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(Freedom) FreedomTrail
Table of Contents
Title Page
Introduction
List of abbreviations
List of Tables
List of Figures
List of Formulae
Fundamentals and terminology
Main concept
Theory of freedom
Condition of interest
Measures of disease occurrence
What we mean by free
Probability and distributions
Prevalence
Quality of estimates
Conditional probability
Bayes theorem
Probability density function
PDF of a dichotomous variable
PDF of a binomial variable
Tests, sensitivity and specificity
Diagnostic test
Evaluation of diagnostic tests
Sensitivity and Specificity
Variance of accuracy measures
Apparent prevalence
Operational diagnostic test parameters
Testing systems
Multiple diagnostic tests
Herd testing
Bayes theorem and predictive values
Positive predictive value
Negative predictive value
The link between pre and posttest probability of disease
Application of predictive values in disease surveillance
Design prevalence
Definition and legal issues
Biological issues
Statistical issues and application
Describing differential risk
Internal time period for analysis
Surveys
Ongoing surveillance
Statistical evidence from surveys and surveillance
Documenting evidence for disease freedom in small herds
Bayesian inference
The beta prior for proportions
How to get the prior?
Obtaining the posterior
Markov chain Monte Carlo
Surveillance, Monitoring and Surveys
Data collection for Surveillance
Targeted Surveillance
The impact of the change in trade regulations on surveillance planning and implementation
Methodological approach
Identifying potential data sources
Drawing up a scenario tree
Estimating branch probabilities and proportions
Analysing results of application of the SSC
Simulated data
Describing surveillance system components
Scope of the model
Unit of analysis
Coverage
Accounting for lack of coverage
Temporal applicability
Outcomes
Specificity
Development of scenario trees
Functions of a scenario tree in analysis of a SSC
Node types
Infection nodes
Detection nodes
Category nodes
Risk category nodes
Detection category nodes
Grouping levels
Ordering of nodes
Factors to include
Estimation of branch probabilities
Using available data
Expert opinion
Design Prevalence
Determining the design prevalence
Small herds
Incorporating differential risk
Multiple risk nodes
Building of scenario trees
Root node
Completion and truncation
Analysing the tree
Analysing the tree assuming independence
Advanced approach  accounting for lack of independence among units
Calculation of unit sensitivity
Stepwise calculation of system sensitivity
Calculation of group level sensitivity
Binomial approach
Hypergeometric approach
Exact method
Calculating sensitivity at higher grouping levels
Binomial
Hypergeometric
Exact
Approaches to calculating component sensitivity
Calculating Countrylevel sensitivity
Category proportions
Sensitivity ratio
Combination of data from multiple sources
Accounting for lack of independence
Incorporating data from representative surveys
Calculation of the probability of country freedom
Selection of a prior
Temporal discounting of historical surveillance data
Introduction
Method
Probability of disease introduction  interface with IRA
?
Acceptable Level of Protection
Stochastic modelling in the context of disease freedom
Stochastic modelling in the context of disease freedom  Principles
Practical implementation
Data from multiple sources
Sampling probability on animal level
Sampling probability on herd level and for population strata
Baseline dependence among surveillance components
Dependence among diagnostic methods
Estimating the surveillance system's sensitivity under dependence
Current issues
Independence of tests
Independence of surveillance system components
Eliciting and combining expert opinion
Nonquantitative analyses
References & Bibliography
Project Credits
Appendices
Suggested notation
Variable names
Design prevalence
Sensitivity notation
Probabilities
Branch proportions
Risk nodes
Stochastic modelling using @Risk
For those not familiar with @Risk
Inputs and Outputs
Distribution functions
@Risk statistics functions
Simulation files
Sensitivity analysis
Correlated inputs
Using PopTools for stochastic spreadsheet simulation
Australian Biosecurity CRC
International EpiLab in Denmark
Projects of the International
EpiLab
related to disease freedom
International EpiLab Project 3 (CSF; Cameron)
International EpiLab Project 4 (HPAI; Martin)
International EpiLab Project 5 (IBR; Salman)
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Page last modified on September 18, 2008, at 03:55 PM by jenny