Credits : 10	Year : 2012
Mode : Internal	Semester : Two
Location : Palmerston North	Online component : None
Coordinator : Dr Mark Stevenson

An introduction to statistical principles and methodology, and their application to veterinary science. Emphasis on interpretation of results presented in the scientific literature. Principles of applied veterinary epidemiology including patterns of disease, investigation of disease in animal populations, interpretation of diagnostic tests, observational studies and critical appraisal of the literature.

Lecture notes, resources, details of assignments and examinations are all now available in Stream. Log in to the 227.407 page using your Massey user name and password. Dates, times and venues for 2012 are as follows:

Date	Time	Location	Instructor	Format	Details
Mon 09 Jul	1100 - 1200	ICLT	JM	Lecture	Introduction to biometrics
Tue 10 Jul	1400 - 1500	ICLT	JM	Lecture	Exploratory data analysis 1
Fri 13 Jul	1000 - 1100	ICLT	JM	Lecture	Exploratory data analysis 2
Mon 16 Jul	1100 - 1200	SSLB2	JM	Lecture	Probability distributions 1
Tue 17 Jul	1400 - 1500	SSLB4	JM	Lecture	Probability distributions 2
Fri 20 Jul	1000 - 1100	SSLB5	JM	Lecture	Probability distributions 3
Mon 23 Jul	1100 - 1200	SSLB2	JM	Lecture	Confidence intervals
Tue 24 Jul	1400 - 1500	SSLB4	JM	Lecture	Statistical inference 1
Fri 27 Jul	1000 - 1100	SSLB5	JM	Lecture	Statistical inference 2
Mon 13 Aug	1100 - 1200	SSLB2	JM	Lecture	Statistical inference 3
Tue 14 Aug	1400 - 1500	SSLB4	JM	Lecture	Statistical inference 4
Fri 17 Aug	1000 - 1100	SSLB5	JM	Lecture	Qualitative data
Mon 20 Aug	1100 - 1200	ICLT	JM	Lecture	ANOVA 1
Tue 21 Aug	1400 - 1500	ICLT	JM	Lecture	ANOVA 2
Fri 24 Aug	1000 - 1100	ICLT	JM	Lecture	ANOVA 3
Mon 27 Aug					Assignment 1 due
Mon 27 Aug	1100 - 1200	ICLT	JM	Lecture	Regression 1
Tue 28 Aug	1400 - 1500	ICLT	JM	Lecture	Regression 2
Fri 31 Aug	1000 - 1100	ICLT	JM	Lecture	Experimental design 1
Mon 10 Sep	1100 - 1200	SSLB2	JM	Lecture	Experimental design 2
Tue 11 Sep	1400 - 1500	SSLB4	MS	Lecture	Introduction to epidemiology
Fri 14 Sep	1000 - 1100	SSLB5	MS	Lecture	Measures of health 1
Mon 17 Sep	1100 - 1200	SSLB2	MS	Lecture	Measures of health 2
Tue 18 Sep	1400 - 1500	SSLB4	MS	Lecture	Observational study design
Fri 21 Sep	1000 - 1100	SSLB5	MS	Lecture	Measures of association 1
Mon 24 Sep	1100 - 1200	SSLB2			Mid-semester test
Mon 24 Sep					Assignment 2 due
Tue 25 Sep	1400 - 1500	SSLB4	MS	Lecture	Measures of association 2
Fri 28 Sep	1000 - 1100	SSLB5	MS	Lecture	Error in epidemiological research
Mon 01 Oct	1100 - 1200	SSLB2	MS	Lecture	Causation
Tue 02 Oct	1400 - 1500	SSLB4	MS	Lecture	Critical appraisal 1
Fri 05 Oct	1000 - 1100	SSLB5	MS	Lecture	Critical appraisal 2
Mon 08 Oct	1100 - 1200	SSLB2	MS	Lecture	Sampling
Mon 08 Oct					Assignment 3 due
Tue 09 Oct	1400 - 1500	SSLB4	MS	Lecture	Diagnostic tests 1
Fri 12 Oct	1000 - 1100	SSLB5	MS	Lecture	Diagnostic tests 2
Mon 15 Oct	1100 - 1200	SSLB2	MS	Lecture	Outbreak investigation 1
Tue 16 Oct	1400 - 1500	SSLB4	MS	Lecture	Outbreak investigation 2
Fri 19 Oct	1000 - 1100	SSLB5	MS	Lecture	Revision

MS: Mark Stevenson

JM: Jonathon Marshall

Exemptions

You can apply for an exemption from the biometrics (or epidemiology) component of this course if you've completed a similar program of study from another university. To apply for an exemption, you'll need to provide the course controller (Mark Stevenson) with a letter detailing the name of the institution and the name (and number) of the course on which the grounds for the exemption are based. This letter should also contain: (1) an outline of the material covered in the course (in lecture-by-lecture format); and (2) evidence that a B grade (or higher) was achieved. Please include a certified copy of your academic transcript.

Students applying for an exemption from biometrics will need to pass a 30 question multiple choice quizz to be held in May 2012 (venue and date to be confirmed). Epidemiology exemptions will be assessed on a case-by case basis.

Students exempt from biometrics will need to complete the epidemiology component of the course, which involves: (1) attending all of the epidemiology lectures; (2) completing the two epidemiology assignments; (3) completing the epidemiology component of the mid-semester test; and (4) completing the epidemiology component of the final exam.

When preparing a case for an exemption, please provide a printed version of your documents. Emailed requests will not be considered. Requests for an exemption must be received before 1 May 2012.

Course notes

An Introduction to Veterinary Epidemiology (updated 11 January 2012).

Veterinary Biometrics (updated 5 December 2007).

A Veterinarian's Guide to MS Excel (updated 22 September 2008).

Reference material:

Green MD, Freedman DM, Gordis L Reference Guide on Epidemiology (from Reference Manual on Scientific Evidence, Federal Judicial Center 2000). The entire volume can be downloaded from the Federal Judicial Center’s web site: http://www.fjc.gov.

Kaye DH, Freedman DA. Reference Guide on Statistics (from Reference Manual on Scientific Evidence, Federal Judicial Center 2000).

Rubinfeld DL. Reference Guide on Multiple Regression (from Reference Manual on Scientific Evidence, Federal Judicial Center 2000).

Diamond SS. Reference Guide on Survey Research (from Reference Manual on Scientific Evidence, Federal Judicial Center 2000).

Recommended texts

It is recommended that students purchase a copy of Petrie and Watson (2005) for the biometrics component of this course. Thrusfield (2007) or Dohoo et al. (2003) are recommended if students wish to purchase an epidemiology text.

Petrie A and Watson P (2005) Statistics for Veterinary and Animal Science. London: Blackwell Science. ISBN-10: 1405127813 | ISBN-13: 978-1405127813.

Thrusfield M (2007) Veterinary Epidemiology, 3rd Edition. London: Blackwell Science. ISBN-10: 1405156279 | ISBN-13: 978-1405156271

Dohoo I, Martin W, and Stryhn H (2009) Veterinary Epidemiologic Research, 2nd Edition. Charlottetown, Prince Edward Island, Canada: AVC Inc.

Resources

Introduction to epidemiology

Snow J (1855) On the Mode of Communication of Cholera, John Churchill, London.

Semmelweis I (1861) The etiology, concept and prophylaxis of childbed fever.

Bowie W, King A, Werker D, Isaac-Renton J, Bell A, Eng S, Marion S (1997) Outbreak of toxoplasmosis associated with municipal drinking water. The Lancet 350, 173 - 177.

Mikami T, Nakagomi T, Tsutsui R, Ishikawa K, Onodera Y, Arisawa K, Nakagomi O (2004) An outbreak of gastroenteritis during school trip caused by serotype G2 group A rotavirus. Journal of Medical Virology 73, 460 - 464

Ruddy M, Davies A, Yates M, Yates S, Balasegaram S, Drabu Y, Patel B, Lozewicz S, Sen S, Bahl M, James E, Lipman M, Duckworth G, Watson J, Piper M, Drobniewski F, Maguire H (2004) Outbreak of isoniazid resistant tuberculosis in north London. Thorax 59, 279 - 285.

Measures of health

VETSTATS_v02.xls: An Excel spreadsheet for calculating point estimates and confidence intervals around measures of disease frequency and measures of association, sample size calculations (for simple random sampling), sampling to detect disease, and various measures of diagnostic test performance (updated 5 November 2009).

Measures of health review questions

A note on Figure 7 in the study guide.

Measures of association

Measures association review questions

Study design

Study design review questions

Cardwell JM (2008) An overview of study design. Journal of Small Animal Practice 49, 217 - 218.

Schulz KF, Grimes DA (2002) Case-control studies: research in reverse. The Lancet 359, 431 - 434.

Yates J, James D (2006) Predicting the 'strugglers': a case-control study of students at Nottingham University Medical School. British Medical Journal doi:10.1136/bmj.38730.678310.63.

Error in epidemiological research

Misclassification spreadsheet

Atwell R, Heath T (2001) Some factors affecting diagnostic accuracy. Australian Veterinary Practitioner 31, 23 - 28.

Fitzmaurice G (2003) Confused by confounding? Nutrition 19, 189 - 191.

Fitzmaurice G (2004) Adjusting for confounding Nutrition 20, 594 - 596.

Causation

Public Policy and the Use of Science. A lecture by Sir John Krebs given at a meeting of the Royal Geographic Society on 7 March 2006.

Sampling

Sampling review questions

Software for sample size calculations (simple random sampling, stratified random sampling, one- and two-stage cluster sampling), ProMESA. Unzip to a temporary folder and then double click on ProMESA_install.msi to install. Alternatively, a web version of the program can be accessed from here.

Diagnostic tests

Diagnostic tests review questions

Leung W-C (2002) Measuring chances. Student British Medical Journal 10, 268 - 270.

Altman D, Bland A (1994) Diagnostic tests 1: sensitivity and specificity. British Medical Journal 308: 1552.

Altman D, Bland A (1994) Diagnostic tests 2: predictive values. British Medical Journal 309: 102.

Deeks J, Altman A (2004) Diagnostic tests 4: likelihood ratios. British Medical Journal 329: 168 - 169.

Halkin A, Reichman J, Schwaber M, Paltiel O, Brezis M (1998) Likelihood ratios: getting diagnostic testing into perspective. The Quarterly Journal of Medicine 91: 247 - 258.

Outbreak investigation

Morris R (1990) Disease outbreak! What can you do? In: Epidemiological Skills in Animal Health. Post Graduate Committee in Veterinary Science, University of Sydney, Australia pp 321 - 327.

Gardner I (1990) Reporting disease outbreaks. In: Epidemiological at Work. Post Graduate Committee in Veterinary Science, University of Sydney, Australia pp 29 - 42.

US Army Medical Department (2003) Military Preventive Medicine: Mobilization and Deployment, Vol 1.

US Army Medical Department (2005) Military Preventive Medicine: Mobilization and Deployment, Vol 2.

Critical appraisal

Greenhalgh T, Taylor R (1997) How to read a paper: Papers that go beyond numbers (qualitative research). British Medical Journal 315: 740 - 743.

Greenhalgh T (1997) How to read a paper: Papers that summarise other papers (systematic reviews and meta-analyses). British Medical Journal 315: 672 - 675.

Greenhalgh T (1997) How to read a paper: Papers that tell you what things cost (economic analyses). British Medical Journal 315: 596 - 599.

Greenhalgh T (1997) How to read a paper: Papers that report diagnostic or screening tests. British Medical Journal 315: 540 - 543.

Greenhalgh T (1997) How to read a paper: Assessing the methodological quality of published papers. British Medical Journal 315: 305 - 308.

Greenhalgh T (1997) How to read a paper: Statistics for the non-statistician. II: "Significant" relations and their pitfalls. British Medical Journal 315: 422 - 425.

Greenhalgh T (1997) How to read a paper: Getting your bearings (deciding what the paper is about). British Medical Journal 315: 243 - 246.

Browne M (2001) Critical appraisal: An Introduction. Mount Sinai Hospital.