Radioactive decay model (Gillespie, 1977)

set.seed(1)
knitr::opts_chunk$set(fig.width = 8, fig.height = 6)

This model is also known as the irreversible isomerization reaction set. It consists of a single species and single reaction channels,

X --c--> 0

Load package

library(GillespieSSA)

Define parameters

parms <- c(k = 0.5)
tf <- 20                                       # Final time
simName <- "Radioactive decay model"

Define initial state vector

x0 <- c(N=1000)

Define state-change matrix

nu <- matrix(c(-1),nrow=1,byrow=TRUE)

Define propensity functions

a <- c("k*N")

Run simulations with the Direct method

set.seed(1)
out <- ssa(
  x0 = x0,
  a = a,
  nu = nu,
  parms = parms,
  tf = tf,
  method = ssa.d(),
  simName = simName,
  verbose = FALSE,
  consoleInterval = 1
) 
ssa.plot(out, show.title = TRUE, show.legend = FALSE)

Run simulations with the Explict tau-leap method

set.seed(1)
out <- ssa(
  x0 = x0,
  a = a,
  nu = nu,
  parms = parms,
  tf = tf,
  method = ssa.etl(tau = .003),
  simName = simName,
  verbose = FALSE,
  consoleInterval = 1
) 
ssa.plot(out, show.title = TRUE, show.legend = FALSE)

Run simulations with the Binomial tau-leap method

set.seed(1)
out <- ssa(
  x0 = x0,
  a = a,
  nu = nu,
  parms = parms,
  tf = tf,
  method = ssa.btl(),
  simName = simName,
  verbose = FALSE,
  consoleInterval = 1
) 
ssa.plot(out, show.title = TRUE, show.legend = FALSE)

Run simulations with the Optimized tau-leap method

set.seed(1)
out <- ssa(
  x0 = x0,
  a = a,
  nu = nu,
  parms = parms,
  tf = tf,
  method = ssa.otl(),
  simName = simName,
  verbose = FALSE,
  consoleInterval = 1
) 
ssa.plot(out, show.title = TRUE, show.legend = FALSE)


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GillespieSSA documentation built on July 27, 2019, 1:02 a.m.