compile_reactions {GillespieSSA2}

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)