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Simulate transmission chains using a stochastic branching process

Source: R/utils.R
dot-chain_sim.Rd

Code modified from the bpmodels::chain_sim() function. The function chain_sim() function from bpmodels is reused with permission and licensed under MIT as is bpmodels. bpmodels is not on CRAN and is retired.

Usage

.chain_sim(
  n,
  offspring,
  stat = c("size", "length"),
  stat_threshold = Inf,
  generation_time,
  tf = Inf,
  ...
)

Arguments

n

Number of simulations to run.

offspring

Offspring distribution: a character string corresponding to the R distribution function (e.g., "pois" for Poisson, where rpois() is the R function to generate Poisson random numbers).

stat

String; Statistic to calculate. Can be one of:

  • "size": the total number of offspring.

  • "length": the total number of ancestors.

stat_threshold

A size or length above which the simulation results should be set to Inf. Defaults to Inf, resulting in no results ever set to Inf.

generation_time

The generation time generator function; the name of a user-defined named or anonymous function with only one argument n, representing the number of generation times to generate.

tf

End time (if generation_time interval is given).

...

Parameters of the offspring distribution as required by R.

Value

A <data.frame> with columns n (simulation ID), id (a unique ID within each simulation for each individual element of the chain), ancestor (the ID of the ancestor of each element), and generation. A time column is also appended if the generation_time interval is supplied to serial.

Author

Sebastian Funk, James M. Azam, Joshua W. Lambert