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
