| 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... |
| n.c.hp | Hypergeometric (HerdPlus) optimum sample size and cut-point... |
| n.freecalc | Freecalc sample size for a finite population and specified... |
| n.freedom | Freedom sample size |
| n.hp | Hypergeometric (HerdPlus) sample size for finite population... |
| n.hypergeo | Hypergeometric sample size |
| n.pfree | Sample size to achieve desired (posterior) probability of... |
| 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... |
| n.rb.2stage.2 | Sample size for 2-stage risk-based surveillance, allowing for... |
| 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 |
| sep | Population sensitivity |
| se.parallel | Sensitivity of tests in parallel |
| 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... |
| sep.hypergeo | Hypergeometric Population sensitivity |
| sep.passive | Passive surveillance sensitivity |
| sep.pfree | Population sensitivity to achieve desired (posterior)... |
| sep.pooled | Pooled population sensitivity |
| sep.prior | Population sensitivity to achieve desired prior probability... |
| sep.rb2.binom | Binomial risk-based population sensitivity for 2 risk factors |
| sep.rb2.hypergeo | Hypergeometric risk-based population sensitivity for 2 risk... |
| sep.rb.bin | Binomial risk-based population sensitivity |
| sep.rb.bin.varse | Binomial risk-based population sensitivity for varying unit... |
| sep.rb.hypergeo | Hypergeometric risk-based population sensitivity |
| sep.rb.hypergeo.varse | Hypergeometric risk-based population sensitivity for varying... |
| sep.sys | 2-stage population sensitivity |
| sep.var.se | Population sensitivity for varying unit sensitivity |
| se.series | Sensitivity of tests in series |
| sph.binom | Binomial population specificity for imperfect test |
| sph.hp | Hypergeometric population specificity calculation |
| spp | Population specificity |
| sp.parallel | Specificity of tests in parallel |
| sp.series | Specficity of tests in series |
| sse.combined | System sensitivity by combining multiple surveillance... |
| sse.rb.2stage | Two-stage risk-based system sensitivity |
| tp | True prevalence |
| tp.normal | Normal approximation confidence limits for true prevalence |
