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...

Functions

as.timedData Man page
BD Man page
Dimer Man page
discretise Man page
gillespie Man page
gillespied Man page
ID Man page
imdeath Man page
LV Man page
LVdata Man page
LVirregular Man page
LVirregularNoise10 Man page
LVnoise10 Man page
LVnoise10Scale10 Man page
LVnoise30 Man page
LVnoise3010 Man page
LVperfect Man page
LVprey Man page
LVpreyNoise10 Man page
LVpreyNoise10Scale10 Man page
mcmcSummary Man page
metrop Man page
MM Man page
mytable Man page
normgibbs Man page
pfMLLik Man page
rcfmc Man page
rdiff Man page
rfmc Man page
simpleEuler Man page
simSample Man page
simTimes Man page
simTs Man page
smfsb Man page
SMfSB Man page
smfsb2e Man page
SMfSB2e Man page
spnModels Man page
StepCLE Man page
StepEuler Man page
StepEulerSPN Man page
StepFRM Man page
StepGillespie Man page
stepLVc Man page
StepODE Man page
StepPTS Man page
StepSDE Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.