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**smfsb**: SMfSB 2e: Stochastic Modelling for Systems Biology, second edition**spnModels**: Example SPN models

# Example SPN models

### Description

Collection of example stochastic Petri net (SPN) models. Includes `LV`

, a Lotka–Volterra
model, `ID`

, an immigration–death process, `BD`

, a birth–death
process, `Dimer`

, a simple dimerisation kinetics model, and
`MM`

, a Michaelis–Menten enzyme kinetic model.

### Usage

1 |

### Format

Each model is a list, with components `Pre`

, `Post`

,
and `h`

. Some models also include an initial state, `M`

. See
`gillespie`

and `StepGillespie`

for further details, and
examples of use.

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- astimedData: Convert a time series object to a timed data matrix
- discretise: Discretise output from a discrete event simulation algorithm
- discretise: Discretise output from a discrete event simulation algorithm
- gillespie: Simulate a sample path from a stochastic kinetic model...
- gillespie: Simulate a sample path from a stochastic kinetic model...
- gillespied: 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...
- imdeath: Simulate a sample path from the homogeneous immigration-death...
- LVdata: Example simulated time courses from a stochastic...
- LVdata: Example simulated time courses from a stochastic...
- mcmcSummary: Summarise and plot tabular MCMC output
- mcmcSummary: Summarise and plot tabular MCMC output
- metrop: Run a simple Metropolis sampler with standard normal target...
- metrop: Run a simple Metropolis sampler with standard normal target...
- mytable: Simple example data frame
- mytable: Simple example data frame
- normgibbs: A simple Gibbs sampler for Bayesian inference for the mean...
- normgibbs: A simple Gibbs sampler for Bayesian inference for the mean...
- pfMLLik: Create a function for computing the log of an unbiased...
- pfMLLik: Create a function for computing the log of an unbiased...
- rcfmc: Simulate a continuous time finite state space Markov chain
- rcfmc: Simulate a continuous time finite state space Markov chain
- rdiff: Simulate a sample path from a univariate diffusion process
- rdiff: Simulate a sample path from a univariate diffusion process
- rfmc: Simulate a finite state space Markov chain
- rfmc: Simulate a finite state space Markov chain
- simpleEuler: Simulate a sample path from an ODE model
- simpleEuler: Simulate a sample path from an ODE model
- simSample: Simulate a many realisations of a model at a given fixed time...
- 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...
- 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...
- simTs: Simulate a model on a regular grid of times, using a function...
- smfsb-package: Stochastic Modelling for Systems Biology, second edition
- smfsb-package: Stochastic Modelling for Systems Biology, second edition
- spnModels: Example SPN models
- spnModels: Example SPN models
- StepCLE: Create a function for advancing the state of an SPN by using...
- StepCLE: 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...
- 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...
- 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...
- 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...
- StepGillespie: Create a function for advancing the state of an SPN by using...
- stepLVc: A function for advancing the state of a Lotka-Volterra model...
- 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...
- 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...
- 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...
- StepSDE: Create a function for advancing the state of an SDE model by...