Description Usage Arguments Value See Also Examples

View source: R/StepGillespie2D.R

This function creates a function for advancing the state of an SPN model
using the Gillespie algorithm. The resulting function (closure) can be
used in conjunction with other functions (such as `simTs2D`

)
for simulating realisations of SPN models in space and time.

1 | ```
StepGillespie2D(N,d)
``` |

`N` |
An R list with named components representing a stochastic
Petri net (SPN). Should contain |

`d` |
A vector of diffusion coefficients - one coefficient for each reacting species, in order. The coefficient is the reaction rate for a reaction for a molecule moving into an adjacent compartment. The hazard for a given molecule leaving the compartment is therefore four times this value (as it can leave in one of 4 directions). |

An R function which can be used to advance the state of the SPN model
`N`

by using the Gillespie algorithm. The function closure has
interface `function(x0,t0,deltat,...)`

, where `x0`

is a 3d array
with dimensions corresponding to species followed by two spatial dimensions,
representing the initial condition, `t0`

represent the initial state and time, and `deltat`

represents the amount of time by which the process should be advanced. The function closure returns an array representing the simulated state of the system at the new time.

`StepGillespie`

,
`simTs2D`

, `StepGillespie1D`

1 2 3 4 5 6 7 8 9 10 11 12 | ```
data(spnModels)
m=20; n=30; T=10
x0=array(0,c(2,m,n))
dimnames(x0)[[1]]=c("x1","x2")
x0[,round(m/2),round(n/2)]=LV$M
stepLV2D = StepGillespie2D(LV,c(0.6,0.6))
xx = simTs2D(x0,0,T,0.2,stepLV2D,verb=TRUE)
N = dim(xx)[4]
op=par(mfrow=c(1,2))
image(xx[1,,,N],main="Prey",xlab="Space",ylab="Time")
image(xx[2,,,N],main="Predator",xlab="Space",ylab="Time")
par(op)
``` |

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