infection.count: Generate whether a participant contracted a infection at...
In SimVitD: Simulation Tools for Planning Vitamin D Studies

infection.count

R Documentation

Generate whether a participant contracted a infection at exposure times.

Generates probabilities of developing infection, the relative risk and whether a participant becomes infected or not at exposure times.

  infection.count( expos, baseline = 0.03, RR = 3, holding.time = 2, lohi.vit = c(10,70) )

`expos`	An object of class `exposure.levels`.
`baseline`	Numeric, baseline prevalence of developing infection at any exposure time. Probability of developing infection when a participant has maximum (fully replete) vitamin D levels.
`RR`	Numeric, the relative risk of the study. The difference between becoming infected at highest and lowest vitamin D levels.
`holding.time`	Numeric, the mean number of weeks for after becoming infected when the participant can not become re-infected. Times are simulated independently from an exponential distribution with this mean.
`lohi.vit`	A vector of length 2 giving the level at which a participant is considered to have insufficient and sufficient vitamin D status levels.

infection.count returns an object of class infection.count that is a list. The list has the following slots.

`baseline`	The baseline prevalence of disease.
`RR`	The relative risk of the study.
`inflection`	The inflection points of the relative risk curve.
`probs`	Matrix, the probability of developing infection at each exposure time for each participant.
`relativerisk`	Matrix, the relative risk of infection at each exposure time for each participant.
`infection`	Matrix, 1 if participant was infected at the corresponding exposure time, 0 if participant was not infected at exposure time.
`count`	Number of infections for each participant over the course of the study.
`mean`	The mean number of infections for the group over the course of the study.