Stochastic Modelling for Systems Biology

abcRun | Run a set of simulations initialised with parameters sampled... |

abcSmc | Run an ABC-SMC algorithm for infering the parameters of a... |

astimedData | Convert a time series object to a timed data matrix |

discretise | Discretise output from a discrete event simulation algorithm |

gillespie | Simulate a sample path from a stochastic kinetic model... |

gillespied | Simulate a sample path from a stochastic kinetic model... |

imdeath | Simulate a sample path from the homogeneous immigration-death... |

LVdata | Example simulated time courses from a stochastic... |

mcmcSummary | Summarise and plot tabular MCMC output |

metrop | Run a simple Metropolis sampler with standard normal target... |

metropolisHastings | Run a Metropolis-Hastings MCMC algorithm for the parameters... |

mytable | Simple example data frame |

normgibbs | A simple Gibbs sampler for Bayesian inference for the mean... |

pfMLLik | Create a function for computing the log of an unbiased... |

pfMLLik1 | Create a function for computing the log of an unbiased... |

rcfmc | Simulate a continuous time finite state space Markov chain |

rdiff | Simulate a sample path from a univariate diffusion process |

rfmc | Simulate a finite state space Markov chain |

simpleEuler | Simulate a sample path from an ODE model |

simSample | Simulate a many realisations of a model at a given fixed time... |

simTimes | Simulate a model at a specified set of times, using a... |

simTs | Simulate a model on a regular grid of times, using a function... |

simTs1D | Simulate a model on a regular grid of times, using a function... |

simTs2D | Simulate a model on a regular grid of times, using a function... |

smfsb-package | Stochastic Modelling for Systems Biology |

spnModels | Example SPN models |

StepCLE | Create a function for advancing the state of an SPN by using... |

StepCLE1D | Create a function for advancing the state of an SPN by using... |

StepCLE2D | Create a function for advancing the state of an SPN by using... |

StepEuler | Create a function for advancing the state of an ODE model by... |

StepEulerSPN | Create a function for advancing the state of an SPN by using... |

StepFRM | Create a function for advancing the state of an SPN by using... |

StepGillespie | Create a function for advancing the state of an SPN by using... |

StepGillespie1D | Create a function for advancing the state of an SPN by using... |

StepGillespie2D | Create a function for advancing the state of an SPN by using... |

stepLVc | A function for advancing the state of a Lotka-Volterra model... |

StepODE | Create a function for advancing the state of an ODE model by... |

StepPTS | Create a function for advancing the state of an SPN by using... |

StepSDE | Create a function for advancing the state of an SDE model by... |

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