Design and Analysis of Disease Surveillance Activities

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Documentation for package ‘RSurveillance’ version 0.2.1

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adj.risk Adjusted risk
adj.risk.sim Adjusted risk for simulation models
ap Apparent prevalence
binom.agresti Agresti-Coull confidence limits
binom.cp Clopper-Pearson exact confidence limits
binom.jeffreys Jeffreys confidence limits
disc.prior Discounted prior probability of freedom
epi.calc Effective probability of infection (EPI)
n.2stage 2-stage freedom sample size
n.ap Sample size for apparent prevalence
n.binom Binomial sample size
n.c.freecalc Freecalc optimum sample size and cut-point number of positives
n.c.hp Hypergeometric (HerdPlus) optimum sample size and cut-point number of positives
n.freecalc Freecalc sample size for a finite population and specified cut-point number of positives
n.freedom Freedom sample size
n.hp Hypergeometric (HerdPlus) sample size for finite population and specified cut-point number of positives
n.hypergeo Hypergeometric sample size
n.pfree Sample size to achieve desired (posterior) probability of freedom
n.pooled Sample size for pooled testing for freedom
n.rb Risk-based sample size
n.rb.2stage.1 sample size for 2-stage risk-based surveillance, risk factor at cluster level only
n.rb.2stage.2 Sample size for 2-stage risk-based surveillance, allowing for risk factors at either or both cluster and unit level
n.rb.varse Risk-based sample size for varying unit sensitivity
n.tp Sample size for true prevalence
pfree.1 Probability of freedom for single time period
pfree.calc Probability of freedom over time
pfree.equ Equilibrium probability of freedom
pstar.calc Design prevalence back-calculation
se.parallel Sensitivity of tests in parallel
se.series Sensitivity of tests in series
sep Population sensitivity
sep.binom Binomial Population sensitivity
sep.binom.imperfect Binomial population sensitivity for imperfect test
sep.exact Population sensitivity for census (all units tested)
sep.freecalc FreeCalc population sensitivity for imperfect test
sep.hp Hypergeometric (HerdPlus) population sensitivity for imperfect test
sep.hypergeo Hypergeometric Population sensitivity
sep.passive Passive surveillance sensitivity
sep.pfree Population sensitivity to achieve desired (posterior) probability of freedom
sep.pooled Pooled population sensitivity
sep.prior Population sensitivity to achieve desired prior probability of freedom
sep.rb.bin Binomial risk-based population sensitivity
sep.rb.bin.varse Binomial risk-based population sensitivity for varying unit sensitivity
sep.rb.hypergeo Hypergeometric risk-based population sensitivity
sep.rb.hypergeo.varse Hypergeometric risk-based population sensitivity for varying unit sensitivity
sep.rb2.binom Binomial risk-based population sensitivity for 2 risk factors
sep.rb2.hypergeo Hypergeometric risk-based population sensitivity for 2 risk factors
sep.sys 2-stage population sensitivity
sep.var.se Population sensitivity for varying unit sensitivity
sp.parallel Specificity of tests in parallel
sp.series Specficity of tests in series
sph.binom Binomial population specificity for imperfect test
sph.hp Hypergeometric population specificity calculation
spp Population specificity
sse.combined System sensitivity by combining multiple surveillance components
sse.rb.2stage Two-stage risk-based system sensitivity
tp True prevalence
tp.normal Normal approximation confidence limits for true prevalence