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. |