Spatial
All functions and utilities relating to spatial simulation
Attributes
- Graph
- Supertypes
- class Objecttrait Matchableclass Any
- Self type
- Spatial.type
Members list
Value members
Concrete methods
The 1d spatial CLE algorithm
The 1d spatial CLE algorithm
Attributes
- 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
Attributes
- 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
Attributes
- 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
Attributes
- 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
Attributes
- 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
Attributes
- 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
Plot the output of a 1d time series simulation. Called solely for the side-effect of rendering a plot on the console.
Plot the output of a 1d time series simulation. Called solely for the side-effect of rendering a plot on the console.
Attributes
- ts
Output from a 1d spatial time series simulation