simTransmission: Simulate a transmission tree considering...

In Huimin-stat/simTransmission: Simulate Transmission Tree

Description

Takes in infection rate, recovery rate of symptomatic and asymptomatic group, asymptomatic proportion among infeted people and number of generation to generate a transmission tree

Usage

simTransmission(
  inf_rate,
  inf_rate_time = 0,
  diag_rate,
  rec_rate_asy,
  rec_rate_sym,
  death_prop,
  death_rate,
  inf_rate_diag,
  asy_prop,
  ngeneration
)

Arguments

inf_rate	per day infective rate per infected capita; could be a constant or vector
inf_rate_time	time points corresponds to the start time of each infectious rate when it is not a constant
diag_rate	per day diagnosis rate per capita for symptomatic/sampled individuals; constant
rec_rate_asy	per day recovery rate per capita for asymptomatic/unsampled individulas; constant
rec_rate_sym	per day recovery rate per capita for symptomatic/unsampled individulas after diagnosis; constant
death_prop	proportion of dead cases among diagnosed people; constant
death_rate	death rate per day per capita (inverse of the average time/days to death); constant
inf_rate_diag	infection rate per day per capita for symptomatic individuals after diagnosis; constant
asy_prop	aysmptomatic propotion among infected individuals; constant
ngeneration	number of generation that get infected counted from the first infected individual

Value

transmission matrix including infection time, recovery/dead time, number of people infected by current individual, current node number of current individual, node number of individual who infected the current person (ancestor), asymptomatic information, diagnosed time and death information of current person

Huimin-stat/simTransmission documentation built on Sept. 23, 2020, 12:43 a.m.