Network Reconstruction and Changepoint Detection

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Documentation for package ‘EDISON’ version 1.1.1

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EDISON-package Allows for network reconstruction and changepoint detection.
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 configurations.
buildXY Builds response Y and predictor X.
CalculateChanges Function to calculate the number of differences between adjaccent network segments.
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 timepoint.
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 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 under the binomial prior.
NetworkProbExp Calculates the prior probability of the network using the exponential prior.
NetworkRatioBino Calculates the ratio of binomial prior probabilites.
NetworkRatioExp Calculates the ratio of exponential network prior probabilities.
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 parameters (edges).
psrf_check_hyper Checks the potential scale reduction factor for the hyperparameters.
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.