ssa.btl {GillespieSSA}R Documentation

Binomial tau-leap method (BTL)

Description

Binomial tau-leap method implementation of the SSA as described by Chatterjee et al. (2005). It is usually called from within ssa, but can be invoked directly.

Usage

ssa.btl(x = stop("missing state vector (x)"),
        a = stop("missing propensity vector (a)"),
       nu = stop("missing state-change matrix (nu)"),
        f = stop("missing coarse-graining factor (f)"))

Arguments

x state vector.
a vector of evaluated propensity functions.
nu state-change matrix.
f coarse-graining factor (see page 4 in Chatterjee et al. 2005).

Details

Performs one time step using the Binomial tau-leap method. Intended to be invoked by ssa.

Value

A list with two elements, 1) the time leap (tau) and 2) the realized state change vector (nu_j).

References

Chatterjee et al. (2005)

See Also

GillespieSSA-package, ssa

Examples

a = function(parms,x){
 b <- parms[1]
 d <- parms[2]
 K <- parms[3]
 N <- x[1]
 return(c(b*N , N*b + (b-d)*N/K))
} 
parms <- c(2,1,1000,500)
x <- 500
nu <- matrix(c(+1, -1),ncol=2)
t <- 0
for (i in seq(100)) {
  out <- ssa.btl(x,a(parms,x),nu,f=10)  
  x <- x + out$nu_j
  t <- t + 1
  cat("t:",t,", x:",x,"\n")
}

[Package GillespieSSA version 0.5-3 Index]