EDISON: Network Reconstruction and Changepoint Detection

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.

AuthorFrank Dondelinger, Sophie Lebre
Date of publication2016-03-30 21:04:12
MaintainerFrank Dondelinger <fdondelinger.work@gmail.com>
LicenseGPL-2
Version1.1.1

View on CRAN

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.

Files in this package

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

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