Biostatistics for Clinical Pharmacology Fellows

Course Goals

1. understand basic concepts, ideas, and techniques often used in statistics, especially biostatistics;
2. develop appreciation of (i) variation, (ii) importance of design to the overall quality of a study, (iii) impact of assumptions on data analysis and interpretation, and (iv) artifacts and caveats in data analysis and interpretation;
3. carry out simple exploratory/graphical/formal/diagnostic analysis; and
4. know when and where to seek statisticians’ help.
5. not to emphasize software but rather concepts and interpretation of statistical results

Textbook and Reading Materials

• Kirkwood BR, Sterne JAC (2003) Essential Medical Statistics, 2nd ed. Blackwell Publishers. $58.95. ISBN: 0865428719. Corrections and four datasets are available at book web site http://www.blackwellpublishing.com/essentialmedstats.
• [SN] Altman DG, Bland JM et al. (1994-2006) Statistics Notes. British Medical Journal. Fifty-two valuable short articles on misuses and correct uses of statistics in medical research. Links at http://www-users.york.ac.uk/~mb55/pubs/pbstnote.htm.
• [LHSP] Dallal G. Little Handbook of Statistical Practice: http://www.StatisticalPractice.com
• [SP] Statistical Problems to Document and to Avoid. A collection of misuses of statistics. http://biostat.mc.vanderbilt.edu/ManuscriptChecklist.

Other Useful Books (not required; asterisks ― highly recommended to read):

• Forthofer RN, Lee ES, and Hernandez M. Biostatistics: A Guide to Design and Discovery. http://www.biostat-edu.com
• Altman DG (1990) Practical Statistics for Medical Research. Chapman & Hall/CRC. [A very good book on medical statistics. The second edition should come out soon.]
• *Altman DG, Machin D, Bryant TN, Gardner MJ (2000) Statistics with Confidence, 2nd ed. Blackwell Publishers. [Short essays on the advantages of using confidence intervals. The book comes with software Confidence Interval Analysis (CIA).]
• Armitage P, Berry G, Matthews JNS (2001) Statistical Methods in Medical Research, 4th ed. Blackwell Publishers. [This book is quite comprehensive, covering more materials than a semester’s course. It may serve as a reference book, but definitely not a cookbook.]
• Bland M (2000) An Introduction to Medical Statistics, 3rd ed. Oxford University Press. [Another popular introductory book on medical statistics.]
• *Motulsky H (1995) Intuitive Biostatistics. Oxford University Press. [This book covers basic materials in biostatistics and explains the basic concepts very well.]
• Rosner B (2005) Fundamentals of Biostatistics, 6th ed. Duxbury Press. [Old style of teaching statistics. Lots of examples from many medical fields.]
• *Freedman D, Pisani R, and Purves R (1997) Statistics, 3rd ed. W. W. Norton & Company. [This is a very good introduction to statistics, without being technical.]
• Moore DS, Notz WI (2005) Statistics: Concepts and Controversies, 6th ed. W. H. Freeman. [Another very good non-technical introduction to statistics.]

Free Online Resources

• Resources from Vanderbilt Biostatistics: Main education page | General statistics ideas
• Glossary of Statistical Terms: http://biostat.mc.vanderbilt.edu/twiki/pub/Main/ClinStat/glossary.pdf
• HyperStat Online (by David Lane): http://davidmlane.com/hyperstat [An online book on basic statistics, with some useful links.]
• SticiGui (by Philip Stark): http://www.stat.berkeley.edu/~stark/SticiGui/ [An online non-technical textbook on introductory statistics, with applets to allow interactive learning.]
• Electronic Statistics Textbook (by StatSoft): http://www.statsoft.com/textbook/stathome.html
• Electronic Encyclopedia of Statistical Examples and Exercises (EESEE): http://www.whfreeman.com/eesee/ [A good site for learning statistics with lots of examples. Developed by folks at an Ohio State University.]

Software

• You can use any software your want other than Excel. We will be demonstrating R and giving out R code.
• R 2.6 (optional, free from http://www.r-project.org): Powerful, versatile, and actively maintained and updated. It may require a longer learning curve than Stata and SPSS, but the effort will pay off later on. To get a feel, look at one of the following: http://cran.r-project.org/doc/manuals/R-intro.pdf 1 (and try the commands in "A Sample Session“) http://cran.r-project.org/other-docs.html 2 3. The Department of Biostatistics has a free R Clinic every Thursday. Print the R http://www.rpad.org/Rpad/Rpad-refcard.pdf reference card to get a list of the most commonly used commands.
• To download R: http://cran.wustl.edu/bin/linux Linux http://cran.wustl.edu/bin/macosx Mac http://cran.wustl.edu/bin/windows/base Windows
• Under R you can use a menu to install new packages. Install the Rcmdr package, which provides a simple SPSS-like menu system to interact with the R language. Load Rcmdr and the main menu will appear. Go http://socserv.socsci.mcmaster.ca/jfox/Misc/Rcmdr here for more information. The first time you load Rcmdr it will ask you if you want to download and install packages that Rcmdr depends on. Answer affirmatively, and specify CRAN as the source. This will take a few minutes but only needs to be done the first time you try to use Rcmdr.
  • Rcmdr http://socserv.mcmaster.ca/jfox/Misc/Rcmdr/installation-notes.html installation instructions especially for Mac
• See SoftwareRecs for more software recommendations
• Chun Li's Stata notes, Need-to-know commands, and R notes
• Leena Choi's Stata notes for classes, Stata Lab info, and R notes for classes

Comments on Other Software Packages

• Stata: Powerful and good graphics with an SPSS-like menu system. A good support site is at http://www.ats.ucla.edu/stat/stata. Cost is $89 for a year and $145 for life, through http://www.stata.com/order/new/edu/gradplans/gp-campus.html GradPlan. Buy Small Stata for $45 if you have to pay by yourself. Stata also is available at the College of Arts & Science Microcomputer Labs.
• SAS: The oldest survivor, with strong legacy. Hard to learn and extend, with outdated structure and the worst graphics of any major package.
• SPSS: Have “standard” methods and good graphical user interface. However, it is difficult to extend beyond the “standard” methods.
• Honorable mention: Epi Info (free from CDC), S-Plus.
• There is a long list of reasons not to use Excel. See ExcelProblems
• See StatComp for more information about statistical computing including links to several online statistical and probability calculators