smfsb: SMfSB 2e: Stochastic Modelling for Systems Biology, second edition

This package contains code and data for modelling and simulation of stochastic kinetic biochemical network models. It contains the code and data associated with the second edition of the book Stochastic Modelling for Systems Biology, published by Chapman & Hall/CRC Press, November 2011.

AuthorDarren Wilkinson
Date of publication2016-02-21 15:34:18
MaintainerDarren Wilkinson <darren.wilkinson@ncl.ac.uk>
LicenseLGPL-3
Version1.2

View on R-Forge

Man pages

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...

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...

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...

smfsb-package: Stochastic Modelling for Systems Biology, second edition

spnModels: Example SPN models

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...

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...

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...

Files in this package

smfsb/CHANGES
smfsb/DESCRIPTION
smfsb/NAMESPACE
smfsb/R
smfsb/R/StepCLE.R smfsb/R/StepEuler.R smfsb/R/StepEulerSPN.R smfsb/R/StepFRM.R smfsb/R/StepGillespie.R smfsb/R/StepODE.R smfsb/R/StepPTS.R smfsb/R/StepSDE.R smfsb/R/astimedData.R smfsb/R/gillespie.R smfsb/R/gillespied.R smfsb/R/imdeath.R smfsb/R/mcmcSummary.R smfsb/R/metrop.R smfsb/R/normgibbs.R smfsb/R/pfMLLik.R smfsb/R/rcfmc.R smfsb/R/rdiff.R smfsb/R/rfmc.R smfsb/R/simpleEuler.R smfsb/R/stepLVc.R
smfsb/build
smfsb/build/vignette.rds
smfsb/data
smfsb/data/LVdata.rda
smfsb/data/mytable.txt.gz
smfsb/data/spnModels.rda
smfsb/demo
smfsb/demo/00Index
smfsb/demo/DimerisationKinetics.R
smfsb/demo/ExtrinsicNoise.R
smfsb/demo/LVdataGen.R
smfsb/demo/LotkaVolterra.R
smfsb/demo/Metropolis.R
smfsb/demo/PMCMC.R
smfsb/inst
smfsb/inst/doc
smfsb/inst/doc/smfsb.Snw
smfsb/inst/doc/smfsb.pdf
smfsb/man
smfsb/man/LVdata.Rd smfsb/man/StepCLE.Rd smfsb/man/StepEuler.Rd smfsb/man/StepEulerSPN.Rd smfsb/man/StepFRM.Rd smfsb/man/StepGillespie.Rd smfsb/man/StepODE.Rd smfsb/man/StepPTS.Rd smfsb/man/StepSDE.Rd smfsb/man/astimedData.Rd smfsb/man/discretise.Rd smfsb/man/gillespie.Rd smfsb/man/gillespied.Rd smfsb/man/imdeath.Rd smfsb/man/mcmcSummary.Rd smfsb/man/metrop.Rd smfsb/man/mytable.Rd smfsb/man/normgibbs.Rd smfsb/man/pfMLLik.Rd smfsb/man/rcfmc.Rd smfsb/man/rdiff.Rd smfsb/man/rfmc.Rd smfsb/man/simSample.Rd smfsb/man/simTimes.Rd smfsb/man/simTs.Rd smfsb/man/simpleEuler.Rd smfsb/man/smfsb-package.Rd smfsb/man/spnModels.Rd smfsb/man/stepLVc.Rd
smfsb/src
smfsb/src/stepLVc.c
smfsb/vignettes
smfsb/vignettes/smfsb.Snw

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