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EDISON (version 1.1.1)

Network Reconstruction and Changepoint Detection

Description

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.

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Version

Install

install.packages('EDISON')

Version

1.1.1

License

GPL-2

Last Published

March 30th, 2016

Functions in EDISON (1.1.1)

BinoHyperRatio

Calculates the MH ratio of the binomial prior.
generateNetwork

Generate a random network.
CalculateChanges

Function to calculate the number of differences between adjaccent network segments.
NetworkRatioBino

Calculates the ratio of binomial prior probabilites.
fix_eigenvalues

Modify network to ensure stationarity.
init

Initialise the MCMC simulation.
calculateEdgeProbabilitiesSegs

Calculate edge probabilities for fixed segments.
cp.shift

Makes a changepoint shift move.
sampleDelta2

Sample delta squared.
NetworkProbExp

Calculates the prior probability of the network using the exponential prior.
addProposalNetworkInfo

Add the proposed new network to the new.nets list.
proposalTuning

Tune the proposal width for betas.
bp.computeAlpha

Computes the acceptance ratio of two changepoint configurations.
sampleBxy

Sample regression coefficients.
buildXY

Builds response Y and predictor X.
sampleSig2

Sample initial sigma squared.
make_structure_move

Makes a structure move.
main

Main function of the MCMC simulation.
calculateEdgeProbabilities

Calculate the edge probabilities.
sampleBinit

Sample initial regression coefficients.
CalculatePriorRatio

Calculates the network prior ratio.
CalculateLikelihoodRatio

Calculates the ratio of two likelihoods in a structure move.
calculateEdgeProbabilitiesTimePoints

Calculate the edge posterior probabilities for each timepoint.
convert_nets

Convert internal representation of networks.
AcceptableMove

Check if move is acceptable.
psrf

Calculates the potential scale reduction factor.
sampleParms

Sample initial parameters for the MCMC simulation.
ExpHyperMove

Makes an exponential hyperparameter move.
cp.birth

Make changepoint birth move.
NetworkProbBino

Calculates the prior probability of the network segments under the binomial prior.
defaultOptions

Set the default options for the MCMC simulation.
EDISON.run

Wrapper function for starting an MCMC simulation
computePx

Compute projection matrix.
runDBN

Setup and run the MCMC simulation.
EDISON-package

Allows for network reconstruction and changepoint detection.
sampleK

Sample initial number of changepoints.
dinvgamma

Calculate inverse gamma distribution.
NetworkRatioExp

Calculates the ratio of exponential network prior probabilities.
psrf_check_hyper

Checks the potential scale reduction factor for the hyperparameters.
phase.update

Make a network structure or hyperparameter move.
cp.death

Make changepoint death move.
HyperparameterMove

Make a hyperparameter move.
output

Collects and saves output.
proposeContinuous

Propose a new real hyperparameter value.
updateSigMulti

Update sigma squared variances.
BinoHyperMove

Makes a binomial hyperparameter move.
ExpHyperRatioTarget

Calculates the ratio of an exponential hyperparameter move.
CollectNetworkInfo

Collects all the network information in one list.
PriorRatioPoisson

Calculate network prior ratio with Poisson prior.
HyperParms

Sets up initial values of hyperparameters.
simulateNetwork

Generate network and simulate data.
ProposeDiscrete

Propose a new discrete value.
updateSigSolo

Sample new values for sigma squared.
psrf_check

Check the potential scale reduction factors for all parameters (edges).
calculateCPProbabilities

Calculate the changepoint probabilities.
rinvgamma

Samples from the inverse gamma distribution.
calculateCPPGlobal

Calculated the global changepoint probabilities.
computeRho4

Calculate proposal frequencies for changepoint moves.
readDataTS

Read target data.