installation
In IBMPopSim: Individual Based Model Population Simulation

The latest stable version can be installed from CRAN:

install.packages('IBMPopSim')

The latest development version can be installed from github:

# install.packages("devtools")
devtools::install_github('DaphneGiorgi/IBMPopSim')

First example to check installation

To illustrate the use of the package and to check the installation, a simple model with Poisson arrivals and exits is implemented. Starting from an initial population pop, we define two events birth and death with intensity of Poisson type, we create the model birth_death and simulate the population evolution over 10 years.

library(IBMPopSim)

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

birth = mk_event_poisson(type = 'birth', intensity = 'lambda')
death = mk_event_poisson(type = 'death', intensity = 'mu')
params = list('lambda' = 100, 'mu' = 100)

# mk_model compiles C++ code using sourceCpp from Rcpp
birth_death <- mk_model(characteristics = get_characteristics(pop_init),
                        events = list(birth, death),
                        parameters = params)

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

num_births <- length(sim_out$population$birth) - init_size
num_deaths <- sum(!is.na(sim_out$population$death))
print(c("births" = num_births, "deaths" = num_deaths))