Simulate a single chain using a branching process while accounting for depletion of susceptibles.
Source:R/simulate_susceptibles.R
chain_sim_susc.RdSimulate a single chain using a branching process while accounting for depletion of susceptibles.
Usage
chain_sim_susc(
offspring = c("pois", "nbinom"),
mn_offspring,
disp_offspring,
serial,
t0 = 0,
tf = Inf,
pop,
initial_immune = 0
)Arguments
- offspring
offspring distribution: a character string corresponding to the R distribution function. Currently only "pois" & "nbinom" are supported. Internally truncated distributions are used to avoid infecting more people than susceptibles available.
- mn_offspring
the average number of secondary cases for each case
- disp_offspring
the dispersion coefficient (var/mean) of the number of secondary cases. Ignored if offspring == "pois". Must be > 1.
- serial
the serial interval. A function that takes one parameter (
n), the number of serial intervals to randomly sample. Value must be >= 0.- t0
start time
- tf
end time
- pop
the population
- initial_immune
the number of initial immunes in the population
Value
a data frame with columns time, id (a unique ID for each
individual element of the chain), ancestor (the ID of the ancestor
of each element), and generation.
Details
This function has a couple of key differences with chain_sim: it can only simulate one chain at a time, it can only handle implemented offspring distributions ("pois" and "nbinom"), it always tracks and returns a data frame containing the entire tree, the maximal length of chains is limited with pop instead of infinite.