R: Network Reconstruction and Changepoint Detection

# Network Reconstruction and Changepoint Detection

## Documentation for package ‘EDISON’ version 1.1.2

- DESCRIPTION file
- Package NEWS

## Help 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 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.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.