Nothing
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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