General Statistical Ideas

• http://fharrell.com/doc/bbr.pdf Biostatistics for Biomedical Research: Primary Notes | http://fharrell.com/code/bbr.zip R Code for Chapters in Notes
• Data science open training
• http://hbiostat.org/doc/glossary.pdf Glossary of Statistical Terms
• Medical Citations for Statistical Issues | Articles Compiled by Vanderbilt Kennedy Center
• Clinical Trials Methodology
• The Pressure to Get It Right: Biases in Biomedical Research - Videocast by John Ioannidis
• Manuscript Checklist for Documenting or Avoiding Statistical Errors
• Doug Altman's http://www.chiroweb.com/archives/12/13/06.html The Scandal of Poor Medical Research
• Waterboarding and Wilcoxon: What Medical Researchers Might Learn About Statistics From the CIA by Andrew Vickers
• Emanuel, Wendler, and Grady's http://www.dartmouth.edu/~cphs/docs/jama-article.pdf What Makes Clinical Research Ethical?
• http://www-users.york.ac.uk/~mb55/pubs/pbstnote.htm Statistics Notes in the http://www.bmj.com British Medical Journal
• Translating statistical findings into plain English
• Interesting http://news.bbc.co.uk/2/hi/uk_news/magazine/7605118.stm statistics articles from the BBC
• Miscellaneous Problems to Avoid and our Checklist
• Recommendations about Statistical Software
• Severe hazards of using Excel for statistical calculations
• Stats Overview for Clinical Researchers
• http://en.wikipedia.org/wiki/Rule_of_three_%28statistics%29 The 3/n rule
• Relationships among http://www.zen89632.zen.co.uk/R/TwoProportions/lambda_delta.pdf risk difference, relative risk, and odds ratios
• Dance of the P-values

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Statistical Thinking in Biomedical Research Short Course

• Overview and Target Audience
• Schedule
• Syllabus, Objectives, Handouts, and Readings
• Discussion Board
• Checklist for Course Organizer
• Checklist for Participants
• Notes for Instructors

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Supplementary Handouts

• The End of Statistical Significance? by Jonathan Sterne, Department of Social Medicine, University of Bristol UK
• Introduction to Statistical Concepts (Frank Harrell) and Clinical Trials and Observational Studies (Viktor Bovbjerg, University of Virginia)
• The Basic Logic in Statistical Inference (Rob Abbott, University of Virginia)
• Principles of Experimental Design (Mark Conaway, University of Virginia; also contains some material on repeated measurements and dropouts). There are also older separate versions of https://biostat.app.vumc.org/wiki/pub/Main/ClinStat/doe.pdf Principles of Experimental Design (Mark Conaway) and https://biostat.app.vumc.org/wiki/pub/Main/ClinStat/repmeas.PDF Repeated Measures Design (Mark Conaway)
• Experimental Design (Jim Patrie, University of Virginia; slides contain description of statistical models useful for analyzing experimental data).
• Bayesian Methods for Clinicians
• Outline of the Bayesian Approach to Randomized Clinical Trials (FE Harrell and M Peruggia)
• http://www.indiana.edu/~kruschke Bayes material from John Kruschke
• Multivariable Modeling Issues
• How Should Change be Measured? (NOTE: Contained in Introduction to Statistical Concepts)
• Analysis of repeated measurements (serial or longitudinal data) (FE Harrell 1987)
• Analysis of Observer Variability
• Reporting Results (Gina Petroni, University of Virginia)
• Possible agenda for a short course or research retreat to be offered to clinical and basic science departments

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Introduction to Biostatistics for Clinical Investigators

Course for Clinical Pharmacology Fellows Fall 2009 - Spring 2010

• 449 PRB, 12:30 - 1:30, Thursdays

Instructors

• Chris Slaughter DrPH, Assistant Professor of Biostatistics
  • mailto:james.c.slaughter@vanderbilt.edu; D-2207 Medical Center North; 322-0439
• Frank Harrell PhD, Professor of Biostatistics, Chairman, Dept. of Biostatistics
  • mailto:f.harrell@vanderbilt.edu; S-2323 Medical Center North; 322-2001

Syllabus

Textbook and reading materials

• [EMS] Essential Medical Statistics Kirkwood and Sterne
• [B] Biostatistics: A Guide to Design, Analysis, and Discovery Forthofer et. al
• [SN] Statistics Notes. Fifty-five (and counting) valuable short articles on misuses and correct uses of statistics in medical research.
• [LHSP] Little Handbook of Statistical Practice
• [SP] Statistical Problems to Document and to Avoid. A collection of misuses of statistics.
• [H] http://fharrell.com/doc/bbr.pdf Handouts
• Glossary of Statistical Terms
• T-test examples, Tests of proportions example
• Power and Sample Size Estimation Software
• Exercises

Lectures

• Key concepts covered during each lecture with review questions

	Date	To read/do before class	Topics	Instructor	edit
1	9/3	EMS 1-2; Optionally download R and install the http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/StatBiomedResSyllabus#Software Rcmdr package	Course description; Introduction (H1); Data Tips	CS & FH	edit
2	9/10	H2, EMS 3-4	Descriptive statistics and distributions; Example Paper; Anscombe's quartet	CS & FH	edit
3	9/17	Online statbook Chapter; The Basic Logic in Statistical Inference; H3; EMS8	Ideas Behind Hypothesis Testing	FH	edit
	9/24		Journal Club	TBA	edit
4	10/1	EMS 6; H3.4 - H3.6; Power and Sample Size Estimation Software	1-sample (paired) t-tests: Power, sample size, confidence intervals, and hypothesis testing; SurfStat p-value calculator	CS & FH	edit
5	10/8	EMS 7-8; H3.7 - H3.10; Power and Sample Size Estimation Software	2-sample t-tests: Power, sample size, confidence intervals, and hypothesis testing	CS & FH	edit
6	10/15	EMS 34 (particularly 34.2 and 34.3)	Finish parametric tests. Also, introduction to study designs including randomized/observational, retrospective/prospective, case-control, crossover, and factorial designs	CS & FH	edit
	10/22		Journal Club	TBA	edit
7	10/29	BMJ article on odds ratio; H4; EMS 16	Categorical data analysis and tests of proportions (H4): Pearson's Chi-squared test, Fisher's exact test, odds ratios, relative risk, and power/sample size calculations	TBA	edit
8	11/5	Parametric vs non-parametric tests; EMS 30.1, 30.2 (through Wilcoxon signed rank test)	Non Parametric Tests I: When to use non-parametric methods; Wilcoxon 1-sample test	TBA	edit
9	11/12		No course (MSCI conflict)	TBA	edit
10	11/19	EMS 30.2, 30.3	Non Parametric Tests II: Wilcoxon 2-sample test, the bootstrap for obtaining confidence intervals	TBA	edit
	12/3		Journal Club	TBA	edit
11	12/10	Measuring change on twiki; Article on measuring change	Measuring Change	TBA	edit
12			Correlation	TBA	edit
13		Paper using Regression	Introduction to regression	TBA	edit
14			Analysis of variance (ANOVA), both parametric and non-parametric	TBA	edit

Student presentations

• One fellow present an introduction to the day's topic at the start of class
• Each presentation should last 15-20 minutes
• Before class, fellows should have read all of the assigned material, but do not try to cover every idea during the student presentation. It is better to provide a good, thorough introduction rather than a brief overview of all topics.
• If appropriate, discuss the portions of the topic that pertain to your research or recent papers that you have read. One nice way of organizing a lecture is to start with a specific example (given in the student presentation), continue with general applications and ideas (handled by the instructors), and finishing with more specifics (by the instructors).
• Highlight any areas that you think are unclear and require further explanation
• If you need assistance getting started, the instructors have provided a set of learning objectives that will be covered each lecture. Again, you do not need to cover all of these ideas in your presentation, but it can be a useful starting point.

Instructor Notes and Plans for Upcoming Course

Additional Material from Previous Course

• Syllabus for biostatistics component
• Handout for session 2:Probability and Estimation
• Quiz and answers for session 2
• Handout for session 5:Regression and Correlation
• Quiz and answers for session 5
• Statistical Calculators
• Dandelions: A good way to present point estimates
• An interactive demonstration of the meaning of confidence intervals
• Slides from Mimi Lam MD explaining the purpose of the Kaplan-Meier estimator

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Links to Other Sites

• St. George's Hospital Medical School http://www.sgul.ac.uk/index.cfm?D7DEB028-B5BE-7536-BD9D-2EC800CE3789 Statistics Guide for Research Grant Applications, including links to Randomization Software and Services
• Canadian Medical Association http://www.cmaj.ca/cgi/collection/statistics_and_research_methods Statistics and research methods articles
• British Medical Journal's http://bmj.bmjjournals.com/collections/statsbk Statistics at Square One
• NIDCR NERI http://symptomresearch.nih.gov Symptom research site, with much material related to clinical research methodology and prognostic modeling
• http://www.ualberta.ca/~pletendr Statistics sites, compiled by Pat Letendre, Medical Laboratory Science, University of Alberta
• http://exploringdata.cqu.edu.au Exploring Data - web-based curriculum for introductory statistics from Rex Boggs of Education Queensland, Australia
• http://www.ruf.rice.edu/~lane/rvls.html Rice University Virtual Lab in Statistics (includes HyperStat Textbook)
• Susan Holmes' http://www-stat.stanford.edu/~susan/surprise graphical applets for teaching probability and statistical concepts
• http://www.math.uah.edu/stat University of Alabama in Huntsville Virtual Laboratory in Probability and Statistics
• http://www.amstat.org/publications/jse Journal of Statistical Education
• http://www.statsoft.com/textbook/stathome.html StatSoft Electronic Statistics Textbook
• http://statistics.cyberk.com CyberGnostics Electronic Statistics Textbook Project
• UC Berkeley's Tools for an Interactive Learning Environment
• Charles Annis' interactive demonstration of the central limit theorem and other information about statistics in engineering
• Gary McClelland's Java applet demonstrating the information loss from dichotomizing a continuous variable
• Jerry Dallal's Little Handbook of Statistical Practice
• American Psychological Association Guidelines for Statistical Methods in Psychology Journals
• http://www.itl.nist.gov/div898/handbook/index.htm NIST Sematech Engineering Statistics Handbook
• http://www.pitt.edu/~wpilib/statfaq.html Frequently Asked Statistical Questions by Rich Ulrich, University of Pittsburgh
• http://www.dartmouth.edu/~chance Dartmouth Chance Case Study Quantitative Literacy Course
• Peter Diggle's highly informative web site for spatial statistics
• Gillian Raab's teaching material on Bayesian inference and the use of BUGS Bayesian analysis software
• Milo Schield's http://www.augsburg.edu/ppages/~schield Statistical Literacy and Evidential Statistics Material
• Mike Fuller's http://www.fmi.uni-sofia.bg/fmi/statist/statlist.html List of Statistical Lists
• http://www.mrc-bsu.cam.ac.uk Cambridge MRC Biostatistics Unit
• Bland and Altman's material on assessing http://www-users.york.ac.uk/~mb55/meas/meas.htm agreement and accuracy
• FE Harrell's http://zotero.com/groups/feh bibliographic database

-- FrankHarrell - 10 Feb, 26-27 Jun, 13 Aug 2004, 13 Feb 2005, 24 Dec 2006, 25 Sep 2007, 7 Apr 2008, 26 Feb, 18 Aug, 17 Dec 2009, 4 Apr 2012, 16 Sep 2012, 4 Feb 2013, 2014-07-15, 2015-02-14, 2015-02-27, 2015-03-03, 2015-06-26, 2015-09-16, 2017-07-18, 2018-01-18, 2018-01-28, 2019-01-10
-- ColeBeck - 08 Mar 2004

• LTD_Paper.pdf: LTD_Paper.pdf