calc_risk_mult: Calculate risk from mulitple pathogen exposures

In bryanmayer/multdr: Simulating and fitting multiple exposure infectious disease dose-response models

Description

This function takes mulitple pathogen exposure and calculates the risk of infection over their persistence within host

Usage

calc_risk_mult(exposure_series, exposure_times, survival_time = Inf,
  hazard_risk, clr, na.zero = F, log.surv = F)

Arguments

exposure_series	The values of repeated pathogen exposures
exposure_times	The times of exposures
survival_time	the final time to calculate survival to (default infinity)
hazard_risk	The per time risk of exposure during persistence
clr	The clearance rate of exposure

Details

The risk for a single exposure is derived in calc_risk. The accumulation of exposure assuming exponential clearance is independent.

S(t) = exp(-β/c *sum(i = 1..n) p_i *(1 - exp(-c(T - t_i))

which simplifies as T -> Inf to

S(T) = exp(-β/c *sum(i = 1..n) p_i)

Value

risk calculation over the time specified in survival time

See Also

calc_risk for single exposures.

Examples

##Single exposure examples
calc_risk_mult(1e8, 0, 1, 1e-8, 1) # should return same as calc_risk(1e8, 1, 1e-8, 1)
calc_risk_mult(1e8, 1, 2, 1e-8, 1) # should return same as calc_risk(1e8, 1, 1e-8, 1)
## multiple exposures
exposures = c(1e7, 1e9, 1e5); exp_times = c(0, 1, 2)
calc_risk_mult(exposures, exp_times, 3, hazard_risk = 1e-9, clr = 1)
calc_risk_mult(exposures, exp_times, hazard_risk = 1e-9, clr = 1) #total risk
1-exp(-1e-9/1 * sum(exposures))

bryanmayer/multdr documentation built on May 13, 2019, 8:11 a.m.