1 School of Population Health POPLHLTH 304 Principles of applied epidemiology Semester 1, 2011 Course Coordinator: Simon Thornley Copyright Warning Notice This course book is protected by copyright and has been copied by and solely for the educational purposes of the University under licence. You may not sell, alter or further reproduce or distribute any part of this course book to any other person. Where provided to you in electronic format, you may only print from it for your own private study and research. Failure to comply with the terms of this warning may expose you to legal action for copyright infringement and/or disciplinary action by the University. 2 Contents Introduction ............................................................................................... 3 Course coordinator ............................................................................................. 3 Course description ..................................................................................... 4 Key course objectives.......................................................................................... 4 Structure of the course .............................................................................. 4 Lecture Schedule ............................................................................................... 6 Tutorial Schedule ............................................................................................... 8 Course Assessment ............................................................................................ 8 Attendance......................................................................................................... 8 Examination ....................................................................................................... 8 Assignments .............................................................................................. 9 Assignment 1 ..................................................................................................... 9 Assignment 2 ..................................................................................................... 9 Assignment 3 ..................................................................................................... 9 Submission of assignments ................................................................................ 9 Late Assignment .............................................................................................. 10 Presentation of assignments ............................................................................ 10 References ....................................................................................................... 10 Guidelines on confidentiality of student material (optional) ............................ 10 Assignment marking ........................................................................................ 11 Reading or Recommended Textbook(s) ................................................... 11 Prescribed texts................................................................................................ 11 Other useful reference texts ............................................................................... 11 Grading .................................................................................................... 12 Moderation of Final Marks .................................................................................. 13 Academic honesty and Turnitin ................................................................ 13 Plagiarism........................................................................................................ 13 Additional information ............................................................................. 14 Study guide ..................................................................................................... 14 Study groups (optional) ..................................................................................... 14 Study problems ................................................................................................ 14 Course evaluation ............................................................................................. 14 Appendix 1: Survival skills ....................................................................... 14 CECIL (http://cecil.auckland.ac.nz ) ................................................................ 14 EC Mail (http://webmail.ec.auckland.ac.nz ) ................................................... 15 Redirect/forward EC Mail ................................................................................... 15 Appendix 2: Useful web URLs ............................................................. 16 Appendix 3: Turnitin ................................................................................ 17 3 Introduction Kia ora and welcome to POPLHLTH 304, Principles of Applied Epidemiology. The course will introduce students to the practical skills required to design, analyse, publish and interpret epidemiological studies. Course coordinator 4 Simon Thornley Lecturer Section of Epidemiology and Biostatistics School of Population Health University of Auckland Private Bag 92019 Auckland Tel: (09) 373 7599 ext 81971 Mobile: 021 2991752 Email: s.thornley@auckland.ac.nz Course description The course focuses on the principles of epidemiology with particular reference to New Zealand. We will explore the different study designs used by epidemiologists to assess the effects of different exposures, and under what circumstances such studies are best used. You will also gain ‘hands on’ experience with the analysis of data from real studies, and presenting the findings for publication. Key course objectives By the end of the course, each participant will be expected to: Become familiar with the main epidemiological study designs, their applications, strength and weaknesses. Be familiar with the methods of calculating main study effect measures and confidence intervals. Gain skills using Epi Info, a public-domain software package, which allows users to develop a questionnaire or form, customize the data entry process, and analyze data. Gain insight into how epidemiological studies have changed the course of medical and public health practice. At the end of the course the student should have an appreciation of: The uses of epidemiological research. The limits of epidemiological methods. Practical steps involved in developing epidemiological studies. Structure of the course The course will consist of approximately 36 contact hours comprising the following teaching modes: One hour lectures Tutorials of one hour duration. Presentations by guest speakers, experts in their field. 5 Lecture Tutorial Wednesday Thursday Wednesday Thursday 10:30-11:30 1:30-2:30 12:30-1:30 2:30 – 3:30 721-201 721-201 730-268 730-268 You only have to attend one tutorial per week as the content will be the same in each. Locations for the lectures and tutorials are available in your class timetable when you log in to Student Services Online. Students are expected to access their course information on Cecil and receive all information on their University email. See Appendix 2 Survival Skills on page 16 for important information on your email. 6 Lecture Schedule Week Date Lecture Topic 1 Course introduction, Epidemiology and Epi info 3 Mar 2 Epidemiological measures and attributable risk; discuss first assignment 9 Mar 3 2 Mar 1 2 10 Mar 4 16 Mar 5 17 Mar 6 3 23 Mar 7 Overview of Epidemiological study design Sharpening your tools – measurement in epidemiology and an introduction to causation Case-control studies (ST) Random error, confidence intervals and power (ST) Bias, Confounding and Effect modification (ST) 4 5 24 Mar 8 30 Mar 9 31 Mar 10 6 Apr 9 7 Apr 10 Epidemiology and progress: The NZ cot death study (RS) Cohort studies (ST) Cohort studies: an example Cohort studies (ST) Cohort studies: an example Readings Chapter 1, Getting started: The anatomy and physiology of Clinical Research Selected excerpts from Freedman “Wrong: Why experts keep failing us and how to know when not to trust them”. Little, Brown and Company, 2010. Epidemiology for the uninitiated; Chapter 2. Available on the web here: http://resources.bmj.com/bmj/readers/r eaders/epidemiology-for-theuninitiated/2-quantifying-disease-inpopulations Hulley, Chapters 7 to 10. Hulley, Chapter 9. Epidemiology for the uninitiated; Chapter 4. http://resources.bmj.com/bmj/readers/r eaders/epidemiology-for-theuninitiated/4-measurement-error-andbias Hulley, Chapter 8. Hulley, Chapters 5 and 6 Hulley, Chapter 9. Epidemiology for the uninitiated; Chapter 8. http://resources.bmj.com/bmj/readers/r eaders/epidemiology-for-theuninitiated/8-case-control-and-crosssectional-studies Scragg R, Stewart AW, Mitchell EA, et al. Public health policy in bed sharing and smoking in the sudden infant death syndrome. NZMJ 1995; 108: 218-22. Hulley, Chapter 7 To be confirmed Hulley, Chapter 7 To be confirmed Semester Break 7 Week Date Lecture 27 April 11 28-Apr 12 6 4 May 13 7 Topic Multivariate analysis (RM) Publication: presenting your results (ST) Epidemiology and Progress: The adverse reactions story (ST) 5 May 14 Epidemiology and Progress: Vitamin D (RS) 11 May 15 Cross-sectional studies (ST) 8 12 May 16 18 May 17 19 May 18 9 25 May Randomised controlled trials (NEWS) (ST) Health data sources and epidemiological studies (ST) Epidemiological research and Maori 1 Jun To be advised Pearce, N. Adverse Reactions: the fenoterol story. 2007. Auckland University Press. Scragg, Robert. Vitamin D Deficiency: A New Risk Factor for Cardiovascular Disease? Australasian Epidemiologist, Vol. 16, No. 1, Apr 2009: 30-34. Hulley, Chapter 8. Thornley S, McRobbie H, Lin RB, Bullen C, Hajek P, Laugesen M, Senior H, Whittaker R. A single blind, randomized, crossover trial of the effects of a nicotine pouch on the relief of tobacco withdrawal symptoms and user satisfaction. Nicotine and Tobacco Research. 2009: ntp054 Hulley, Chapter 13 To be confirmed Woodward A, McMichael AJ. Passive smoking and cancer risk: the nature and uses of epidemiological evidence. European Journal of Cancer and Clinical Oncology 1991;27(11):1472-1479. Chapter 10, Who sank the boat? Association and Causation pp 215 to 248 Mente A, de Koning L, Shannon HS, Anand SS. A Systematic Review of the Evidence Supporting a Causal Link Between Dietary Factors and Coronary Heart Disease. Arch Intern Med 2009;169(7):659-669. 19 20 Causation: Bradford Hill, Rothman and Bayesian views. 21 Ethical considerations, project management and grant applications (ST) Hulley, Chapters 13,14,15, 17. 22 Epidemiology and progress: recalibrating CVD risk assessment (RJ) Jackson R, Lawes CMM, Bennett DA, Milne RJ, Rodgers A. Treatment with drugs to lower blood pressure and blood cholesterol based on an individual's absolute cardiovascular risk. The Lancet 2005;365(9457):434-441 11 2 Jun Slides and handouts to be provided Epidemiology and progress: the passive smoking story 10 26 May Readings 8 Tutorial Schedule Week Date Topic 1 2/3 Mar Introduction; discussion of first assignment. 2 8/9 Mar Questionnaire Design 3 15/16 Mar Cot death study: introduction 4 22/23 Mar Cot death study: basic effect measures 5 30/31 Mar Cot Death study: confounding and interaction (1) 6 27/28 Apr Cot death study: confounding and interaction (2) 7 4/5 May Cot death study: multivariate analysis (1) 8 11/12 May Cot death study: multivariate analysis (2) 9 13/14 May Sample size calculation 10 25/26 May Revision 11 1/2 Jun Semester Break Review for exam Course Assessment The assessment of this course is 50% on-course, and 50% final examination. The assessment consists of: Three Assignments: worth 10%, 10% and 30% Final examination: 50%. There is a choice of questions to answer during a two hour period. Books are not permitted in the exam, although scientific calculators are required. Date to be announced. Attendance A fundamental principle of the course is the assimilation of knowledge and the acquiring of new skills within a cooperative, collegial learning environment. It is therefore expected that students will attend all the sessions. Examination The final two-hour examination is worth 50% of the final mark for the module. This will be similar to the papers available in the library, will comprise 10 multiple choice questions and 4 (out of a possible 5) short answer questions, will be two hours long and will focus on both the principles of epidemiology, as well as some of the applications covered in this course only. Examination papers are peer reviewed and a sample of examination questions and/or assignments double-marked by an external assessor. The role of the external assessor is to ensure that questions/assignments are appropriate and marks given reflect the standards expected. 9 The 2011 semester one examination period is Thursday June 9 – Monday June 27. Note that the examination timetables are not finalised and available to students until 6-8 weeks into the semester. Assignments There will be three assignments for this paper: Assignment 1 (10% of the final mark) Due by 5pm Monday 21 March 2011 Assignment 2 (10% of the final mark) Due by 5pm Monday 4 April 2011 Assignment 3 (30% of the final mark) Due by 5pm Monday 16 May 2011 Assignment 1 You will be provided with a reading from this book (1), which describes the main reasons why scientific studies fail to come up with the correct answers. In less than one thousand words, briefly summarise the main reasons that Freedman cites that result in scientists drawing the wrong conclusions. This assignment is due by 5pm Monday 21 March 2011 (10 marks). The word limit is 1000 words (excluding references). Assignment 2 You will be given a worksheet along with a dataset, and be asked to work out some basic effect measures. This assignment is due by 5pm Monday 4 April 2011 (10 marks). Short answers, along with working is all that is required. Assignment 3 You will be given a case control study, in which researchers were investigating potential risk factors for coronary artery disease. You will be asked to present the findings of the study as you would in a brief scientific publication, including background, aims, method, results and discussion. This assignment is due by Monday 16 May 2011 (30 marks). The word limit is 2500 words (excluding references and tables). Submission of assignments A hard copy of each of your assignments is required for marking purposes. You are also required to submit an electronic copy of your report to www.turnitin.com (see appendix 3). DO NOT email assignments directly to the course co-ordinator or tutor unless by prior approval. The School Policy on submission of assignments is as follows: 1. Due dates for assignments must be strictly observed. 10 2. Extensions will only be given in very exceptional and unavoidable circumstances, and if approved by the Course Coordinator prior to the assignment due date. 3. No assignments will be accepted after 2 weeks. Late Assignment The School policy in relation to late assignments will be applied. Extensions will be considered only in exceptional circumstances and where the request is made within a reasonable timeframe prior to the assignment due date. Assignments received more than 2 weeks after the due date will not be marked and will be graded 0. Problems Illness or Circumstances Minor – documentation Moderate - evidence Severe – lots of evidence and get assessed Extension Up to 1 week* Up to 2 weeks Help as much as possible Late (Do not have a valid reason) Turnitin 5% a day (working days) 2 weeks limit *5 working days as a week The extension application should be in 24 hours before the due date. One or another (hard copy and Turnitin) is late, punishment applies. Presentation of assignments You must type/word-process your assignments Please use two sides of the page to preserve paper Please use double spacing (to allow for marker’s comments) Please use size 12 font Ensure all pages are numbered If your graphs and/or diagrams need to be in colour to be interpreted, please ensure you print them in colour Please leave an good sized margin down the side for the marker's comments Please number the pages and include your ID on each page (header or footer) – do not put your name on the body of your assignment Please work within the word limit (you will be penalised for being significantly under or over) Please use the cover sheet downloadable from Cecil, and the declaration form. References Either the APA system (author, date) or the Vancouver system (numbers) may be used for citing references. Please refer the library website for further details on referencing systems: http://www.library.auckland.ac.nz/subjects/med/referencing-fmhs.htm Either end notes or footnotes may be used, but stay with one system on a particular assignment. Guidelines on confidentiality of student material (optional) Some student assignments may draw on or cite confidential material. The University has prepared general guidelines for the use of information contained in student assignments and thesis material. 11 The following guidelines apply to student assignments: 1. In general, student assignments are not subject to the provisions of the Official Information Act. 2. Students and staff should however be conscious of the provisions of the Act, particularly if discussing documents in class. 3. Where a document is discussed in class, then any person named in that document could claim access to the document under the personal information provisions of the Act. 4. This places an obligation on staff and students particularly regarding the use of personal information, but may also extend to other information subject to confidentiality requirements. 5. Students should not use confidential information without permission of their employer and/or the person(s) to whom the information belongs or refers. 6. Staff should not allow the discussion of confidential information in class or tutorials. Assignment marking The assignment marking guide is shown below. Students should complete all coursework and the examination, and obtain a minimum overall mark of 50% in order to obtain a pass. Reading or Recommended Textbook(s) A list of recommended readings is given for each session. Students will be expected to have read these prior to the sessions, and to be prepared to discuss the issues and questions arising from them. This is intended to help students expand their reading on each topic, and is also designed to assist with assignment work. Students are, however, encouraged to read much more widely. In preparing assignments, students will be expected to have gone well beyond the references listed. Given the rapidly changing nature of each topic, it is certain that significant readings will become available after the preparation of this course manual. Where these become part of the recommended reading, students will be advised. Prescribed texts Hulley SB, Cummings SR, Browner WS, Grady DG, Newman TB. Designing Clinical Research, 3rd edition. Wolters Kluwer, 2007. This is a very practical, hands on, guide to epidemiological research. Although it is targeted at clinicians, I think it is the best introductory epidemiology text I can find. Recommended Books Kleinbaum, DG, Sullivan K, Barker N. A Pocket Guide to Epidemiology. New York: Springer: 2007 (available from the university library website, for free, here: http://www.springerlink.com.ezproxy.auckland.ac.nz/content/j01w4x/ Coggon D, Rose G, Barker DJP. Epidemiology for the Uninitiated. London: BMJ Publishing Group: 2003. Available free at: http://www.bmj.com/collections/epidem/ Other useful reference texts Other Resources For those interested in delving into the statistical background of the some of the methods taught, then I recommend: Kirkwood BR, Sterne JAC. Essential Medical Statistics. Oxford: Blackwell Science Ltd: 2003. 12 Neil Pearce is a remarkable New Zealand Epidemiologist who has published a free text online: Pearce N. A Short Introduction to Epidemiology. 2nd ed. Wellington. Massey University: 2005. Available free at: http://www.massey.ac.nz/~wwwcphr/publications/introepi.pdf I also recommend his book about the fenoterol controversy in New Zealand in the early 80s, in which epidemiological evidence provided the basis for banning a drug that was killing people with asthma. We will discuss the study during the course. Pearce N. Adverse Reactions: the fenoterol story. Auckland: Auckland University Press: 2007. Useful websites (list websites important for this course) If you are running either a Windows or Linux operating system, then you may download and install Epiinfo for free on your home computer. Sorry Mac users, you will need a windows emulator or virtual environment, with windows, to run epiinfo. See the following website for details: http://wwwn.cdc.gov/epiinfo/ Most of the study materials, along with lecture notes will be available on Course builder or Cecil. I have put the material on Course builder here: http://flexiblelearning.auckland.ac.nz/poplhlth304/ Grading Grading System and descriptors relating to student attainment GRADE % VALUE DESCRIPTION A+ 90 – 100 A 85 – 89 A- 80 – 84 Work is of high to exceptionally high quality showing excellent knowledge and understanding of subject matter and appreciation of issues. Arguments are well formulated and based on strong and sustained evidence. Maps and diagrams, graphs and tables, etc included where appropriate. Relevant literature is referenced. There is a high level of creative ability, originality, and critical thinking. Excellent communication and presentation skills are evident. B+ 75 – 79 B 70 – 74 B- 65 – 69 C+ 60 – 64 Work shows a good to strong grasp of subject matter and understanding of major issues, though not necessarily of the finer points. Arguments are clearly developed and based on convincing evidence. Relevant literature is referenced. There is evidence of creative ability, originality, and critical thinking. Good communication and presentation skills are evident. Work shows some knowledge of subject matter and appreciation of main issues, though possibly with some lapses and inadequacies. 13 C 55 – 59 C- 50 – 54 D+ 45 – 49 D 40 – 44 D- 0 – 39 Arguments are developed and supported by some evidence and references. Creative ability, originality, and critical thinking is present, but limited. Adequate communication and presentation skills are evident. Work lacks breadth and depth. Work generally has gaps. Frequently work of this grade takes a simple factual approach and understanding, and coverage of material is inadequate. Does not attempt to interpret the material. At the lower end, indicates a need for considerable effort to achieve improvement. Communication and presentation skills are poor. Highly unsatisfactory. Work shows a lack of knowledge about, and understanding of, the topic. Inadequate in degree of relevance, completeness, or both. Communication and presentation skills are weak. Moderation of Final Marks Most courses run by the University use the University Grading Scale as an indicative scale for students. All courses are examined and assessed to ensure that all results are accurate and fair, not just for the course but across the entire programme in the current and previous years. Therefore the Examiners and Assessors are able to moderate the grading scale to ensure that the final results are fair and consistent. This is does mean that sometimes that the grading scale is adjusted, as is allowed by the University Regulations. Therefore, although the grading scale may appear to be definitive in its grade boundaries, these boundaries are indicative only. Scaling/moderation can occur at the end of the semester on all or only some parts of the course assessments. Academic honesty and Turnitin You are also required to submit an electronic copy of your report to www.turnitin.com for assessment of originality and to discourage plagiarism. These are to be submitted by the same assignments’ due dates as above. The Turnitin Class ID is: 3552272 and Class Password: Epidemiology. Instructions for the use of Turnitin are included in the back of this coursebook. Assignments not submitted to Turnitin.com cannot be marked and shall be marked a Fail. A hard copy of each of your assignments is still required for marking purposes (see above). Plagiarism Plagiarism (copying from another person’s work) is not acceptable, and the University of Auckland takes instances of plagiarism seriously. Plagiarism can also mean not acknowledging the full extent of indebtedness to a source. Work can be plagiarised from many sources - including books, articles, the internet, and other students' assignments. Plagiarism can easily occur unconsciously or inadvertently. To find out more about Turnitin, plagiarism, and our procedures and penalties for academic dishonesty (often detected by Turnitin) please look carefully at this website: www.auckland.ac.nz/academic_honesty 14 Additional information Study guide Although it is difficult to give a general estimate of study time commitment to the course, it is suggested for this course that six to seven hours be set aside each week outside of direct contact time. Overall, a 15 point undergraduate course is estimated to require 10 hours a week over a 12 week semester, including campus attendance, reading, assignments, study and exams. Study groups (optional) Study groups may be set up as a means of study support. Students may arrange regular meetings - for example, to discuss the issues raised in the sessions or discovered through personal study or to collaborate on some assignments. Individual study problems may be discussed within the group. Study problems From time to time, students may feel anxious about their study progress, and it is important that these anxieties be resolved promptly. If the problem is academic in nature (e.g. assignment problems, specific course content, etc.), the matter should be raised with the course coordinator/lecturer in the first instance. If the problem is likely to affect your ability to complete the course, please contact the School of Population Health Undergraduate Teaching Office for advice and options – it is important to seek help earlier rather than later as your whole programme may be affected. Course evaluation Student’s experience of the course may be formally evaluated at the conclusion of the course. This evaluation is applied to all courses taught by the School of Population Health and is usually scheduled on the last day of the course. This evaluation is strictly confidential. The collated results will not be available to the lecture/tutor until after the final examination paper has been marked and course marks finalised. Appendix 1: Survival skills CECIL (http://cecil.auckland.ac.nz ) We use CECIL extensively for this course, and it is important you become familiar with it. To logon and use CECIL you will need your NetID and password. Cecil can be used to access information such as: Course information Contact information for lecturer and administrator The library and your course readings Your course marks Announcements and discussions Selected lecture notes and handouts Difficult to find readings 15 EC Mail (http://webmail.ec.auckland.ac.nz ) All students at The University of Auckland are given a University email account. The University uses your NetID@aucklanduni.ac.nz email address for all official email communications. Redirect/forward EC Mail To redirect/forward your EC Mail to your regular email account (eg, Gmail, Hotmail, Yahoo), follow the steps below: Step 1: Sign into your EC Mail account at http://webmail.ec.auckland.ac.nz Step 2: Click “Settings” at the top of your EC Mail page Step 3: Click on the “Forwarding and POP/IMAP” tab Step 4: Select “Forward a copy of incoming mail to” and enter the email address you would like your messages to be forwarded to. A verification email will be sent to your forwarding email address. Step 5: Open your verification email and click the confirmation link. Step 6: Return to your EC Mail account settings and to “Forwarding and POP/IMAP”; click on “Forward a copy of incoming mail to” and select the verified email address Step 7: Click “Save changes” Note: This function will not work until the forwarding email address is verified (see Steps 4–7). All information will be sent to your University email address only – Cecil, Student Services Online, examination timetables, admission and all other information, so the above steps are very important if you are a part-time student. 16 Appendix 2: Useful web URLs To find The University of Auckland URLs www.auckland.ac.nz Faculty of Medical and Health Sciences www.fmhs.auckland.ac.nz SOPH Website http://www.fmhs.auckland.ac.nz/soph/default.aspx http://www.fmhs.auckland.ac.nz/soph/undergrad/default.aspx BHSc Website http://www.fmhs.auckland.ac.nz/soph/undergrad/bhsc.aspx SOPH course outlines www.fmhs.auckland.ac.nz , selecting Future undergraduates, Undergraduate Study options, then selecting the link Search for courses in Undergraduate courses Academic Information http://www.auckland.ac.nz/uoa/home/for/current-students/csacademic-information/ Student Services Online www.auckland.ac.nz/studentservicesonline www.studentservices.auckland.ac.nz Tāmaki Campus www.tamaki.auckland.ac.nz University Calendar www.auckland.ac.nz/calendar Careers Services www.auckland.ac.nz/careers Changing your enrolment www.auckland.ac.nz/change-enrolment Counselling services www.auckland.ac.nz/personalsupport EC Mail University emails http://webmail.ec.auckland.ac.nz/ Examinations www.auckland.ac.nz/exams Fees www.auckland.ac.nz/fees Forms www.auckland.ac.nz/studentforms Graduation www.auckland.ac.nz/graduation graduation@auckland.ac.nz ID Cards www.auckland.ac.nz/it-essentials Library www.library.auckland.ac.nz Plagiarism and Turnitin www.auckland.ac.nz/academic_honesty Public transport www.maxx.co.nz Referencing styles See www.library.auckland.ac.nz And select Study & Research Help for more information. 17 Scholarships www.auckland.ac.nz/scholarships Student Learning Centre www.slc.auckland.ac.nz Student bus service www.auckland.ac.nz/transport Tāmaki Campus student services www.tamaki.auckland.ac.nz/studentservices University health and counselling www.auckland.ac.nz/personalsupport Appendix 3: Turnitin If you are a new user, here is the Turnitin guide for students: http://www.auckland.ac.nz/uoa/tl-turnitin-faq. The guidelines will also be available at the BHSc website http://www.fmhs.auckland.ac.nz/soph/undergrad/bhsc.aspx and on Cecil as well.