543 will be reviewed and other new methods will be presented. We will also introduce a few bivariate analyses (equivalence testing and survival analyses), if time permits. The primary statistical methods that will be covered in this course include the following:

• One-way and two-way Analysis of Variance (ANOVA)
• Repeated-measures ANOVA
• Simple and multiple linear regression
• The Analysis of Covariance (ANCOVA)
• Logistic regression
• Equivalence Analysis (optional)
• Survival Analysis (optional)

IMRaD

If you have already taken the first part of the series with us you are familiar with the IMRaD format. Those of you who did not take BIOS 543 with us will need to work on their own and with the TAs and the professors to become more acquainted with the format. The IMRaD structure is currently the norm for the structure of a scientific paper; most scientific journals now require this structure . While we do not expect you to fill in the “non-statistical” parts (e.g. literature search or comparison of your results to other published results), you do need to focus on the statistical parts and understand how it all comes together in the big picture. In short, all assignments (unless otherwise stated) are to be typed with a separate heading and section for the following:

• Introduction
• This section includes a statement of the research question and why it is important to address this question as well as a description of the population of interest.
• Methods
• This section includes a clear and concise description of what was done to get the data and how it was analyzed.
• More specifically this would include describing the following: the type of study conducted; the population of interest and how the sample was obtained; what variables were measured and how; a description of how the data was analyzed to address each of the research questions; the overall type I error rate and any methods for post-hoc comparisons or analyses; and a statement of what software (and version) were used to analyze the data.
• Results
• This section will typically include a description of the sample to assess the representativeness of the population, the results from any preliminary analyses that were conducted, and the results for the primary analyses that address the research questions of interest. Follow-up, post hoc analyses may also be included.
• Discussion
• This section addresses what the results mean and why they are important.

While this is not a statistical literacy course, your statistical literacy and proficiency will greatly improve though this process. Furthermore, your understanding of the concepts and how they fit into the bigger picture of research will be enriched.

Textbooks and Course Notes

There are not any required textbooks for this course; however there are two suggested textbooks for you to purchase if you can. The course will be taught using course notes provided by the professors and uploaded as PDF files to Blackboard for students to download. These are required readings; you must save them on your computer. You may print them out to take notes on and/or take notes in a separate notebook.
The first suggested textbook is “How to Report Statistics in Medicine” by Thomas A. Lang and Michelle Secic (2nd Edition; ISBN 978-1930513693). This text is useful in understanding most of the basic concepts in biostatistics in general, and is an excellent tool to help you with your writing. The second book “Biostatistics: A Foundation for Analysis in the Health Sciences” by Wayne W. Daniel (9th Edition; ISBN 978-0-470-10582-5) is an excellent reference for the statistical methods presented here, as well as many more. Furthermore, many of our homework problems use data from this book. All of the scanned homework pages needed from the book will be provided to you in Blackboard in case you did not buy the book. Data from his book are also available on the web .

Software

We teach this course as if we were in a computer lab. We assume that everyone is able to at least see a computer screen during class and has access to a computer out of class. If you have a laptop computer, you are strongly encouraged to bring it to every class. We expect you to “work along” with the professor during class. Much of the course will be hands on, using software to analyze data. Working along with us in class will familiarize you with the process of analyzing data more quickly. The following is a list of software you must have access to in order to do your homework assignments.

• You may obtain JMP (or SAS) for free through the university. See the Technology Services website for more information.
  To obtain and/or renew JMP v.9.0.2 see http://www.ts.vcu.edu/software/2544.html.
  To obtain and/or renew SAS v.9.3 see http://www.ts.vcu.edu/software/2558.html.
  Important: Be sure to install the latest Patch (JMP) and/or Hot Fixes (SAS); see the related sites above for more information. You are responsible for grading discrepancies due to this.
• Adobe Acrobat Reader to view the course notes provided by the professor.
• A word processing tool such as Microsoft Word. All homework and exams are to be typed and printed versions are submitted to be graded. No hand-written assignments are permitted.

Attendance

Attendance is not required or monitored but clearly an essential part of your learning process. It is helpful to let us know in advance of any planned absences and we are happy to work with you to keep you on schedule. The M/W section and the Tu/Th section are taught in conjunction, with the material always presented in the M/W section first. If you cannot attend your own section feel free to attend the other section. The teaching style of the professors may differ, but the topics and material presented will be the same. In these cases however, homework and exams must be handed in by the due date for you during your original section and you will need to make arrangements to turn it in on time (do not expect the other TAs or the professor to deliver it to your grader). There are always cases where unplanned absences occur and/or you cannot attend the other section. It is your responsibility to make up the missed material, but you may meet with the TAs or instructors to fill in any missing holes or answer additional questions from the reading IF you have done the required reading beforehand. If you are arriving late or leaving early please sit on the side of the room opposite the podium so as not to disrupt the lecture. Also please keep phones and pagers OFF (or, if necessary, on vibrate).
Be aware of Team Based Learning days – these are required attendance days, and you are expected to participate in a team in your original section. Please mark them on your calendar and do your best not to miss these; it will have a detrimental effect on your team since you are not there to contribute and participate; be respectful of this.

Grading

Homework

The purpose of homework is to give you an opportunity to better understand and ultimately master the course material with additional data. Furthermore, it is when you will practice writing the IMRaD reports and get feedback from your assigned grader.
There will be 10 equally weighted homework assignments, each due at the beginning of class. All homework assignments, unless otherwise stated, are to be typed up on a word processor (at least 1.5 spacing) and printed, with the pages stapled together in the top left corner.
Each student will be assigned to TA in their section who will grade their homework throughout the entire semester. On the table in the front of the classroom will be a folder for each grader with a list of the students assigned to that grader. It is your responsibility to put your homework in your grader’s folder and sign the homework “sign-in” sheet. This sheet is not an attendance sheet; rather it is a method of tracking which assignments were turned in and which were not. If you arrive late, quietly hand your assignment to your grader and sign the sheet (at that point located next to the TAs seated in the back of the room) before sitting down.
You are allowed to collaborate with other students in the current class (either section) on homework assignments; however the IMRaD report that is turned in must be a reflection of your own individual understanding, presentation, and interpretation of the results. You are encouraged to meet with the TAs or the professors for homework guidance after you have given it an honest attempt; that is, you may not come to office hours just to do your homework.
As there may be unplanned absences that occur we allow one opportunity to write “one-day late” on your HW and turn it in within 48 hours. It is up to you to determine how it will get to your grader however. Any other homework that is late will incur a 5% reduction for every 48 hours it is late (always rounding up).
The goal of this course is for each of you to understand the material and be able to perform the analyses when necessary in the future for your own work or research. We are not interested in ranking each of you according to how quickly you are able to do this; rather we are interested in each of you meeting that goal. As such, we will allow you to redo any homework assignments for which you received lower than a 90%. In these cases, you typically have 3 class periods (about 10 days) from the day it was passed back to turn in back in to your grader for a re-grade. You will only be allowed to receive up to a 90% on any redo homework, but you may retain any “extra-credit” points you may have earned on the first attempt. When turning in a redo you must include (i) the original assignment, (b) the original grade sheet, and (c) the redo of the assignment.
The grade sheet is usually passed back with the original graded assignment to aid in interpretation of your score and to further improve your learning. In cases where a homework assignment is turned in with minimal effort, the grader may choose to hold back the grade sheet until a homework reflecting more substantial effort is submitted.
Please address any grading disputes with the grader first, and if needed the professors.

Midterm and Final Exam

There will be one mid-term exam and one final exam for this course. While the final exam will be cumulative, it will emphasize the latter half of the course, with the midterm emphasizing the first half of the course. Both exams are take-home, open-book/notes exams and you will have a week to complete the exam. You may not collaborate with any person except the professors for the two sections (Dr.’s Ketchum and Wan) when working on the exam. You may refer to your homework, notes, and textbooks, and ask the TAs about related questions, but they will not answer any content questions regarding the exam. There are not opportunities to redo either the midterm or the final exam.
If you have any grading disputes please bring them up with your grader; TAs grade the midterm and your Professors grade the final exam.

Team Based Learning Activities

There will be 5 Team Based Learning (TBL) activities. The purpose of TBL is to enrich the traditional lecture style content with applications and problem solving skills while allowing for you to develop interpersonal skills. In general you will be given something to read at least a week before the TBL class (e.g. a journal article) and then you will participate in the TBL activities during the class. During each TBL class you will start by taking an individual quiz over the reading material (usually 10-15 minute time limit depending on quiz), then group-up with your assigned teams to repeat the same quiz as a unit. At this point you will have the opportunity to hear how other students in your team think about the question as well as express your own opinion. Each team must come to an agreement, however, and assign a “speaker” to defend your team’s response on each quiz item before turning the quiz in. The time limit for the team quiz is usually about 30 minutes. Finally, the teams will come together as a class and we will discuss the correct responses to the quiz items. Rather than have the professor tell you what the correct answers are, the teams will reveal their responses and their speakers will debate their answers until the class reaches agreement. At the end of each class, the grades from the quiz will be posted by team. For the individual quiz, the team score will reflect the average score by the members of the team on the individual quiz. For the team quiz, the grade will reflect the percentage correct by the team. For each student, the TBL grade for that class will be computed as a weighted average of their own individual score (20%) and their team score (80%). Students will be randomized to their teams at the beginning of the semester (after the drop date) and remain in the same team throughout the semester. Teams will consist of 4 to 5 members each. If you miss a TBL class, first you should apologize to your team members for not being there to contribute (they need you). After that, given you have a reasonable excuse for missing class, you may take the individual quiz at some point before the end of the semester. You should make arrangements with your professor to do so. This score will reflect 100% of your TBL score for that quiz; you will not benefit from the team’s score.

Final Grade

Each student’s final grade will be determined as a weighted average of their homework (65%), midterm (15%), final exam (15%), and TBL grade (5%); see the table below. Letter grades based on the overall score will be reported at the end of the semester

Extra Credit

At several points during the semester you will have the opportunity to earn extra credit points to increase your grade. Participation in these activities will never decrease your score. Opportunities for extra credit include the following: going above and beyond on homework or exam; doing an additional extra credit assignment the professor has designed; or finding a journal article with data (or using data from your own research), performing an analysis similar to what you have learned in class recently, and providing an IMRaD report. Do not ask for additional extra credit opportunities towards the end of the semester; it is your responsibility to keep up with the course material.

Seeking Help

There are 7 TAs and 2 professors for the two sections of the course on the MCV campus. Each TA will regularly provide 3 hours of assistance each week in One Capitol Square (7th Floor, Rooms 700B/C). In addition, both professors will provide 4 hours of assistance each week. Please see the schedule on the first page of the syllabus for the specific times. We strongly encourage that you utilize the assistance provided to you. We are here to help you understand, and ultimately master, the material. However, you must come prepared, having put forth effort beforehand and be ready to actively ask questions to move you in the right direction. While each of you is assigned to one grader and one professor, you are more than welcome to see any of the TAs or professors during their designated office hours.

SAS Assistance

Some of you may want or need to use SAS in the future and this class is a great opportunity to so. While the entire class will be taught using the JMP software, students needing to learn SAS are encouraged to use SAS to do data management and analysis. There is a SAS component that accompanies the course notes and we encourage you to use it to help you learn SAS. It is important that you go still through the process in JMP (it doesn’t take very long) and make sure you are getting the same results in SAS. The grading sheet is based on JMP output and you are responsible for any discrepancies between the results. While we don’t anticipate the results to differ depending on JMP or SAS, there are some instances where this may occur (e.g. you have not correctly installed the latest patches/hotfixes). The professors will not spend time in class instructing on SAS, but we are willing to answer questions you may have. There is one TA devoted to offering 3 hours of assistance to those students using SAS to work through the HW assignments. You may ask questions about the HW in addition to SAS, but it must be in the context of SAS and not JMP.

Participation in Class, Communication, and Boundaries

We strongly encourage that you always bring your laptop to class ready to perform analyses during class along with the professor. Evidence suggests that this type of active learning can increase your understanding and retention of the material. It is not OK to use your laptop to cruise on the internet, check Facebook, or read the news. If you are not listening to the lecture you are not learning, and you are wasting your time. Furthermore, this sort of activity distracts the people seated behind you (and the TAs can see you).
There are occasions where you may have questions and we strongly encourage you to raise your hand and ask them. Chances are someone else is wondering the same thing. It could also be the case that the professor was not clear in how they explained something. Bottom line: don’t be shy to ask questions at any time. If there is question that is better answered after class the professor will say so and move on. You may find that TAs to be less intimidating than the professors and they are there to answer questions before and after class as well as during office hours. Please take advantage of these opportunities as well. Feel free to email the professors at anytime, and you may email the TAs with short questions (e.g. may I speak with you for a few minutes after class about my HW grade?), but see them or the professors during the office hours for more detailed questions. Remember there are very few “simple questions” that allow for a “quick answer”. It is usually less time consuming and more helpful for you to ask concept and homework questions in person rather than through email.
We are all very busy, juggling many tasks at any given time. We recognize that this is just one of perhaps several classes and you may also have a job and/or a family. We respect this and try to give you the appropriate amount of work to, so that your learning is optimized and your time spent doing so is minimized. It may seem like a lot of work at first, but we promise you will get better and it will get easier the more you practice and the more you learn. On the same note, it is important for you to recognize that this course is just one of the many duties of the Professors and the TAs. Please respect our time and our space. We are here to help you, but boundaries are very important.

Email Policy

You are required to use and check your VCU email frequently. That is, you must use your EID@vcu.edu email address. Electronic mail or "email" is considered an official method for communication at VCU because it delivers information in a convenient, timely, cost effective, and environmentally aware manner. This policy ensures that all students have access to this important form of communication. It ensures students can be reached through a standardized channel by faculty and other staff of the University as needed. Mail sent to the VCU email address may include notification of University-related actions, including disciplinary action. Please read the policy in its entirety: http://www.ts.vcu.edu/kb/3407.html

VCU Honor System: Plagiarism and Academic Integrity

The VCU honor system policy describes the responsibilities of students, faculty, and administration in upholding academic integrity, while at the same time respecting the rights of individuals to the due process offered by administrative hearings and appeals. According to his policy, “members of the academic community are required to conduct themselves in accordance with the highest standards of academic honesty and integrity.” In addition, “All members of the VCU community are presumed to have an understanding of the VCU Honor System and are required to:

• Agree to be bound by the Honor System policy and its procedures;
• Report suspicion or knowledge of possible violations of the Honor System;
• Support an environment that reflects a commitment to academic integrity;
• Answer truthfully when called upon to do so regarding Honor System cases, and,
• Maintain confidentiality regarding specific information in Honor System cases.”

Most importantly, “All VCU students are presumed upon enrollment to have acquainted themselves with and have an understanding of the Honor System.” (The VCU INSIDER, VCU Honor System 131-132).
The Honor System in its entirety can be reviewed on the Web at http://www.provost.vcu.edu/pdfs/Honor_system_policy.pdf or it can be found in the 2011-12 VCU Insider at http://www.students.vcu.edu/insider.html.
In this class, because coursework will be collaborative at times, particular issues of integrity arise. You should not copy or print another student’s work without permission. Any material (this includes IDEAS and LANGUAGE) from another source must be credited, whether that material is quoted directly, summarized, or paraphrased. In other words, you should respect the work of others and in no way present it as your own.

Student Conduct in the Classroom

According to the VCU Resource Guide, “The instructional program at VCU is based upon the premise that students enrolled in a class are entitled to receive instruction free from interference by other students. Accordingly, in classrooms, laboratories, studies, and other learning areas, students are expected to conduct themselves in an orderly and cooperative manner so that the faculty member can proceed with their [sic] customary instruction. Faculty members (including graduate teaching assistants) may set reasonable standards for classroom behavior in order to serve these objectives. If a student believes that the behavior of another student is disruptive, the instructor should be informed.” Among other things, cell phones and beepers should be turned off while in the classroom. Also, the University Rules and Procedures prohibit anyone from having “…in his possession any firearm, other weapon, or explosive, regardless of whether a license to possess the same has been issued, without the written authorization of the President of the university..." See http://www.students.vcu.edu/docs/policy_student_conduct.pdf and the VCU Resource Guide for more information: http://www.students.vcu.edu/insider.html.
Certainly the expectation in this course is that students will attend class with punctuality, proper decorum, required course material, and studious involvement.
The VCU Resource Guide contains additional important information about a number of other policies with which students should be familiar, including Guidelines on Prohibition of Sexual Harassment, Grade Review Procedure, and Ethics Policy on Computing. It also contains maps, phone numbers, and information about resources available to VCU students. The VCU Resource Guide is available online at the link above or through the Division of Student Affairs.

Students with Disabilities

SECTION 504 of the Rehabilitation Act of 1973 and the Americans with Disabilities Act of 1990 require that VCU provide an “academic adjustment” and/or a “reasonable accommodation” to any individual who advises us of a physical and/or mental disability. To receive accommodations, students must declare their need for disability-related accommodations with the Disability Support Services Office (DSS). The DSS office is located in the Student Commons, Room 102. The office phone number is 828-2253. The Director of Disability Support Services is Joyce Knight. More information is available at the Disability Support Services webpage: http://www.students.vcu.edu/dss/.
If you have a physical or mental impairment that requires an academic adjustment or accommodation, arrange a meeting with your Professor within the first 10 days of class. Additionally, if your coursework requires you to work in a lab environment, you should advise your Professor or department chairperson of any concerns you may have regarding safety issues related to your limitation(s). This statement applies not only to this course but also to every other course in this University.
Statement on Military Short-Term Training or Deployment
Military students may receive orders for short-term training or deployment. These students are asked to inform and present their orders to their professor(s). For further information on policies and procedures contact Military Services at 828-5993 or access the corresponding policies at http://www.pubapps.vcu.edu/bulletins/about/?Default.aspx?uid=10096&iid=30704 and http://www.pubapps.vcu.edu/BULLETINS/undergraduate/?uid=10096&iid=30773.
Excused Absences for Students Representing the University
Since most of you are graduate students, you may be called away to present your work at a conference. If so, you will know these dates in advance and you must notify the professor well ahead of time so that we can agree on how you will be able to make up your work or exam.
We are aware that students who represent the university (athletes and others) do not choose their schedules. Student athletes are required to attend games and/or meets. All student athletes will give their professor their schedule in the beginning of the semester. The Intercollegiate Athletic Council (IAC) strongly encourages professors to treat missed classes or exams (because of a scheduling conflict) as excused absences and urges us to work with the students to make up the work or exam.
Campus Emergency information

• What to know and do to be prepared for emergencies at VCU: Sign up to receive VCU text messaging alerts (http://www.vcu.edu/alert/notify). Keep your information up-to-date. Within the classroom, the professor will keep her phone on to receive any emergency transmissions.
• Know the safe evacuation route from each of your classrooms. Emergency evacuation routes are posted in on-campus classrooms.
• Listen for and follow instructions from VCU or other designated authorities. Within the classroom, follow your professor’s instructions.
• Know where to go for additional emergency information (http://www.vcu.edu/alert).
• Know the emergency phone number for the VCU Police (828-1234). Report suspicious activities and objects.

Important Dates

Important dates for the Spring 2012 semester are available at: http://academiccalendars.vcu.edu/ac_fullViewAll.asp?term=Spring+2012.

VCU Mobile

The VCU Mobile application is a valuable tool to get the latest VCU information on the go. The application contains helpful information including the VCU directory, events, course schedules, campus maps, athletics and general VCU news, emergency information, library resources, Blackboard and more. To download the application on your smart phone or for more information, please visit http://m.vcu.edu/.
Class registration required for attendance
Please remember that students may only attend those classes for which they have registered. Faculty may not add students to class rosters. Therefore, if students are attending a class for which they have not registered, they must stop attending.

Concluding Remarks

This will be a long semester and you will work hard. You will get out of this class what you put into it. The tools you will take from this course will empower you to design your own studies, perform many of your own complex data analyses, interpret and communicate the results from your analyses, be critical of the literature, and be more marketable. In the end, you will learn a lot and I believe you will have fun doing it.