Skip to contents

Calculate probability of infection given physical contact \(\sigma^{DC}\)

Source: R/calc_sigma_dc.R
calc_sigma_dc.Rd

calc_sigma_dc will calculate one value for probability of infection using defaults if no arguments are provided. Defaults are described in the sir_model_description document and are sourced from the literature or expert elicitation.

Usage

calc_sigma_dc(
  V_DC = NULL,
  C_nu = NULL,
  pfu_conv = NULL,
  k = NULL,
  nsamples = NULL,
  seed = NULL
)

Arguments

V_DC

Transferred volume (ml). Default is 0.1

C_nu

viral load in sputum; RNA copies/ml. Default samples from expert elicited distribution of parameter 'Viral Load'. Concentration of infectious particles in sputum (gc per ml)

pfu_conv

conversion value (PFU per GC). Set to 1/10^5.2

k

set to 410 as the default

nsamples

number of samples wanted. Default is set to 1

seed

sets a seed for random draws of parameter from default distributions.

Value

returns a number or vector of probability values for probability of infection via direct contact.

Details

Mathematical background to calculate this infection probability given physical contact. We use a Wells-Riley dose response model that estimates infection probability as a log-logistic function of dose (\(d^{dc}\); plaque-forming units, PFU) and the dose-response function (\(k\); Watanabe et al. 2010). The dose received is the product of a typical volume of sputum transferred given contact (\(V^{DC}\)) and the concentration of SARS-CoV-2 in sputum (\(C_{\nu}\)). We initially assume that at each contact \(100\mu l\) of sputum is transferred between individuals making contact. $$\sigma^{DC} = 1 - e^{-(d^{DC}/k)}$$ where $$d^{DC} = V^{DC} \cdot C_{\nu} \cdot pfuConv$$

Examples