smfsb: SMfSB 2e: Stochastic Modelling for Systems Biology, second edition
Version 1.1

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.

Browse man pages Browse package API and functions Browse package files

AuthorDarren Wilkinson
Date of publication2013-12-11 21:07:39
MaintainerDarren Wilkinson <darren.wilkinson@ncl.ac.uk>
LicenseLGPL-3
Version1.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("smfsb")

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

BD Man page
Dimer Man page
ID 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
MM Man page
SMfSB Man page
SMfSB2e Man page
StepCLE Man page Source code
StepEuler Man page Source code
StepEulerSPN Man page Source code
StepFRM Man page Source code
StepGillespie Man page Source code
StepODE Man page Source code
StepPTS Man page Source code
StepSDE Man page Source code
as.timedData Man page Source code
discretise Man page Source code
gillespie Man page Source code
gillespied Man page Source code
imdeath Man page Source code
mcmcSummary Man page Source code
metrop Man page Source code
mytable Man page
normgibbs Man page Source code
pfMLLik Man page Source code
rcfmc Man page Source code
rdiff Man page Source code
rfmc Man page Source code
simSample Man page Source code
simTimes Man page Source code
simTs Man page Source code
simpleEuler Man page Source code
smfsb Man page
smfsb2e Man page
spnModels Man page
stepLVc Man page Source code

Files

inst
inst/doc
inst/doc/smfsb.Snw
inst/doc/smfsb.pdf
src
src/stepLVc.c
NAMESPACE
demo
demo/PMCMC.R
demo/LVdataGen.R
demo/00Index
demo/DimerisationKinetics.R
demo/ExtrinsicNoise.R
demo/LotkaVolterra.R
demo/Metropolis.R
data
data/spnModels.rda
data/mytable.txt.gz
data/LVdata.rda
R
R/stepLVc.R
R/gillespied.R
R/rcfmc.R
R/astimedData.R
R/rdiff.R
R/StepEuler.R
R/imdeath.R
R/normgibbs.R
R/pfMLLik.R
R/mcmcSummary.R
R/rfmc.R
R/gillespie.R
R/metrop.R
R/simpleEuler.R
R/StepPTS.R
R/StepODE.R
R/StepEulerSPN.R
R/StepCLE.R
R/StepGillespie.R
R/StepSDE.R
R/StepFRM.R
vignettes
vignettes/smfsb.Snw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/LVdata.Rd
man/pfMLLik.Rd
man/simTimes.Rd
man/StepFRM.Rd
man/simSample.Rd
man/StepEuler.Rd
man/astimedData.Rd
man/StepGillespie.Rd
man/rdiff.Rd
man/gillespied.Rd
man/StepCLE.Rd
man/stepLVc.Rd
man/metrop.Rd
man/StepPTS.Rd
man/simTs.Rd
man/normgibbs.Rd
man/discretise.Rd
man/spnModels.Rd
man/imdeath.Rd
man/mytable.Rd
man/smfsb-package.Rd
man/StepSDE.Rd
man/rfmc.Rd
man/mcmcSummary.Rd
man/simpleEuler.Rd
man/StepEulerSPN.Rd
man/rcfmc.Rd
man/gillespie.Rd
man/StepODE.Rd
CHANGES
smfsb documentation built on May 30, 2017, 3:42 a.m.