TiPS (version 1.2.3)

build_simulator: Build a simulator of dynamics of population-model

Description

A simulator is built by supplying reactions of the model described by our formalism or described by differential equations The returned function will be used to simulate trajectories, that can further be used to simulate phylogenies.

Usage

build_simulator(reactions, functions = NULL)

Value

An object of class simulation, which is a function that can be used to simulate trajectories from the model.

Arguments

reactions

A character vector of reactions describing the input model.

functions

A named vector where functions are defined.

Author

Gonche Danesh

Examples

if (FALSE) {
# Build a simulator for an SIR model
reactions <- c('S [beta * S * I] -> I',
               'I [gamma * I] -> R')

sir.simu <- build_simulator(reactions = reactions)

# Run a simulation of a trajectory
sir_traj <- sir.simu(paramValues = c(gamma = 1, beta = 2e-4),
                     initialStates = c(I = 1, S = 9999, R = 0),
                     times = c(0, 20), ,
                     method = "exact",
                     seed = 166)

# The output is a named list containing the trajectory, the algorithm used,
# the parameter values and the reactions of the model.
names(sir_traj)

# Print head of the simulated trajectory
head(sir_traj$traj)

# Plot the trajectory
plot(sir_traj)
}