epiR - RSurveillance function mapping

Evan Sergeant and Mark Stevenson

2021-11-10

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`