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.gitignore template for the examples Jul 20, 2018
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README.md

scala-smfsb Examples directory

Directory containing runnable examples illustrating use of the scala-smfsb library

Just doing sbt run from this directory should build and run the examples. That is (assuming you have sbt installed and working), you should clone or fork the repo and then execute sbt run from your OS command line, with the current working directory set to inside the examples directory:

scala-smfsb/examples$ sbt run

Then just select the number of the example you want to run.

Examples

Basics

Spatial reaction-diffusion simulation

  • Gillespie1d - 1d exact spatial Gillespie simulation
  • Cle1d - 1d spatial CLE simulation
  • Gillespie2d - 2d exact spatial Gillespie simulation
  • Cle2d - 2d spatial CLE simulation
  • Cle2dfine - 2d spatial CLE (SPDE) simulation on a fine grid, animated
  • Euler2dfine - 2d spatial Euler (PDE) simulation on a fine grid, animated

Bayesian parameter inference using time course data

  • PMCMC - Parameter estimation from data using a PMMH particle MCMC algorithm (applied to a LV model)
  • AbcLv - A naive rejection ABC algorithm for the LV model based on Euclidean distance between trajectories
  • AbcSsLv - A rejection ABC algorithm using summary statistics
  • AbcSmcLv - An ABC-SMC algorithm using summary statistics

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