## ---- setseed, echo=FALSE-----------------------------------------------------
set.seed(1)
knitr::opts_chunk$set(fig.width = 6, fig.height = 4)
if("package:GillespieSSA" %in% search()) detach("package:GillespieSSA", unload=TRUE) 

## -----------------------------------------------------------------------------
library(GillespieSSA2)
sim_name <- "Decaying-Dimerizing Reaction Set"
final_time <- 10
params <- c(c1 = 1.0, c2 = 0.002, c3 = 0.5, c4 = 0.04)
initial_state <- c(s1 = 10000, s2 = 0, s3 = 0)

## -----------------------------------------------------------------------------
reactions <- list(
  reaction("c1 * s1",        c(s1 = -1)),
  reaction("c2 * s1 * s1",   c(s1 = -2, s2 = +1)),
  reaction("c3 * s2",        c(s1 = +2, s2 = -1)),
  reaction("c4 * s2",        c(s2 = -1, s3 = +1))
)

## ----exact--------------------------------------------------------------------
set.seed(1)
out <- ssa(
  initial_state = initial_state,
  reactions = reactions,
  params = params,
  final_time = final_time,
  method = ssa_exact(),
  sim_name = sim_name
)
plot_ssa(out)

## ----etl----------------------------------------------------------------------
set.seed(1)
out <- ssa(
  initial_state = initial_state,
  reactions = reactions,
  params = params,
  final_time = final_time,
  method = ssa_etl(tau = 0.003),
  sim_name = sim_name
) 
plot_ssa(out)

## ----btl----------------------------------------------------------------------
set.seed(1)
out <- ssa(
  initial_state = initial_state,
  reactions = reactions,
  params = params,
  final_time = final_time,
  method = ssa_btl(),
  sim_name = sim_name
) 
plot_ssa(out)