Credits : 10	Year : 2011
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 2011 are as follows:

Date	Time	Location	Instructor	Format	Details
Mon 11 Jul	1100 - 1200	ICLT	MS	Lecture	Introduction to epidemiology
Tue 12 Jul	1400 - 1500	ICLT	SG	Lecture	Introduction to biometrics
Fri 15 Jul	1000 - 1100	ICLT	SG	Lecture	Exploratory data analysis 1
Mon 18 Jul	1100 - 1200	SSLB2	SG	Lecture	Exploratory data analysis 2
Tue 19 Jul	1400 - 1500	SSLB4	SG	Lecture	Probability distributions 1
Fri 22 Jul	1000 - 1100	SSLB5	SG	Lecture	Probability distributions 2
Mon 25 Jul	1100 - 1200	SSLB2	SG	Lecture	Probability distributions 3
Tue 26 Jul	1400 - 1500	SSLB4	SG	Lecture	Confidence intervals
Fri 29 Jul	1000 - 1100	SSLB5	SG	Lecture	Statistical inference 1
Mon 15 Aug	1100 - 1200	SSLB2	JM	Lecture	Statistical inference 2
Tue 16 Aug	1400 - 1500	SSLB4	JM	Lecture	Statistical inference 3
Fri 19 Aug	1000 - 1100	SSLB5	JM	Lecture	Statistical inference 4
Mon 22 Aug	1100 - 1200	ICLT	JM	Lecture	Qualitative data
Tue 23 Aug	1400 - 1500	ICLT	JM	Lecture	ANOVA 1
Fri 26 Aug	1000 - 1100	ICLT	JM	Lecture	ANOVA 2
Fri 26 Aug					Assignment 1 due
Mon 29 Aug	1100 - 1200	ICLT	JM	Lecture	ANOVA 3
Tue 30 Aug	1400 - 1500	ICLT	JM	Lecture	Regression 1
Fri 02 Sep	1000 - 1100	ICLT	JM	Lecture	Regression 2
Mon 12 Sep	1100 - 1200	SSLB2	JM	Lecture	Experimental design 1
Tue 13 Sep	1400 - 1500	SSLB4	JM	Lecture	Experimental design 2
Fri 16 Sep	1000 - 1100	SSLB5	MS	Lecture	Measures of health 1
Mon 19 Sep	1100 - 1200	SSLB2	MS	Lecture	Measures of health 2
Tue 20 Sep	1400 - 1500	SSLB4	MS	Lecture	Observational study design
Fri 23 Sep	1000 - 1100	SSLB5	MS	Lecture	Measures of association 1
Mon 26 Sep	1100 - 1200	SSLB2			Mid-semester test
Tue 27 Sep	1400 - 1500	SSLB4	MS	Lecture	Measures of association 2
Fri 30 Sep	1000 - 1100	SSLB5	MS	Lecture	Error in epidemiological research
Mon 03 Oct	1100 - 1200	SSLB2	MS	Lecture	Causation
Mon 03 Oct					Assignment 2 due
Tue 04 Oct	1400 - 1500	SSLB4	MS	Lecture	Sampling
Fri 07 Oct	1000 - 1100	SSLB5	MS	Lecture	Diagnostic tests 1
Mon 10 Oct	1100 - 1200	SSLB2	MS	Lecture	Diagnostic tests 2
Tue 11 Oct	1400 - 1500	SSLB4	MS	Lecture	Critical appraisal 1
Fri 14 Oct	1000 - 1100	SSLB5	MS	Lecture	Critical appraisal 2
Mon 17 Oct	1100 - 1200	SSLB2	MS	Lecture	Outbreak investigation 1
Mon 17 Oct					Assignment 3 due
Tue 18 Oct	1400 - 1500	SSLB4	MS	Lecture	Outbreak investigation 2
Fri 21 Oct	1000 - 1100	SSLB5	MS	Lecture	Revision lecture
Fri 04 Nov	0915 - 1230				Final examination

MS: Mark Stevenson

SG: Siva Ganesh

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 2011 (venue and date to be confirmed). Epidemiology exemptions will be assessed on a case-bycase 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 2011.

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.

Thrusfield M (2007) Veterinary Epidemiology, 3rd Edition. London: Blackwell Science.

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.