Design and Analysis of Disease Surveillance Activities
Adjusted risk
Adjusted risk for simulation models
Apparent prevalence
Agresti-Coull confidence limits
Clopper-Pearson exact confidence limits
Jeffreys confidence limits
Discounted prior probability of freedom
Effective probability of infection (EPI)
2-stage freedom sample size
Sample size for apparent prevalence
Binomial sample size
Freecalc optimum sample size and cut-point number of positives
Hypergeometric (HerdPlus) optimum sample size and cut-point number of ...
Freecalc sample size for a finite population and specified cut-point n...
Freedom sample size
Hypergeometric (HerdPlus) sample size for finite population and specif...
Hypergeometric sample size
Sample size to achieve desired (posterior) probability of freedom
Sample size for pooled testing for freedom
sample size for 2-stage risk-based surveillance, risk factor at cluste...
Sample size for 2-stage risk-based surveillance, allowing for risk fac...
Risk-based sample size
Risk-based sample size for varying unit sensitivity
Sample size for true prevalence
Probability of freedom for single time period
Probability of freedom over time
Equilibrium probability of freedom
Design prevalence back-calculation
Sensitivity of tests in parallel
Sensitivity of tests in series
Binomial population sensitivity for imperfect test
Binomial Population sensitivity
Population sensitivity for census (all units tested)
FreeCalc population sensitivity for imperfect test
Hypergeometric (HerdPlus) population sensitivity for imperfect test
Hypergeometric Population sensitivity
Passive surveillance sensitivity
Population sensitivity to achieve desired (posterior) probability of f...
Pooled population sensitivity
Population sensitivity to achieve desired prior probability of freedom
Binomial risk-based population sensitivity
Binomial risk-based population sensitivity for varying unit sensitivit...
Hypergeometric risk-based population sensitivity
Hypergeometric risk-based population sensitivity for varying unit sens...
Binomial risk-based population sensitivity for 2 risk factors
Hypergeometric risk-based population sensitivity for 2 risk factors
Population sensitivity
2-stage population sensitivity
Population sensitivity for varying unit sensitivity
Specificity of tests in parallel
Specficity of tests in series
Binomial population specificity for imperfect test
Hypergeometric population specificity calculation
Population specificity
System sensitivity by combining multiple surveillance components
Two-stage risk-based system sensitivity
Normal approximation confidence limits for true prevalence
True prevalence
A range of functions for the design and analysis of disease surveillance activities. These functions were originally developed for animal health surveillance activities but can be equally applied to aquatic animal, wildlife, plant and human health surveillance activities. Utilities are included for sample size calculation and analysis of representative surveys for disease freedom, risk-based studies for disease freedom and for prevalence estimation. This package is based on Cameron A., Conraths F., Frohlich A., Schauer B., Schulz K., Sergeant E., Sonnenburg J., Staubach C. (2015). R package of functions for risk-based surveillance. Deliverable 6.24, WP 6 - Decision making tools for implementing risk-based surveillance, Grant Number no. 310806, RISKSUR (<https://www.fp7-risksur.eu/sites/default/files/documents/Deliverables/RISKSUR_%28310806%29_D6.24.pdf>). Many of the 'RSurveillance' functions are incorporated into the 'epitools' website: Sergeant, ESG, 2019. Epitools epidemiological calculators. Ausvet Pty Ltd. Available at: <http://epitools.ausvet.com.au>.