Winter 2014 (Wednesdays 10-11:30 am, Purvis 48)

January 22, 2014

Sahir Rai Bhatnagar 

 

Reproducible research and Biostatistics
Biostat-2009-Peng-405-8.pdf
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Presentation:

Slides
rrslides.pdf
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February 5, 2014

Luc Villandre 

Phylogenetic Clustering of HIV and its Connection to Sexual Contact Networks

 

Background Reading:

Inferring Epidemic Contact Structure from Phylogenetic Trees
Leventhal2012.pdf
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February 19, 2014

Dr. Michael Wallas 

An introduction to Measurement Error

 

Introducing Measurement Error
(Three chapters of Michael's Ph.d thesis)
MeasurementError.pdf
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March 19, 2014

Maxime Turgeon

Mendelian randomization

Mendelian randomization’: can genetic epidemiology contribute to understanding environmental determinants of disease?
George Davey Smith and Shah Ebrahim 2003
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April 2, 2014

Dr. Hela Romdhani

On the association between variables with lower

detection limits

On the association between variables with lower detection limits
sim4319.pdf
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April 9, 2014

Raymond Griner

An Introduction to Group Sequential Methods.

Monitoring Response Variables
Book: "Fundamentals of Clinical Trials" by Friedman, Furberg, and DeMets.
Note: start on page 22 of the pdf document.
ch16_new.pdf
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Fall 2013 (Wednesdays 2:30-4 pm, Purvis 48)

September 25, 2013

Dr. James Hanley

Driving under the (Cellular) Influence
CellPhoneAfter9pm.pdf
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Background Reading:

A statistician plays darts
TibshiraniDartsArticle.pdf
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October 2, 2013

Dr. Heungsun Hwang

FUNCTIONAL MULTIPLE-SET CANONICAL CORRELATION ANALYSIS
reprint_FMCCA.pdf
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October 9, 2013

Dr. Madhukar Pai

 

Assessing the value of diagnostic tests: a framework for designing and evaluating trials
diRuffano BMJ 2012.pdf
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October 30, 2013

Maarten Van Smeden

 

A cautionary note on the robustness of latent class models for estimating diagnostic error without a gold standard
Albert2004.pdf
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November 6 , 2013

Dr. Tibor Schuster 

 

Matching Methods for Causal Inference: A Review and a Look Forward.

 

http://projecteuclid.org/DPubS/Repository/1.0/Disseminate?view=body&id=pdfview_1&handle=euclid.ss/1280841730

Slides
Matching methods for causal inference TS
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November 20 , 2013

Giuseppe Lamberti 

PATHMOX a New Approach to the Heterogeneity Problem: a Linear Regression Example
G_Lamberti_paper.pdf
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Winter 2013 (Mondays 12-1:15 pm, Purvis 48)

January 7, 2013

Dr. Nandini Dendukuri

Bayesian Meta-Analysis of the Accuracy of a Test for Tuberculous Pleuritis in the Absence of a Gold Standard Reference
Dendukuri2012.pdf
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Presentation
Dendukuri2013.pdf
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January 14, 2013

Dr. Benjamin Rich

High-dimensional Propensity Score Adjustment in Studies of Treatment Effects Using Health Care Claims Data
Schneeweiss2009.pdf
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Presentation
Rich2013.pdf
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Background Reading:

The central role of the propensity score in observational studies for causal effects
Rosenbaum_Rubin1983.pdf
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Variable selection for propensity score models
Brookhart2006.pdf
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January 21, 2013
Dr. Erica Moodie

Estimating optimal treatment regimes from a classification perspective
Zhang2012.pdf
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Presentation
Moodie2013.pdf
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Tutorial:

Dynamic Treatment Regimes for Managing Chronic Health Conditions: A Statistical Perspective
Chakraborty2011.pdf
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January 28, 2013

Dr. Ashley Naimi

Estimation of the time-dependent accelerated failure time model in the presence of confounding factors
Robins1992.pdf
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Presentation
Naimi2013.pdf
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February 4, 2013

Dr. Olli Miettinen

 

Epidemiological Research: An Introduction
Chapter 5 Etiologic Studies' Essentials

Chapter 6 Etiologic Studies' Typology

February 11, 2013

Dr. David Stephens

Advances in Markov Chain Monte Carlo
Griffin_Stephens.pdf
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Reversible jump Markov chain Monte Carlo computation and Bayesian model determination
Green1995.pdf
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February 18, 2013

Dr. Tibor Schuster 

 

The Elements of Statistical Learning (Hastie, Tibshirani, and Friedman)

Chapter 7 Model Assessment and Selection

http://www-stat.stanford.edu/~tibs/ElemStatLearn

Presentation
Schuster2013.pdf
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February 25, 2013

Dr. Olli Miettinen 

 

Epidemiological Research: An Introduction
Chapter 11 Studies on Screening for a Cancer

March 11, 2013
Dr. William Astle

Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
Falush2003.pdf
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Control of confounding of genetic associations in stratified populations
Hoggart2003.pdf
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Presentation
Astle2013.pdf
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March 18, 2013 (12:30-1:45 pm)
Dr. Robert Platt

Principles of Research
SIM_Cornfield2012.pdf
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Commentaries and Featured Articles:

SIM_Armitage2012.pdf
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SIM_Cox2012.pdf
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SIM_Ellenberg2012.pdf
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SIM_Gail2012.pdf
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SIM_Greenhouse2012.pdf
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SIM_Greenland2012.pdf
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SIM_Rubin2012.pdf
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SIM_Vandenbroucke2012.pdf
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SIM_Wittes2012.pdf
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March 25, 2013

Dr. Andrea Benedetti

 

How to Program Simulations in SAS

SAS_code.pdf
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April 8, 2013

Dr. David Buckeridge

Notes for Discussion
Notes.pdf
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Enhancing time-series detection algorithms for automated biosurveillance
Tokars2009.pdf
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Assessing surveillance using sensitivity, specificity and timeliness
Kleinman2006.pdf
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TBA, 2013

Dr. Robert Platt

Fall 2012 (Wed. 12:30-13:55 at Purvis 24)

September 12, 2012

Dr. Erica Moodie

Models for Longitudinal Data: A Generalized Estimating Equation Approach
Zeger1988.pdf
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Background Reading:

Liang1986.pdf
Adobe Acrobat Document [1.1 MB]
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September 19, 2012

Dr. James Hanley

Hanley1982.pdf
Adobe Acrobat Document [1.0 MB]
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Background Reading:

Swets1973.pdf
Adobe Acrobat Document [2.3 MB]
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Metz1978.pdf
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Background Stories:

"This week is the 32nd anniversary of my introduction to ROC analysis. At home in Natick, Mass, on the evening of Aug 27, 1980, while the intervals between AnnMarie's contractions were getting shorter, I was reading the manual for the FORTRAN program by Dorfman and Alf, as Barbara McNeil has contacted me to ask how to deal with the fact that 1 of the 4 radiology readers in the 'is a radiologist more accurate if (s)he reads CT scan with patient's history in hand vs. if not?' study had not used all 5 rating categories. At 4 a.m. on the 28th, we went to Framingham Union Hospital, where Stephen (already 9 days late, with McGill calling every day to know when was I going to show up to teach EPIB607) arrived that p.m. We arrived in Montreal on Sept. 10th, 1980, so 607 started a bit late.

Barbara gave me two very helpful papers for orietation, the (now very heavily cited) one by Charles Metz,
http://news.uchicago.edu/article/2012/07/10/charles-metz-pioneer-imaging-science-1942-2012
http://radiology.uchicago.edu/page/metz-roc-software
who died this summer, and one by John Swets, whom I consider the founder of ROC analysis, and whose book
http://metz-roc.uchicago.edu/MetzROC/publications/review-of-john-swets-new-book
I must get and read.

I attach both of these papers as background reading, along with (as the primary reading) my own 1st roc paper, which I developed in 1980-1981 while I was still relatively unknown and not yet involved in that many activities at McGill. For the computations, carried out in FORTRAN, I did not have any grant money to pay the mainframe computing bills, so I used some of the small amount of computing money I was allocated for teaching 607 that Fall, and 621 (data analysis for epi students, Winter '81) while the usual teacher (Stan Shapiro) was on sabbatical in Boston in 80-81. Programming steps and data were entered on punched cards.

Some reasons that 1st roc paper of mine became a citation classic: it was self contained; it had a worked example; it was distribution-free and was easy to explain to, and be used by radiologists; it came at a time when VisiCalc (first spreadsheet, developed at MIT for repetitive 'what if' calculations in case studies in business plan projections; forerunner to Quattro, and ultimately, when Bill Gates saw how much $$ he could make form it, Excel) was becoming popular on Apple II personal computers and liberated users from the mainframe and FORTRAN.."

 

Jim, 2012-08-31

September 26, 2012

Please note that at the beginning of this meeting, Professor Andrew Piper, from the Department of Languages, Literatures, and Cultures, has been invited to briefly talk about his work (http://literarytopologies.org/) and how statistics can be useful in his area of research.

Luc Villandré

Episodic Sexual Transmission of HIV Revealed by Molecular Phylodynamics
Lewis2008.pdf
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Presentation
Villandre2012.pdf
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October 3, 2012

Dr. Robert Platt

Quantifying discrimination of Framingham risk functions with different survival C statistics
Pencina2012.pdf
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Background Reading:

Pencina2010.pdf
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Pencina2008.pdf
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October 10, 2012

Dr. David Stephens

Maximum Likelihood from Incomplete Data via the EM Algorithm
DLR1977-JRSSB.pdf
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The EM Algorithm--An Old Folk-Song Sung to a Fast New Tune
MengVanDyk1997-JRSSB.pdf
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Presentation
Stephens2012.pdf
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October 17, 2012

Dr. William Astle

Common SNPs explain a large proportion of the heritability for human height
Yang2010.pdf
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Presentation
Astle2012.pdf
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Background Reading:

Manolio2009.pdf
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Pritchard2002.pdf
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October 24, 2012

Dr. Russell Steele

Multiple imputation: a primer
Schafer1999.pdf
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Review of inverse probability weighting for dealing with missing data
Seaman2001.pdf
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A comparison of multiple imputation and doubly robust estimation for analyses with missing data
Carpenter2006.pdf
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October 31, 2012

Dr. Olli Saarela

Spearman and the origin and development of factor analysis
Bartholomew1995.pdf
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Presentation
Saarela2012.pdf
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November 7, 2012

Dr. Benjamin Rich

Estimating treatment effects for individual patients based on the results of randomised clinical trials
Dorresteijn2011.pdf
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Presentation
Rich2012.pdf
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Appendix1.pdf
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Appendix2.pdf
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Appendix3.pdf
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Background Reading:

Julien2008.pdf
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November 14, 2012

Dr. Andrea Benedetti

Using generalized additive models to reduce residual confounding
Benedetti2004.pdf
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Tutorial in biostatistics: spline smoothing with linear mixed models
Gurrin2005.pdf
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November 21, 2012

Dr. Aurélie Labbe

 

Q&A: Promise and pitfalls of genome-wide association studies
Brookfield2010.pdf
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Learning from our GWAS mistakes: from experimental design to scientific method
Lambert2012.pdf
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Presentation
Labbe2012.pdf
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November 28, 2012

Dr. Celia Greenwood

Controlling the false discovery rate: a practical and powerful approach to multiple testing
Benjamini1995.pdf
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Presentation
Greenwood2012.pdf
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