epiR - RSurveillance function mapping

Evan Sergeant and Mark Stevenson

2021-07-19

The following tables lists each of the functions in RSurveillance and their equivalent in epiR.

Representative sampling

Sample size estimation

Functions to estimate sample size using representative population sampling data.
Sampling Outcome RSurveillance epiR
Representative Prob disease freedom n.pfree rsu.sspfree.rs
Representative SSe n.freedom rsu.sssep.rs
Two stage representative SSe n.2stage rsu.sssep.rs2st
Representative SSe n.freecalc rsu.sssep.rsfreecalc
Pooled representative SSe n.pooled rsu.sssep.rspool

Estimation of surveillance system sensitivity

Functions to estimate surveillance system sensitivity (SSe) using representative population sampling data.
Sampling Outcome RSurveillance epiR
Representative SSe sep.binom rsu.sep.rs
Representative SSe sep.hypergeo rsu.sep.rs
Representative SSe sep rsu.sep.rs
Two stage representative SSe sep.sys rsu.sep.rs2st
Representative SSe sse.combined rsu.sep.rsmult
Representative SSe sep.freecalc rsu.sep.rsfreecalc
Representative SSe sep.binom.imperfect rsu.sep.rsfreecalc
Pooled representative SSe sep.pooled rsu.sep.rspool
Representative SSe sep.var.se rsu.sep.rsvarse
Representative SSp spp rsu.spp.rs
Representative SSp sph.hp rsu.spp.rs

Estimation of the probability of disease freedom

Functions to estimate the probability of disease freedom using representative population sampling data.
Sampling Outcome RSurveillance epiR
Representative Prob disease of freedom pfree.1 rsu.pfree.rs
Representative Prob disease of freedom pfree.calc rsu.pfree.rs
Representative Equilibrium prob of disease freedom pfree.equ rsu.pfree.equ

Risk based sampling

Sample size estimation

Functions to estimate sample size using risk based sampling data.
Sampling Outcome RSurveillance epiR
Risk-based SSe n.rb rsu.sssep.rbsrg
Risk-based SSe n.rb.varse rsu.sssep.rbmrg
Risk-based SSe n.rb.2stage.1 rsu.sssep.rb2st1rf
Risk-based SSe n.rb.2stage.2 rsu.sssep.rb2st2rf

Estimation of surveillance system sensitivity

Functions to estimate surveillance system sensitivity (SSe) using risk based sampling data.
Sampling Outcome RSurveillance epiR
Risk-based SSe sep.rb.bin.varse rsu.sep.rb
Risk-based SSe sep.rb.bin rsu.sep.rb1rf
Risk-based SSe sep.rb.hypergeo rsu.sep.rb1rf
Risk-based SSe sep.rb2.bin rsu.sep.rb2rf
Risk-based SSe sep.rb2.hypergeo rsu.sep.rb2rf
Risk-based SSe sep.rb.hypergeo.varse rsu.sep.rbvarse
Risk-based SSe sse.rb2stage rsu.sep.rb2stage

Census data

Estimation of surveillance system sensitivity

Functions to estimate surveillance system sensitivity (SSe) using census data.
Sampling Outcome RSurveillance epiR
Risk-based SSe sep.exact rsu.sep.cens

Passive surveillance data

Functions to estimate surveillance system sensitivity (SSe) using passively collected surveillance data.
Sampling Outcome RSurveillance epiR
Risk-based SSe sep.passive rsu.sep.pass

Miscellaneous functions

Miscellaneous functions.
Details RSurveillance epiR
Adjusted risk adj.risk rsu.adjrisk
Adjusted risk adj.risk.sim rsu.adjrisk
Series test interpretation, Se se.series rsu.dxtest
Parallel test interpretation, Se se.parallel rsu.dxtest
Series test interpretation, Sp sp.series rsu.dxtest
Parallel test interpretation, Sp sp.parallel rsu.dxtest
Effective probability of infection epi.calc rsu.epinf
Design prevalence back calculation pstar.calc rsu.pstar
Prob disease is less than design prevalence rsu.sep