.new_epichains {epichains}R Documentation

Construct an ⁠<epichains>⁠ object

Description

new_epichains() constructs an ⁠<epichains>⁠ object from a supplied ⁠<data.frame>⁠ and extra attributes passed as individual arguments. It is meant to be lazy and performant, by creating the object without checking the arguments for correctness. It is not safe to call new_epichains() on its own as is called within epichains() after the arguments have been checked. To create an ⁠<epichains>⁠ object, use epichains().

Usage

.new_epichains(
  sim_df,
  n_chains,
  statistic,
  offspring_dist,
  stat_threshold,
  track_pop
)

Arguments

sim_df

a ⁠<data.frame>⁠ containing at least columns for "infectee_id", "infector_id", and "generation". Also has optional columns for "time", and "chain_id".

n_chains

Number of chains to simulate.

statistic

The chain statistic to track as the stopping criteria for each chain being simulated when stat_threshold is not Inf; A ⁠<string>⁠. It can be one of:

  • "size": the total number of cases produced by a chain before it goes extinct.

  • "length": the total number of generations reached by a chain before it goes extinct.

offspring_dist

Offspring distribution: a ⁠<function>⁠ like the ones provided by R to generate random numbers from given distributions (e.g., rpois for Poisson). More specifically, the function needs to accept at least one argument, n, which is the number of random numbers to generate. It can accept further arguments, which will be passed on to the random number generating functions. Examples that can be provided here are rpois for Poisson distributed offspring, rnbinom for negative binomial offspring, or custom functions.

stat_threshold

A stopping criterion for individual chain simulations; a positive number coercible to integer. When any chain's cumulative statistic reaches or surpasses stat_threshold, that chain ends. Defaults to Inf. For example, if statistic = "size" and stat_threshold = 10, then any chain that produces 10 or more cases will stop. Note that setting stat_threshold does not guarantee that all chains will stop at the same value.

track_pop

Was the susceptible population tracked? Logical.

Author(s)

James M. Azam


[Package epichains version 0.1.1 Index]