Spatial
All functions and utilities relating to spatial simulation
Value members
Concrete methods
The 1d spatial CLE algorithm
The 1d spatial CLE algorithm
- Value Params
- d
A vector of diffusion coefficients - one for each species
- dt
Time step of the simulation algorithm
- n
A
Spn[DoubleState]model for simulation
- Returns
A function with type signature
(x0: GenSeq[DoubleState], t0: Time, deltat: Time) => GenSeq[DoubleState]which will simulate the state of the system at timet0+deltatgiven initial statex0and initial timet0
The 2d spatial CLE algorithm
The 2d spatial CLE algorithm
- Value Params
- d
A vector of diffusion coefficients - one for each species
- dt
Time step of the simulation algorithm
- n
A
Spn[DoubleState]model for simulation
- Returns
A function with type signature
(x0: PMatrix[DoubleState], t0: Time, deltat: Time) => PMatrix[DoubleState]which will simulate the state of the system at timet0+deltatgiven initial statex0and initial timet0
The 1d spatial Euler algorithm
The 1d spatial Euler algorithm
- Value Params
- d
A vector of diffusion coefficients - one for each species
- dt
Time step of the simulation algorithm
- n
A
Spn[DoubleState]model for simulation
- Returns
A function with type signature
(x0: GenSeq[DoubleState], t0: Time, deltat: Time) => GenSeq[DoubleState]which will simulate the state of the system at timet0+deltatgiven initial statex0and initial timet0
The 2d spatial Euler algorithm
The 2d spatial Euler algorithm
- Value Params
- d
A vector of diffusion coefficients - one for each species
- dt
Time step of the simulation algorithm
- n
A
Spn[DoubleState]model for simulation
- Returns
A function with type signature
(x0: PMatrix[DoubleState], t0: Time, deltat: Time) => PMatrix[DoubleState]which will simulate the state of the system at timet0+deltatgiven initial statex0and initial timet0
The 1d spatial Gillespie algorithm
The 1d spatial Gillespie algorithm
- Value Params
- d
A vector of diffusion coefficients - one for each species
- maxH
Threshold for terminating simulation early
- minH
Threshold for treating hazard as zero
- n
A
Spn[IntState]model for simulation
- Returns
A function with type signature
(x0: GenSeq[IntState], t0: Time, deltat: Time) => GenSeq[IntState]which will simulate the state of the system at timet0+deltatgiven initial statex0and initial timet0
The 2d spatial Gillespie algorithm
The 2d spatial Gillespie algorithm
- Value Params
- d
A vector of diffusion coefficients - one for each species
- maxH
Threshold for terminating simulation early
- minH
Threshold for treating hazard as zero
- n
A
Spn[IntState]model for simulation
- Returns
A function with type signature
(x0: PMatrix[IntState], t0: Time, deltat: Time) => PMatrix[IntState]which will simulate the state of the system at timet0+deltatgiven initial statex0and initial timet0