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.

Author
Darren Wilkinson
Date of publication
2016-02-21 15:34:18
Maintainer
Darren Wilkinson <darren.wilkinson@ncl.ac.uk>
License
LGPL-3
Version
1.2

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