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.

Functions

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

Files

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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