Nothing
set.seed(1) knitr::opts_chunk$set(fig.width = 8, fig.height = 6)
The Decaying-Dimerization Reaction Set consists of three species and four reaction channels.
S1 --c1--> 0 S1 + S1 --c2--> S2 S2 --c3--> S1 + S1 S2 --c4--> S3
Load package
library(GillespieSSA)
Define parameters
parms <- c(c1=1.0, c2=0.002, c3=0.5, c4=0.04) tf <- 10 # Final time simName <- "Decaying-Dimerizing Reaction Set" # Name
Define initial state vector
x0 <- c(s1=10000, s2=0, s3=0)
Define state-change matrix
nu <- matrix(c(-1, -2, +2, 0, 0, +1, -1, -1, 0, 0, 0, +1), nrow=3,byrow=TRUE)
Define propensity functions
a <- c("c1*s1", "c2*s1*s1", "c3*s2", "c4*s2")
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 = 0.003), 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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