PathogenDose: Probability of illness from exposure to wastewater

In kcrank1/QMRAswim: Model Illness Probability from Swimming in Sewage-Impacted Water

Description

Calculates the probability of illness for a specific pathogen based the amount of wastewater consumed during the swimming event

Usage

PathogenDose(doseresp = "exp", alpha, beta = 0, Pillinf,
  path_sewage_dist = "lunif", p_alpha, p_beta, dose)

Arguments

doseresp	The dose response model being used. Type "exp" for single parameter exponential, "bp" for two parameter beta-poisson, or "f1" for the two parameter hypergeometric1F1, commonly used for norovirus
alpha	First parameter for the dose response
beta	Second parameter for the dose response. Leave blank if using single paramter exponential dose response
Pillinf	The fraction of infections that become illnesses If Pillinf is a distribution not a single value, use the function Fraction to generate a monte carlo table. Can be a single value or a monte carlo vector generated from the frac function. P _ill/inf The probability of illness if infected. Fraction in decimal form. i.e. for norovirus, 60 percent of infections become illnesses, so frac=0.6 (McBride et al. 2013)
path_sewage_dist	The distribution of the pathogen in sewage. Choose either 'lunif' for a uniform distribution or 'lnorm' for a normal distribution
p_alpha	The first parameter value for the distribution of pathogen in sewage. For 'lunif' alpha_sew is the min concentration in log 10 copies/L, for 'lnorm' it is the mean value in log 10 copies/L.
p_beta	The second parameter value for the distribution of pathogen in sewage. For 'lunif' beta_sew is the max concentration in log 10 copies/L, for 'lnorm' it is the standard deviation in log 10 units.
dose	Returned dose from Wastewater Dose function. Defaults to WWdose

Details

This function computes the probability of illness from exposure to wastewater

Value

Probability of illness pill1. Vector contains count number of samplings. To calculate illness from n number of pathogens, use the formula totpill=1-((1-pill1)(1-pill2)(1-pill3)(1-pill4)...)

kcrank1/QMRAswim documentation built on Aug. 1, 2020, 5:07 a.m.