popsim: Simulation of a model.
In IBMPopSim: Individual Based Model Population Simulation

popsim

R Documentation

Simulation of a model.

Description

This function simulates the random evolution of an IBM.

Usage

popsim(
  model,
  initial_population,
  events_bounds,
  parameters = NULL,
  age_max = Inf,
  time,
  multithreading = FALSE,
  num_threads = NULL,
  clean_step = NULL,
  clean_ratio = 0.1,
  seed = NULL,
  verbose = FALSE
)

Arguments

`model`	Model resulting from a call to the function `mk_model`.
`initial_population`	Object of population class representing the initial population.
`events_bounds`	Named vector of events bounds, with names corresponding to events names.
`parameters`	List of model parameters.
`age_max`	Maximum age of individuals in the population (`Inf` by default).
`time`	Final time (Numeric). Can be of length 1 or a vector of simulation discretized times.
`multithreading`	Logical for multithread activation, `FALSE` by default. Should be only activated for IBM simulation with no interactions.
`num_threads`	(Optional) Number of threads used for multithreading. Set by default to the number of concurrent threads supported by the available hardware implementation.
`clean_step`	(Optional) Optional parameter for improving simulation time. Time step for removing dead (or exited) individuals from the population. By default, equal to age_max.
`clean_ratio`	(Optional) Optional parameter for improving simulation time. 0.1 by default.
`seed`	(Optional) Random generator seed, random by default.
`verbose`	(Optional) Activate verbose output, FALSE by default.

Value

List composed of

arguments: Simulation inputs (initial population, parameters value, multithreading...)
logs: Simulation logs (algorithm duration, accepted/rejected events...).
population: If time is of length 1, population is an object of type population containing of all individuals who lived in the population in the time interval [0,time]. If time is a vector (time[1], ..., time[n]), population is a list of n objects of type population, each representing the state of the population at time time[i], for i = 1,..., n.

Examples


init_size <- 100000
pop_df <- data.frame(birth = rep(0, init_size), death = NA)
pop <- population(pop_df)

birth = mk_event_poisson(type = 'birth', intensity = 'lambda')
death = mk_event_poisson(type = 'death', intensity = 'mu')
params = list('lambda' = 100, 'mu' = 100)
birth_death <- mk_model(events = list(birth, death),
                       parameters = params)

sim_out <- popsim(model = birth_death,
                 initial_population = pop,
                 events_bounds = c('birth' = params$lambda, 'death' = params$mu),
                 parameters = params,
                 time = 10)

IBMPopSim documentation built on Oct. 15, 2024, 5:07 p.m.