RSurveillance: Design and Analysis of Disease Surveillance Activities

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.

AuthorEvan Sergeant
Date of publication2016-10-04 00:15:41
MaintainerEvan Sergeant <evan@ausvet.com.au>
LicenseGPL-2 | GPL-3
Version0.2.0

View on CRAN

Man 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...

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

Files in this package

RSurveillance
RSurveillance/tests
RSurveillance/tests/RSurveillance.R
RSurveillance/NAMESPACE
RSurveillance/R
RSurveillance/R/prevalence_functions.R RSurveillance/R/n_rb2stage.R RSurveillance/R/adj_risk_sim.R RSurveillance/R/freedom_functions_2.R RSurveillance/R/risk_based_functions.R RSurveillance/R/sep_passive.R RSurveillance/R/freedom_functions_1.R RSurveillance/R/sse_rb2stage.R
RSurveillance/MD5
RSurveillance/DESCRIPTION
RSurveillance/man
RSurveillance/man/sep.prior.Rd RSurveillance/man/disc.prior.Rd RSurveillance/man/n.2stage.Rd RSurveillance/man/sep.exact.Rd RSurveillance/man/binom.jeffreys.Rd RSurveillance/man/sph.binom.Rd RSurveillance/man/epi.calc.Rd RSurveillance/man/sep.pooled.Rd RSurveillance/man/sse.combined.Rd RSurveillance/man/sep.pfree.Rd RSurveillance/man/n.rb.varse.Rd RSurveillance/man/n.freecalc.Rd RSurveillance/man/n.rb.Rd RSurveillance/man/pfree.calc.Rd RSurveillance/man/tp.Rd RSurveillance/man/n.pooled.Rd RSurveillance/man/pstar.calc.Rd RSurveillance/man/n.c.hp.Rd RSurveillance/man/sep.binom.imperfect.Rd RSurveillance/man/binom.agresti.Rd RSurveillance/man/sep.var.se.Rd RSurveillance/man/tp.normal.Rd RSurveillance/man/sep.rb.hypergeo.Rd RSurveillance/man/n.rb.2stage.2.Rd RSurveillance/man/sph.hp.Rd RSurveillance/man/sep.passive.Rd RSurveillance/man/se.series.Rd RSurveillance/man/sep.Rd RSurveillance/man/spp.Rd RSurveillance/man/sep.hypergeo.Rd RSurveillance/man/adj.risk.sim.Rd RSurveillance/man/adj.risk.Rd RSurveillance/man/sse.rb.2stage.Rd RSurveillance/man/sep.rb2.binom.Rd RSurveillance/man/binom.cp.Rd RSurveillance/man/n.binom.Rd RSurveillance/man/n.hypergeo.Rd RSurveillance/man/n.freedom.Rd RSurveillance/man/pfree.equ.Rd RSurveillance/man/pfree.1.Rd RSurveillance/man/sp.series.Rd RSurveillance/man/n.tp.Rd RSurveillance/man/ap.Rd RSurveillance/man/sep.sys.Rd RSurveillance/man/sep.freecalc.Rd RSurveillance/man/n.c.freecalc.Rd RSurveillance/man/n.ap.Rd RSurveillance/man/sep.rb.bin.Rd RSurveillance/man/sep.rb2.hypergeo.Rd RSurveillance/man/se.parallel.Rd RSurveillance/man/sep.hp.Rd RSurveillance/man/n.pfree.Rd RSurveillance/man/sep.rb.bin.varse.Rd RSurveillance/man/sep.rb.hypergeo.varse.Rd RSurveillance/man/sep.binom.Rd RSurveillance/man/sp.parallel.Rd RSurveillance/man/n.rb.2stage.1.Rd RSurveillance/man/n.hp.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.