EDISON: Network Reconstruction and Changepoint Detection
Version 1.1.1

Package EDISON (Estimation of Directed Interactions from Sequences Of Non-homogeneous gene expression) runs an MCMC simulation to reconstruct networks from time series data, using a non-homogeneous, time-varying dynamic Bayesian network. Networks segments and changepoints are inferred concurrently, and information sharing priors provide a reduction of the inference uncertainty.

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AuthorFrank Dondelinger, Sophie Lebre
Date of publication2016-03-30 21:04:12
MaintainerFrank Dondelinger <fdondelinger.work@gmail.com>
LicenseGPL-2
Version1.1.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("EDISON")

Man pages

AcceptableMove: Check if move is acceptable.
addProposalNetworkInfo: Add the proposed new network to the new.nets list.
BinoHyperMove: Makes a binomial hyperparameter move.
BinoHyperRatio: Calculates the MH ratio of the binomial prior.
bp.computeAlpha: Computes the acceptance ratio of two changepoint...
buildXY: Builds response Y and predictor X.
CalculateChanges: Function to calculate the number of differences between...
calculateCPPGlobal: Calculated the global changepoint probabilities.
calculateCPProbabilities: Calculate the changepoint probabilities.
calculateEdgeProbabilities: Calculate the edge probabilities.
calculateEdgeProbabilitiesSegs: Calculate edge probabilities for fixed segments.
calculateEdgeProbabilitiesTimePoints: Calculate the edge posterior probabilities for each...
CalculateLikelihoodRatio: Calculates the ratio of two likelihoods in a structure move.
CalculatePriorRatio: Calculates the network prior ratio.
CollectNetworkInfo: Collects all the network information in one list.
computePx: Compute projection matrix.
computeRho4: Calculate proposal frequencies for changepoint moves.
convert_nets: Convert internal representation of networks.
cp.birth: Make changepoint birth move.
cp.death: Make changepoint death move.
cp.shift: Makes a changepoint shift move.
defaultOptions: Set the default options for the MCMC simulation.
dinvgamma: Calculate inverse gamma distribution.
EDISON-package: Allows for network reconstruction and changepoint detection.
EDISON.run: Wrapper function for starting an MCMC simulation
ExpHyperMove: Makes an exponential hyperparameter move.
ExpHyperRatioTarget: Calculates the ratio of an exponential hyperparameter move.
fix_eigenvalues: Modify network to ensure stationarity.
generateNetwork: Generate a random network.
HyperparameterMove: Make a hyperparameter move.
HyperParms: Sets up initial values of hyperparameters.
init: Initialise the MCMC simulation.
main: Main function of the MCMC simulation.
make_structure_move: Makes a structure move.
NetworkProbBino: Calculates the prior probability of the network segments...
NetworkProbExp: Calculates the prior probability of the network using the...
NetworkRatioBino: Calculates the ratio of binomial prior probabilites.
NetworkRatioExp: Calculates the ratio of exponential network prior...
output: Collects and saves output.
phase.update: Make a network structure or hyperparameter move.
PriorRatioPoisson: Calculate network prior ratio with Poisson prior.
proposalTuning: Tune the proposal width for betas.
proposeContinuous: Propose a new real hyperparameter value.
ProposeDiscrete: Propose a new discrete value.
psrf: Calculates the potential scale reduction factor.
psrf_check: Check the potential scale reduction factors for all...
psrf_check_hyper: Checks the potential scale reduction factor for the...
readDataTS: Read target data.
rinvgamma: Samples from the inverse gamma distribution.
runDBN: Setup and run the MCMC simulation.
sampleBinit: Sample initial regression coefficients.
sampleBxy: Sample regression coefficients.
sampleDelta2: Sample delta squared.
sampleK: Sample initial number of changepoints.
sampleParms: Sample initial parameters for the MCMC simulation.
sampleSig2: Sample initial sigma squared.
simulateNetwork: Generate network and simulate data.
updateSigMulti: Update sigma squared variances.
updateSigSolo: Sample new values for sigma squared.

Functions

AcceptableMove Man page Source code
BinoHyperMove Man page Source code
BinoHyperRatio Man page Source code
CalculateChanges Man page Source code
CalculateLikelihoodRatio Man page Source code
CalculatePriorRatio Man page Source code
CollectNetworkInfo Man page Source code
EDISON Man page
EDISON-package Man page
EDISON.run Man page Source code
ExpHyperMove Man page Source code
ExpHyperRatioTarget Man page Source code
HyperParms Man page Source code
HyperparameterMove Man page Source code
NetworkProbBino Man page Source code
NetworkProbExp Man page Source code
NetworkRatioBino Man page Source code
NetworkRatioExp Man page Source code
PriorRatioPoisson Man page Source code
ProposeDiscrete Man page Source code
addProposalNetworkInfo Man page Source code
bp.computeAlpha Man page Source code
buildXY Man page Source code
calculateCPPGlobal Man page Source code
calculateCPProbabilities Man page Source code
calculateEdgeProbabilities Man page Source code
calculateEdgeProbabilitiesSegs Man page Source code
calculateEdgeProbabilitiesTimePoints Man page Source code
computePx Man page Source code
computeRho4 Man page Source code
convert_nets Man page Source code
cp.birth Man page Source code
cp.death Man page Source code
cp.shift Man page Source code
defaultOptions Man page Source code
dinvgamma Man page Source code
fix_eigenvalues Man page Source code
generateNetwork Man page Source code
init Man page Source code
main Man page Source code
make_structure_move Man page Source code
output Man page Source code
phase.update Man page Source code
proposalTuning Man page Source code
proposeContinuous Man page Source code
psrf Man page Source code
psrf_check Man page Source code
psrf_check_hyper Man page Source code
readDataTS Man page Source code
rinvgamma Man page Source code
runDBN Man page Source code
sampleBinit Man page Source code
sampleBxy Man page Source code
sampleDelta2 Man page Source code
sampleK Man page Source code
sampleParms Man page Source code
sampleSig2 Man page Source code
simulateNetwork Man page Source code
updateNetworkInfo Source code
updateSigMulti Man page Source code
updateSigSolo Man page Source code

Files

inst
inst/CITATION
tests
tests/testthat
tests/testthat/test-structure-moves.r
tests/testthat/test-fixed-edges.r
tests/test-all.R
NAMESPACE
NEWS
R
R/sampleK.R
R/calculateCPProbabilities.R
R/proposalTuning.R
R/EDISON-package.R
R/cp.shift.R
R/computeRho4.R
R/ProposeDiscrete.R
R/output.R
R/CalculateChanges.R
R/psrf_check_hyper.R
R/calculateEdgeProbabilities.R
R/BinoHyperMove.R
R/updateSigMulti.R
R/calculateEdgeProbabilitiesSegs.R
R/fix_eigenvalues.R
R/CollectNetworkInfo.R
R/PriorRatioPoisson.R
R/psrf_check.R
R/HyperparameterMove.R
R/sampleBxy.R
R/updateNetworkInfo.R
R/sampleBinit.R
R/bp.computeAlpha.R
R/rinvgamma.R
R/cp.death.R
R/readDataTS.R
R/NetworkRatioExp.R
R/NetworkProbExp.R
R/proposeContinuous.R
R/simulateNetwork.R
R/EDISON.run.R
R/defaultOptions.R
R/NetworkProbBino.R
R/CalculateLikelihoodRatio.R
R/BinoHyperRatio.R
R/make_structure_move.R
R/init.R
R/CalculatePriorRatio.R
R/generateNetwork.R
R/sampleDelta2.R
R/sampleParms.R
R/NetworkRatioBino.R
R/sampleSig2.R
R/ExpHyperMove.R
R/dinvgamma.R
R/convert_nets.R
R/buildXY.R
R/phase.update.R
R/runDBN.R
R/calculateCPPGlobal.R
R/updateSigSolo.R
R/computePx.R
R/calculateEdgeProbabilitiesTimePoints.R
R/ExpHyperRatioTarget.R
R/psrf.R
R/addProposalNetworkInfo.R
R/AcceptableMove.R
R/main.R
R/cp.birth.R
R/HyperParms.R
MD5
DESCRIPTION
man
man/psrf_check.Rd
man/NetworkProbBino.Rd
man/fix_eigenvalues.Rd
man/defaultOptions.Rd
man/readDataTS.Rd
man/proposalTuning.Rd
man/ExpHyperMove.Rd
man/init.Rd
man/NetworkRatioExp.Rd
man/convert_nets.Rd
man/NetworkProbExp.Rd
man/calculateEdgeProbabilitiesTimePoints.Rd
man/addProposalNetworkInfo.Rd
man/EDISON.run.Rd
man/cp.shift.Rd
man/calculateEdgeProbabilitiesSegs.Rd
man/main.Rd
man/sampleK.Rd
man/calculateCPProbabilities.Rd
man/proposeContinuous.Rd
man/calculateEdgeProbabilities.Rd
man/NetworkRatioBino.Rd
man/PriorRatioPoisson.Rd
man/CollectNetworkInfo.Rd
man/ExpHyperRatioTarget.Rd
man/psrf_check_hyper.Rd
man/cp.birth.Rd
man/updateSigMulti.Rd
man/BinoHyperRatio.Rd
man/computeRho4.Rd
man/EDISON-package.Rd
man/buildXY.Rd
man/CalculateChanges.Rd
man/output.Rd
man/sampleSig2.Rd
man/runDBN.Rd
man/AcceptableMove.Rd
man/HyperparameterMove.Rd
man/HyperParms.Rd
man/phase.update.Rd
man/BinoHyperMove.Rd
man/CalculatePriorRatio.Rd
man/psrf.Rd
man/generateNetwork.Rd
man/sampleBinit.Rd
man/ProposeDiscrete.Rd
man/CalculateLikelihoodRatio.Rd
man/calculateCPPGlobal.Rd
man/rinvgamma.Rd
man/sampleBxy.Rd
man/cp.death.Rd
man/computePx.Rd
man/make_structure_move.Rd
man/sampleParms.Rd
man/bp.computeAlpha.Rd
man/dinvgamma.Rd
man/sampleDelta2.Rd
man/updateSigSolo.Rd
man/simulateNetwork.Rd
EDISON documentation built on May 19, 2017, 1:40 p.m.