Lawrence Joseph
Bayesian statistics


Please Note: Prof. Joseph has retired.
These pages are left up in case they prove
useful, but the pages and software will
no longer be updated. All material and
software is "as is" with no guarantees
of functionality or correctness.
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Bayesian Sample Size Change-point methods and applications Diagnostic testing
See related papers		 Diagnostic testing in Genetics
Complete CV
Research interests
Courses taught
Previous courses taught
EPIB-607 Principles of Inferential Statistics in Medicine
EPIB-613 Introduction to Statistical Software
EPIB-621 Data Analysis in the Health Sciences
EPIB-651 Bayesian Analysis in Medicine
EPIB-668 Introduction to Bayesian Analysis in the Health Sciences
EPIB-669 Intermediate Bayesian Analysis for the Health Sciences
EPIB-675 Bayesian Analysis in the Health Sciences
EPIB-682 Introduction to Bayesian Analysis in the Health Sciences
EPIB-683 Intermediate Bayesian Analysis for the Health Sciences
Publications
Methodological publications
Bayesian Sample Size
Change-point methods and applications
Diagnostic testing
Meta analysis
Other topics
Medical publications
Allergy and immunology
Asthma
Cardiology
Gastroenterology
Osteoporosis
Quality of Life
Rheumatology
Other
Book
Bayesian software
Bayesian Sample Size
Change-point methods and applications
Diagnostic testing
Diagnostic testing in Genetics
Links
Please Note: Prof. Joseph has retired. These software packages remain available in case they prove
useful, but the software will no longer be updated or supported. All material and software is "as is"
with no guarantees of functionality or correctness.
ExposureAssessment
Exposure Assessment from continuous data in the absence of a gold standard test
Version 2.1, September 2017
A software package for estimating exposure probabilities in a series of subjects where one or more continuous test measurements relating to the exposure of interest are available for each subject
This package is an implementation of the methods presented in
Bayesian estimation of the probability of asbestos exposure from lung fiber counts
Weichenthal S, Joseph L, Bélisle P, Dufresne A
Biometrics 2010;66(2):603-612
Instructions
InstructionManual.pdf
Files
ExposureAssessment.zip
Install instructions
  1. follow these install instructions for software necessary for this package to work properly (and ignore the Install Instructions found in the files provided with the package as they are slightly outdated)
  2. download and unzip the zipped file (above)
  3. double-click setup.exe
BayesDiagnosticTests
Estimation of Disease Prevalence and the Parameters of One, Two or Three Diagnostic Tests
Version 3.11.1, September 2017
A package to calculate Bayesian posterior distributions via Gibbs sampling for the prevalence of a disease, and sensitivity, specificity, positive and negative predictive values for each test used for that disease, in the absence of a gold standard; requires that the free software packages Winbugs and Perl be installed.
Replaces tt1, tt2 and tt3.
Instructions
InstructionManual.pdf
Files
BayesDiagnosticTests.zip
Install instructions
  1. follow these install instructions for software necessary for this package to work properly (and ignore the Install Instructions found in the files provided with the package as they are slightly outdated)
  2. download and unzip the zipped file (above)
  3. double-click setup.exe
BayesContinuousDiagnosticTest
Estimation of Disease Prevalence and the Parameters of a Continuous Diagnotic Test and One or Two Dichotomous Diagnostic Test(s)
Version 3.9, September 2017
A software package to calculate marginal Bayesian posterior distributions via Gibbs sampling when data are available from a continuous diagnostic test and one or two dichotomous diagnostic test(s) in the absence of a gold standard; requires that the free software packages R, Winbugs and Perl be installed.
Instructions
InstructionManual.pdf
Files
BayesContinuousDiagnosticTest.zip
Install instructions
  1. follow these install instructions for software necessary for this package to work properly (and ignore the Install Instructions found in the files provided with the package as they are slightly outdated)
  2. download and unzip the zipped file (above)
  3. double-click setup.exe
BayesLatentClassModels
A program for estimating diagnostic test properties and disease prevalence in the presence of possibly correlated tests
Version 1.13, December 2015
A software package for estimating diagnostic test properties and disease prevalence in the presence of possibly correlated tests in the absence of a gold standard; requires that the free software packages R and Perl be installed.
Please refer to Nandini Dendukuri's webpage for instructions and files for this software.
PredictiveValues
Computation of Predictive Values when using One, Two or Three Diagnostic Tests
Version 2.1, September 2017
A program designed to convert information on a disease prevalence and one, two or three diagnosic tests into information on predictive values (i.e., on the probability for a patient of being truly positive given a series of diagnostic tests results)
Instructions
InstructionManual.pdf
Files
PredictiveValues.zip
Install instructions
  1. download and unzip the zipped file (above)
  2. double-click setup.exe
  3. follow the instructions in file doc\InstructionManual.pdf
Sample size determination for inference on prevalence or diagnostic test sensitivity or specificity
A package to calculate sample sizes based on highest posterior density intervals in the context of diagnostic testing in presence of one or two imperfect tests; requires that the free software packages R, Winbugs and Perl be installed.
See