R: Design and Analysis of Disease Surveillance Activities

# Design and Analysis of Disease Surveillance Activities

## Documentation for package ‘RSurveillance’ version 0.2.1

- DESCRIPTION file

## Help Pages

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