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.

Author
Evan Sergeant
Date of publication
2016-10-04 00:15:41
Maintainer
Evan Sergeant <evan@ausvet.com.au>
License
GPL-2 | GPL-3
Version
0.2.0

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