get_infect_mat: Create infect matrix

In HopkinsIDD/tti: Test-trace-isolate Recursive Equations

Create infect matrix

Description

This function will create the INFECT matrix

Usage

get_infect_mat(
  alpha = 0.2,
  R = 2.5,
  kappa = 0.5,
  eta = 0.5,
  nu = 4,
  t_ds = 3,
  t_da = 3,
  t_qcs = 3,
  t_qca = 3,
  t_qhs = 3,
  t_qha = 3,
  t_q = 3,
  t_incubation = 5.5,
  offset = -2.31,
  shape = 1.65,
  rate = 0.5,
  isolation_days = Inf
)

Arguments

alpha	Numeric value between 0 and 1. The probability of an asymptomatic infection. Default 0.2.
R	Positive numeric value. Reproduction number. Default: 2.5.
kappa	Positive numeric value. Relative transmissibility of an asymptomatic individual compared to a symptomatic individual. Default: 0.5.
eta	Numeric value between 0 and 1. Probability contact is a household contact. Default: 0.5
nu	Positive numeric value. Relative risk of infection for a household contact compared to a community contact. Default: 4.
t_ds	Non-negative numeric value. Time delay from symptom onset to isolation in detected symptomatic person. Default: 3.
t_da	Non-negative numeric value. Time delay from symptom onset to isolation in detected asymptomatic person. Default: 3.
t_qcs	Non-negative numeric value. Time delay from symptomatic index cases's symptom onset to quarantine of community contacts. Default: 3.
t_qca	Non-negative numeric value. Time delay from asymptomatic index cases's symptom onset to quarantine of community contacts. Default: 3.
t_qhs	Non-negative numeric value. Time delay from symptomatic index cases's symptom onset to quarantine of household contacts. Default: 3.
t_qha	Non-negative numeric value. Time delay from asymptomatic index cases's symptom onset to quarantine of community contacts. Default: 3.
t_q	Non-negative numeric value. Time delay from quarantined index cases's symptom onset to quarantine of contacts. Default: 3.
t_incubation	Non-negative numeric value. The estimated average incubation time. Default: 5.5.
offset	Numeric. Offset of infectiousness compared to symptoms onset. Default is -2.31.
shape	Numeric. Shape of the gamma distribution of infectious period. Default is 1.65.
rate	Numeric. Rate of the gamma distribution of infectious period. Default is 0.5.
isolation_days	Numeric greater than 0. Number of days from symptom onset to end of isolation. Default is Inf implying isolation until no longer infectious.

Value

Matrix

HopkinsIDD/tti documentation built on May 24, 2022, 1:11 a.m.