compile_reactions: Precompile the reactions
In GillespieSSA2: Gillespie's Stochastic Simulation Algorithm for Impatient People

compile_reactions

R Documentation

Precompile the reactions

Description

By precompiling the reactions, you can run multiple SSA simulations repeatedly without having to recompile the reactions every time.

Usage

compile_reactions(
  reactions,
  state_ids,
  params,
  buffer_ids = NULL,
  hardcode_params = FALSE,
  fun_by = 10000L,
  debug = FALSE
)

Arguments

`reactions`	'reaction' A list of multiple `reaction()` objects.
`state_ids`	`[character]` The names of the states in the correct order.
`params`	`[named numeric]` Constants that are used in the propensity functions.
`buffer_ids`	`[character]` The order of any buffer calculations that are made as part of the propensity functions.
`hardcode_params`	`[logical]` Whether or not to hardcode the values of `params` in the compilation of the propensity functions. Setting this to `TRUE` will result in a minor sacrifice in accuracy for a minor increase in performance.
`fun_by`	`[integer]` Combine this number of propensity functions into one function.
`debug`	`[logical]` Whether to print the resulting C++ code before compiling.

Value

A list of objects solely to be used by ssa().

x[["state_change"]]: A sparse matrix of reaction effects.
x[["reaction_ids"]]: The names of the reactions.
x[["buffer_ids"]]: A set of buffer variables found in the propensity functions.
x[["buffer_size"]]: The minimum size of the buffer required.
x[["function_pointers"]]: A list of compiled propensity functions.
x[["hardcode_params"]]: Whether the parameters were hard coded into the source code.'

Examples


initial_state <- c(prey = 1000, predators = 1000)
params <- c(c1 = 10, c2 = 0.01, c3 = 10)
reactions <- list(
  #        propensity function     effects                       name for reaction
  reaction(~c1 * prey,             c(prey = +1),                 "prey_up"),
  reaction(~c2 * prey * predators, c(prey = -1, predators = +1), "predation"),
  reaction(~c3 * predators,        c(predators = -1),            "pred_down")
)

compiled_reactions <- compile_reactions(
  reactions = reactions,
  state_ids = names(initial_state),
  params = params
)

out <-
  ssa(
    initial_state = initial_state,
    reactions = compiled_reactions,
    params = params,
    method = ssa_exact(),
    final_time = 5,
    census_interval = .001,
    verbose = TRUE
  )

plot_ssa(out)

GillespieSSA2 documentation built on Jan. 24, 2023, 1:10 a.m.