transCurrent: Generate the first infected individual in a transmission tree...

In Huimin-stat/simTransmission: Simulate Transmission Tree

Description

Generate the first infected individual in a transmission tree with consideration of asyptomatic/unsampled individuals

Usage

transCurrent(
  inftime = 0,
  inf_rate,
  inf_rate_timeInt,
  diag_rate,
  rec_rate_asy,
  rec_rate_sym,
  death_prop,
  death_rate,
  inf_rate_diag,
  asy_prop,
  currentnode,
  ancestor
)

Arguments

inftime	the start time of infection/outbreak
inf_rate	per day infective rate per infected capita; could be a constant or vector
inf_rate_timeInt	time intervals correspond to the start and end time of each infectious rate; matrix
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
currentnode	current node number of infected individual
ancestor	node number of individual who infected the current person

Value

a list containing transmission information vector and input parameter vector to generate random numbers/times of next generation from uniform distribution

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