UNIVERSITY OF MASSACHUSETTS Department Of Biostatistics .
BIOSTATS 640 Intermediate BiostatisticsSpring 2021Syllabus REVISED v2 3-22-21UNIVERSITY OF MASSACHUSETTSDepartment of Biostatistics and EpidemiologyBIOSTATS 640 - Intermediate BiostatisticsSpring 2021Title:Course website:Number of credits:Instructor:BIOSTATS 640 – Intermediate Biostatisticshttp://people.umass.edu/ biep640w3Carol Bigelow, PhDDepartment of Biostatistics & EpidemiologyEmail: cbigelow@schoolph.umass.eduTeaching Assistant: Derrick Liu, Graduate Student - BiostatisticsEmail: derrickliu@umass.eduAt a GlanceAttendance is encouraged but NOT mandatoryMondays (beginning 2/8/2021) Office Hour (Host: Derrick Liu)4:30 – 5:30 pm Learning RWednesdays (beginning 2/3/2021) Lecture Presentation4:00 – 5:30 pm (recorded)Wellness Wednesdays: No lecture on Wed 2/24 or Wed 4/14Makeups:Lectures will be made up on Mon 2/22 and Mon 4/12Fridays (beginning 2/5/20201) Discussion and Group Work4:00 – 5:00 pm Unit content, homework, exam hintsCourse Description .ADA Accommodation Policy .Covid-19 Impact on this Course .Policies on Classes and Work Missed for Extenuating Circumstances .Getting Started with Remote Learning . . Course Units, Objectives and Outcome Competencies .Textbook, R, and Other Resources . . .Important Dates to Remember . .Course Schedule (Units, Homeworks, Exams) . . .Course Expectations (Instructor, Teaching Assistant, and Students) . . Grade Determination . . .Policy on Late Submissions .Policy on Academic Dishonesty . .Valuing, Recognizing, and Encouraging Diversity .Names and Pronouns . Title IX Statement . .Copyright Protection . .Syllabus 640 2021 Bigelow revised March 22.docx22233356799101011111112Page 1 of 12
BIOSTATS 640 Intermediate BiostatisticsSpring 2021Syllabus REVISED v2 3-22-21Course DescriptionContent. BIOSTATS 640 is the second of a two-semester sequence of introductory biostatistics. Similar toBIOSTATS 540, the overall goal is statistical literacy and skills in selected, basic, analyses of biological and healthdata. Topics include: review of introductory biostatistics, selected discrete distributions, introduction tononparametric tests, analysis of epidemiological tables, single and multiple predictor normal theory regression,logistic regression and introduction to survival analysis. If time allows (this has not happened in recent years) Iwill also provide an introduction to mixed models. Software. We will be using R in illustrations of data analysis.However, no prior experience with R is required and you will not be required to use R on any examination. If youare already a SAS or Stata (or other software) user, you are welcome to use that instead.ADA Accommodation PolicyThe University of Massachusetts Amherst is committed to making reasonable, effective and appropriateaccommodations to meet the needs of students with disabilities and help create a barrier-free campus. If you have adisability and require accommodations, please register with Disability Services (161 Whitmore Administrationbuilding; phone 413-545-0892) to have an accommodation letter sent to me. Information on services and materialsfor registering are also available on their website, here: www.umass.edu/disability.If, because of a disability, you may require special arrangements in order to meet course requirements, pleasecontact me as soon as possible (email: cbigelow@schoolph.umass.edu) so that we can develop an accommodationplan that will work for you.COVID-19 Impact on this CourseIn light of the ongoing COVID-19 pandemic and the challenges it presents, here are some key things to knowabout BIOSTATS 640. This is a remote only course. You must complete a “one-time” registration to access Zoom. Our Zoom meetings will bescheduled as recurring meetings that require a one-time registration. Attendance is not required but, of course, is strongly encouraged! Recordings of the Wednesday lecture presentations and Friday group work will be provided The Monday office hours will not be recorded I will be using your UMass email address only. All announcements and correspondence with theentire class will be sent to you to your UMass email address only. Please be aware that I will not bekeeping track of any other email addresses (e.g – “gmail”) you might have.Syllabus 640 2021 Bigelow revised March 22.docxPage 2 of 12
BIOSTATS 640 Intermediate BiostatisticsSpring 2021Syllabus REVISED v2 3-22-21Policies on Classes and Work Missed for Extenuating Circumstances.Per University of Massachusetts Academic Regulations, “Students absent due to extenuating circumstancesincluding jury duty, military obligations, scheduled activities for other classes, the death of a family member, orverifiable health-related incapacity-remain responsible for meeting all class requirements and contacting thefaculty member in a timely fashion about making up missed work. Faculty shall offer such students reasonableassistance in making up missed classes (i.e., making arrangements for attendance at labs or discussion sectionswhich meet at other times; providing makeup exams or labs where feasible or offer mutually agreeable alternativesto make up work).”If any extenuating circumstances prevent you from completing any work on time, please contact me as soon aspossible (email: cbigelow@schoolph.umass.edu) so that we can make alternative arrangements.Getting Started with Remote LearningPlease be sure to familiarize yourself with the following resources and technologies before the first week of class(February 3-5, 2021).1. Public Course Website: https://people.umass.edu/ biep640w/2. UMass Amherst Blackboard Learn: e for Learning Blackboard Learn:(source: Rowan University, Campbell Library) Blackboard Tutorials for Students3. UMass Amherst Zoom Login: https://www.umass.edu/it/zoomResource for Learning Zoom:(source: https://support.zoom.us) Zoom Video TutorialsTip: Be sure to watch these two tutorials, here: “Join a Meeting” and “Meeting Controls”Course Units, Objectives, and Outcome CompetenciesCourse Units. This course has 8 units (plus a 9th unit, time permitting)1. Review of BIOSTATS 540, Introductory Biostatistics2. Discrete Distributions3. Introduction to Nonparametrics4. Categorical Data Analysis5. Normal Theory Regression6. Analysis of Variance7. Logistic Regression8. Introduction to Survival Analysis9. (time permitting) Introduction to Mixed ModelsObjectives.By the end of this course, you should be able to perform, interpret, and report the findings of selected simplestatistical analyses: description, hypothesis testing (including nonparametric tests), epidemiologic tables, simpleand multiple predictor normal theory regression, analysis of variance, logistic regression, and some simple survivalanalysis techniques.Syllabus 640 2021 Bigelow revised March 22.docxPage 3 of 12
BIOSTATS 640 Intermediate BiostatisticsSpring 2021Syllabus REVISED v2 3-22-21Outcome Competencies.The specific outcome competencies include, but are not limited to, the following:1. Explain the conceptual framework of selected, basic methods, of biostatistical analysis. This is“statistical literacy”. You will be introduced to the underlying principles, rationale, and relevance. Forexample, you will learn that a fitted model is likely to be wrong, but nevertheless useful. It might yieldimportant insights into the nature and strength of associations that might exist.2. Develop a conceptual framework that integrates techniques and methods in biostatistics. You will learnthat the principles of biostatistics (and epidemiology, too) are grounded in scientific reasoning (and the goalof causal inference). You will also learn that the ideas of estimation and statistical hypothesis testing arerelated to the notion of “signal” and “noise”.3. Integrating analysis strategies in biostatistics with principles and issues in epidemiology. Thepresentation of the topics in this course will highlight their relevance to key issues in epidemiology,including: confounding, effect modification, discovery of intermediary pathways, and reduction of bias.4. Apply biostatistical methods to the design of studies in public health. We will integrate the principles ofstatistical literacy with those of epidemiological research to gain practice in developing data analysis plans.And we will see that these vary, depending on the data type and the questions of interest.5. Use computers to appropriately store, manage, manipulate and process data for a research study usingmodern software. This course includes an introduction to the use of R.6. Apply descriptive techniques commonly used to summarize public health data. I will emphasize theimportance of graphical summaries and the use of R.7. Describe the basic concepts of probability, random variation and selected, commonly used, probabilitydistributions – You will learn additional concepts of sampling distributions and additional applications ofthe central limit theorem. Specifically, you will learn how these ideas are the foundation of modeling,estimation, and hypothesis testing.8. Select and perform the appropriate descriptive and inferential statistical methods in selected basic studydesign settings. I will provide data sets for you to explore and will encourage you to give them a try!Specifically, I will encourage you to try your hand at developing your own analysis plan, doing theprogramming necessary for analysis, interpreting your results (especially with respect to the analysis goalsand associated issues of confounding, bias, effect modification, and precision) and generating a report ofyour findings.9. Interpret results and critically evaluate basic statistical aspects of public health research and practicereported in the literature. You will gain practice in being a statistically literate consumer of publishedexamples of data analyses.10. Effective communication. The utility of biostatistics rests, ultimately, in its effective communication!In the weekly homework assignments and in the exams, you will gain practice in the communication ofbiostatistics work to the lay reader. Specifically, you will learn how to write the following types ofdescriptions: analysis question, rationale, method used, statistical findings, and subject matter relevance.Syllabus 640 2021 Bigelow revised March 22.docxPage 4 of 12
BIOSTATS 640 Intermediate BiostatisticsSpring 2021Syllabus REVISED v2 3-22-21Textbook, R, and Other ResourcesThere is no required text. Here are some useful resources:(1) Course contentWhitlock MC and Schluter DThe Analysis of Biological Data, Third EditionMacmillan Learning2020ISBN: 978 1319 226 237(2) Course contentGelman A and Hill JData Analysis Using Regression and Multilevel/Hierarchical ModelsCambridge2007ISBN: 978 0 521 68689 1(3) BIOSTATS 540 – Introductory Biostatisticshttp://people.umass.edu/ biep540w/(4) R for Beginners - BookLi, QuanOxford University Press, 2018ISBN: 978-0-1906-5622-5Using R for Data Analysis in Social 5) Quick-R for Beginners – Online TutorialsSource: DataCamphttps://www.statmethods.net/index.html(6) How to Download and Install R and R StudioWindows Users (pdf, 4 pp)MAC Users (pdf, 4 pp)You will not be tested on R or any other statistical software; andUse of R or any other statistical software will not be necessary in any exam.Syllabus 640 2021 Bigelow revised March 22.docxPage 5 of 12
BIOSTATS 640 Intermediate BiostatisticsSpring 2021Syllabus REVISED v2 3-22-21Important Dates to RememberFirst Week of ClassFebruary 3-5, 2021Last Day to Drop with NO RecordFriday February 12, 2021President’s DayOur Monday office hour WILL BE HELDMonday February 15, 2021Wellness WednesdayNo class – This lecture will be made up on MondayFebruary 22Wednesday February 24, 2021Last Day to Drop with “DR”Monday March 29, 2021Wellness WednesdayNo class – This lecture will be made up on MondayApril 12Wednesday April 14, 2021President’s DayOur Monday office hour WILL BE HELDMonday April 19, 2021Last MeetingMonday May 3, 2021Final Exam (Test #3) DUEFriday May 7, 2021Last date for submissions for credit.Monday May 10, 2021Syllabus 640 2021 Bigelow revised March 22.docxPage 6 of 12
BIOSTATS 640 Intermediate BiostatisticsSpring 2021Syllabus REVISED v2 3-22-21Course Schedule (Units, Homeworks, Exams)Units (Please note: I do not post lecture notes or exams ahead of schedule. Sorry.)WeekDatesSchedule1February 1-5, 2021Unit 1: Review of BIOSTATS 540Mon: no meeting Wed: Lecture (4:00 – 5:30)2February 8-12, 2021Fri: Group work (4:00 – 5:00)Unit 2: Discrete DistributionsMon: R (4:30 – 5:30) Wed: Lecture (4:00 – 5:30) Fri: Group work (4:00 – 5:00)3February 15-19, 2021Unit 3: Introduction to NonparametricsMon: R (4:30 – 5:30) Wed: Lecture (4:00 – 5:30) Fri: Group work (4:00 – 5:00)4February 22-26, 2021Unit 4: Categorical Data Analysis, 1 of 2Mon: Lecture (4:30 – 5:30) Wed: DAY OFF Fri: Group work & R (4:00 – 5:00)5March 1-5, 2021Unit 4: Categorical Data Analysis, 2 of 2Mon: R (4:30 – 5:30) Wed: Lecture (4:00 – 5:30) Fri: Group work (4:00 – 5:00)6March 8-12, 2021Unit 5: Normal Theory Regression, 1 of 3Mon: R (4:30 – 5:30) Wed: Lecture (4:00 – 5:30) Fri: Group work (4:00 – 5:00)7March 15-19, 2021Unit 5: Normal Theory Regression, 2 of 3Mon: R (4:30 – 5:30) Wed: Lecture (4:00 – 5:30) Fri: Group work (4:00 – 5:00)8RevisedMarch 22-26, 2021RevisedUnit 5: Normal Theory Regression, 3 of 3Mon: R (4:30 – 5:30) Wed: Lecture (4:00 – 5:30) Fri: Group work (4:00 – 5:00)9RevisedMarch 29 – April 2, 2021RevisedUnit 6: Analysis of Variance, 1 of 2Mon: R (4:30 – 5:30) Wed: Lecture (4:00 – 5:30) Fri: Group work (4:00 – 5:00)10RevisedApril 5-9, 2021RevisedUnit 6: Analysis of Variance, 2 of 2Mon: R (4:30 – 5:30) Wed: Lecture (4:00 – 5:30) Fri: Group work (4:00 – 5:00)11RevisedApril 12-16, 2021RevisedUnit 7: Logistic Regression, 1 of 2Mon: Lecture (4:30 – 5:30) Wed: DAY OFF Fri: Group work & R (4:00 – 5:00)12RevisedApril 19-23, 2021RevisedUnit 7: Logistic Regression, 2 of 2Mon: R (4:30 – 5:30) Wed: Lecture (4:30 – 5:30) Fri: Group work (4:00 – 5:00)13RevisedApril 26-30, 2021RevisedUnit 8: Introduction to Survival AnalysisMon: R (4:30 – 5:30) Wed: Lecture (4:00 – 5:30) Fri: Group work (4:00 – 5:00)14RevisedMay 3-4, 2021Syllabus 640 2021 Bigelow revised March 22.docxMonday: Last meetingWrap up (Final exam prep, Other content questions, R help (4:30 – 5:30)Page 7 of 12
BIOSTATS 640 Intermediate BiostatisticsSpring 2021HomeworksHomeworkPostingDueTopics CoveredWednesday February 3, 2021Friday February 12, 20211 – Review of BIOSTATS 5401Syllabus REVISED v2 3-22-21Last date for submission for creditwith (-20 points): Friday 2/19/212Wednesday February 10, 2021Friday February 19, 20212 – Discrete DistributionsLast date for submission for creditwith (-20 points): Friday 2/26/213Wednesday February 17, 2021Friday February 26, 2021Last date for submission for creditwith (-20 points): Friday 3/5/214Wednesday February 24, 2021Friday March 12, 20213 – Introduction toNonparametrics4 – Categorical Data AnalysisLast date for submission for creditwith (-20 points): Friday 3/19/215Wednesday March 10, 2021Friday March 26, 20215 – Normal Theory RegressionLast date for submission for creditwith (-20 points): Friday 4/2/216RevisedWednesday March 31, 2021RevisedFriday April 16, 20216 – Analysis of VarianceLast date for submission for creditwith (-20 points): Friday 4/23/217RevisedWednesday April 14, 2021RevisedFriday April 30, 20217 - Logistic RegressionLast date for submission for creditwith (-20 points): Friday 5/7/218Wednesday April 21, 2021Friday May 7, 2021Last date for submission for creditwith (-10 points): Monday 5/10/218 - Introduction to SurvivalAnalysisExamsAll exams are “open book”, “take home”. Use of R is NOT required in any exam.ExamPostingDueTopics Covered12Monday February 22, 2021New Posting DateMonday March 29, 20201Monday March 8, 2021Last date for submission for creditwith (-20 points): Monday 3/15/211 - Review of BIOSTATS 5402 - Discrete Distributions3 - Introduction to NonparametricsNew Due DateMonday April 12, 20214 - Categorical Data Analysis5 - Normal Theory RegressionLast date for submission for creditwith (-20 points): Monday 4/19/213Friday April 23, 2021Friday May 7, 2021Last date for submission for creditwith (-10 points): Monday 5/10/21Syllabus 640 2021 Bigelow revised March 22.docx6 - Analysis of Variance7 - Logistic Regression8 - Introduction to Survival AnalysisPage 8 of 12
BIOSTATS 640 Intermediate BiostatisticsSpring 2021Syllabus REVISED v2 3-22-21Course Expectations (Instructor, Teaching Assistant, and Students)Instructor We will respond to all emails and Blackboard messages every day, except for SaturdaysI will provide a regularly scheduled Zoom office hour, Mondays 4:30 – 5:30 pmI will also provide Zoom meeting office hours by appointment, as appropriateTeaching Assistant (TA) We will respond to Blackboard discussion thread questions every day, except for SaturdaysOur TA will record homework submissions within one week of their due dates.Our TA will respond to questions in homework submissions within one week of their due datesStudents Attendance at weekly Zoom classes is not requiredStudents will abide by the University of Massachusetts policy on academic dishonestyStudents will abide by the policy on late submissions (see below)To earn full credit on the homework, students must submit 8 homework assignmentsGrade Determination (Course Score Determination and Letter Grade Determination)Course Score determinationPercent of GradeHomeworksBIOSTATS 640 has 8 assignments, one per unit. Each will be graded pass/fail and the solutionsare provided (and you are welcome to consult the solutions as you go along!). Thus, thehomeworks are the participation portion of your grade.25%, sub-totalLate policy. If you submit your work on the due date or within 48 hours, your score will be100. Late homework submitted late, but no later than one week, will be given a score of 80.Homeworks submitted more than one week late will be given a score of 0.To earn full homework credit, you must complete eight (8) assignments.Exams (all open book)There are 3 tests, all open book. For each test, you are welcome to consult any resource youlike, but you are not allowed to consult any person except me.Late policy If you submit your exam on the due date, you will earn full credit for your work.Exams submitted late but within 48 hours will have 10 points deducted from their score. Examssubmitted late but between 48 hours and 1 week will have 20 points deducted from their score.Exams submitted more than one week late will be given a score of 0.Syllabus 640 2021 Bigelow revised March 22.docx75%, sub-totalas follows:Best test – 40%2nd best – 20%3rd best – 15%Page 9 of 12
BIOSTATS 640 Intermediate BiostatisticsSpring 2021Syllabus REVISED v2 3-22-21Letter grade determination. Your course score will be converted to a letter grade as follows:AAB BBC CF95 and over90 - 9487 - 8983 – 8680 - 8277 – 7970 – 76Below 70Policy on Late SubmissionsMy policy on late submissions aims to be fair while at the same time accommodating those who, for whateverreason, need an extension.On TimeUp to 48 hours late3-7 days late8 days lateCredit Policy - HomeworksGrading Policy - ExamsFull Credit for points ScoredFull Credit for points ScoredPoints Scored – 20 points0 points (no credit)Full Credit for points ScoredPoints Scored – 10 pointsPoints Scored – 20 points0 points (no credit)Policy on Academic DishonestySince the integrity of the academic enterprise of any institution of higher education requires ho
BIOSTATS 640 Intermediate Biostatistics Spring 2021 Syllabus v1 1-18-21 Syllabus 640 2021 Bigelow.docx Page 2 of 12 Course Description Content. BIOSTATS 640 is the second of a two-semester sequence of introductory biostatistics.
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