Network Reconstruction and Changepoint Detection

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Documentation for package ‘EDISON’ version 1.1.1

• DESCRIPTION file.
• Package NEWS.

Help Pages

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.