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RSurveillance (version 0.2.1)

Design and Analysis of Disease Surveillance Activities

Description

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. This package is based on Cameron A., Conraths F., Frohlich A., Schauer B., Schulz K., Sergeant E., Sonnenburg J., Staubach C. (2015). R package of functions for risk-based surveillance. Deliverable 6.24, WP 6 - Decision making tools for implementing risk-based surveillance, Grant Number no. 310806, RISKSUR (). Many of the 'RSurveillance' functions are incorporated into the 'epitools' website: Sergeant, ESG, 2019. Epitools epidemiological calculators. Ausvet Pty Ltd. Available at: .

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install.packages('RSurveillance')

Monthly Downloads

148

Version

0.2.1

License

GPL-2 | GPL-3

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Last Published

June 30th, 2020

Functions in RSurveillance (0.2.1)

n.ap

Sample size for apparent prevalence
epi.calc

Effective probability of infection (EPI)
n.2stage

2-stage freedom sample size
binom.jeffreys

Jeffreys confidence limits
binom.agresti

Agresti-Coull confidence limits
adj.risk

Adjusted risk
n.freedom

Freedom sample size
disc.prior

Discounted prior probability of freedom
binom.cp

Clopper-Pearson exact confidence limits
ap

Apparent prevalence
se.series

Sensitivity of tests in series
n.hp

Hypergeometric (HerdPlus) sample size for finite population and specified cut-point number of positives
n.pooled

Sample size for pooled testing for freedom
pfree.calc

Probability of freedom over time
se.parallel

Sensitivity of tests in parallel
n.hypergeo

Hypergeometric sample size
n.rb.2stage.1

sample size for 2-stage risk-based surveillance, risk factor at cluster level only
pfree.1

Probability of freedom for single time period
n.binom

Binomial sample size
adj.risk.sim

Adjusted risk for simulation models
sep.binom.imperfect

Binomial population sensitivity for imperfect test
n.c.freecalc

Freecalc optimum sample size and cut-point number of positives
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.pfree

Sample size to achieve desired (posterior) probability of freedom
n.rb

Risk-based sample size
pfree.equ

Equilibrium probability of freedom
sep.binom

Binomial Population sensitivity
n.freecalc

Freecalc sample size for a finite population and specified cut-point number of positives
n.c.hp

Hypergeometric (HerdPlus) optimum sample size and cut-point number of positives
sep

Population sensitivity
sep.exact

Population sensitivity for census (all units tested)
sep.rb.hypergeo.varse

Hypergeometric risk-based population sensitivity for varying unit sensitivity
sse.rb.2stage

Two-stage risk-based system sensitivity
sep.rb2.binom

Binomial risk-based population sensitivity for 2 risk factors
sse.combined

System sensitivity by combining multiple surveillance components
sep.pfree

Population sensitivity to achieve desired (posterior) probability of freedom
pstar.calc

Design prevalence back-calculation
sep.freecalc

FreeCalc population sensitivity for imperfect test
sep.prior

Population sensitivity to achieve desired prior probability of freedom
sep.hp

Hypergeometric (HerdPlus) population sensitivity for imperfect test
sep.rb.bin

Binomial risk-based population sensitivity
sep.rb.bin.varse

Binomial risk-based population sensitivity for varying unit sensitivity
n.rb.varse

Risk-based sample size for varying unit sensitivity
sep.pooled

Pooled population sensitivity
sep.sys

2-stage population sensitivity
spp

Population specificity
sep.rb2.hypergeo

Hypergeometric risk-based population sensitivity for 2 risk factors
sph.hp

Hypergeometric population specificity calculation
n.tp

Sample size for true prevalence
sep.rb.hypergeo

Hypergeometric risk-based population sensitivity
sep.var.se

Population sensitivity for varying unit sensitivity
sep.hypergeo

Hypergeometric Population sensitivity
sep.passive

Passive surveillance sensitivity
tp

True prevalence
sp.parallel

Specificity of tests in parallel
sph.binom

Binomial population specificity for imperfect test
sp.series

Specficity of tests in series
tp.normal

Normal approximation confidence limits for true prevalence