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.
|Date of publication||2016-10-04 00:15:41|
|Maintainer||Evan Sergeant <firstname.lastname@example.org>|
|License||GPL-2 | GPL-3|
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