{ "_id": "6a1edda1b401979e73410158", "Package": "EDISON", "Type": "Package", "Title": "Network Reconstruction and Changepoint Detection", "Version": "1.1.2", "Date": "2025-12-20", "Authors@R": "c(\nperson(given = \"Frank\",\nfamily = \"Dondelinger\",\nrole = c(\"aut\", \"cre\"),\nemail = \"fdondelinger.work@gmail.com\"),\nperson(given = \"Sophie\",\nfamily = \"Lebre\",\nrole = \"aut\"))", "Description": "Package EDISON (Estimation of Directed Interactions from\nSequences Of Non-homogeneous gene expression) runs an MCMC\nsimulation to reconstruct networks from time series data, using\na non-homogeneous, time-varying dynamic Bayesian network.\nNetworks segments and changepoints are inferred concurrently,\nand information sharing priors provide a reduction of the\ninference uncertainty.", "License": "GPL-2", "LazyLoad": "yes", "Packaged": { "Date": "2026-05-20 08:10:40 UTC", "User": "root" }, "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "NeedsCompilation": "no", "Author": "Frank Dondelinger [aut, cre], Sophie Lebre [aut]", "Maintainer": "Frank Dondelinger ", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2025-12-21 06:10:34 UTC", "RemoteUrl": "https://github.com/cran/EDISON", "RemoteRef": "HEAD", "RemoteSha": "ec3764e535addeda937b46b748088e7849f90578", "MD5sum": "20b43945205c6d3d7ac7669910ee6d96", "_user": "cran", "_type": "src", "_file": "EDISON_1.1.2.tar.gz", "_fileid": "7907205c7248e5e82210a43965e55b4e4a8d42e135bdf8d24e234401bfc64042", "_filesize": 269023, "_sha256": "7907205c7248e5e82210a43965e55b4e4a8d42e135bdf8d24e234401bfc64042", "_created": "2026-05-20T08:10:40.000Z", "_published": "2026-06-02T13:41:53.658Z", "_distro": "noble", "_jobs": [ { "job": 79084564221, "time": 120, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7104651607" }, { "job": 79084562814, "time": 139, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7104658379" }, { "job": 79084561973, "time": 182, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7104609071" }, { "job": 79084561989, "time": 105, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7359377386" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/26149854075", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/EDISON", "_commit": { "id": "ec3764e535addeda937b46b748088e7849f90578", "author": "Frank Dondelinger ", "committer": "cran-robot ", "message": "version 1.1.2\n", "time": 1766297434 }, "_maintainer": { "name": "Frank Dondelinger", "email": "fdondelinger.work@gmail.com" }, "_registered": true, "_dependencies": [ { "package": "corpcor", "role": "Depends" }, { "package": "MASS", "role": "Depends" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 1, "_updates": [ { "week": "2025-51", "n": 1 } ], "_tags": [ { "name": "1.1.2", "date": "2025-12-21" } ], "_stars": 2, "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 547, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/EDISON" }, "_mentions": 7, "_searchresults": 15, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/EDISON.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2012-07-16" }, { "version": "1.1", "date": "2014-09-14" }, { "version": "1.1.1", "date": "2016-03-30" }, { "version": "1.1.2", "date": "2025-12-21" } ], "_exports": [ "AcceptableMove", "addProposalNetworkInfo", "BinoHyperMove", "BinoHyperRatio", "bp.computeAlpha", "buildXY", "CalculateChanges", "calculateCPPGlobal", "calculateCPProbabilities", "calculateEdgeProbabilities", "calculateEdgeProbabilitiesSegs", "calculateEdgeProbabilitiesTimePoints", "CalculateLikelihoodRatio", "CalculatePriorRatio", "CollectNetworkInfo", "computePx", "computeRho4", "convert_nets", "cp.birth", "cp.death", "cp.shift", "defaultOptions", "dinvgamma", "EDISON.run", "ExpHyperMove", "ExpHyperRatioTarget", "fix_eigenvalues", "generateNetwork", "HyperparameterMove", "HyperParms", "init", "main", "make_structure_move", "NetworkProbBino", "NetworkProbExp", "NetworkRatioBino", "NetworkRatioExp", "output", "phase.update", "PriorRatioPoisson", "proposalTuning", "proposeContinuous", "ProposeDiscrete", "psrf", "psrf_check", "psrf_check_hyper", "readDataTS", "rinvgamma", "runDBN", "sampleBinit", "sampleBxy", "sampleDelta2", "sampleK", "sampleParms", "sampleSig2", "simulateNetwork", "updateSigMulti", "updateSigSolo" ], "_help": [ { "page": "AcceptableMove", "title": "Check if move is acceptable.", "topics": [ "AcceptableMove" ] }, { "page": "addProposalNetworkInfo", "title": "Add the proposed new network to the new.nets list.", "topics": [ "addProposalNetworkInfo" ] }, { "page": "BinoHyperMove", "title": "Makes a binomial hyperparameter move.", "topics": [ "BinoHyperMove" ] }, { "page": "BinoHyperRatio", "title": "Calculates the MH ratio of the binomial prior.", "topics": [ "BinoHyperRatio" ] }, { "page": "bp.computeAlpha", "title": "Computes the acceptance ratio of two changepoint configurations.", "topics": [ "bp.computeAlpha" ] }, { "page": "buildXY", "title": "Builds response Y and predictor X.", "topics": [ "buildXY" ] }, { "page": "CalculateChanges", "title": "Function to calculate the number of differences between adjaccent network segments.", "topics": [ "CalculateChanges" ] }, { "page": "calculateCPPGlobal", "title": "Calculated the global changepoint probabilities.", "topics": [ "calculateCPPGlobal" ] }, { "page": "calculateCPProbabilities", "title": "Calculate the changepoint probabilities.", "topics": [ "calculateCPProbabilities" ] }, { "page": "calculateEdgeProbabilities", "title": "Calculate the edge probabilities.", "topics": [ "calculateEdgeProbabilities" ] }, { "page": "calculateEdgeProbabilitiesSegs", "title": "Calculate edge probabilities for fixed segments.", "topics": [ "calculateEdgeProbabilitiesSegs" ] }, { "page": "calculateEdgeProbabilitiesTimePoints", "title": "Calculate the edge posterior probabilities for each timepoint.", "topics": [ "calculateEdgeProbabilitiesTimePoints" ] }, { "page": "CalculateLikelihoodRatio", "title": "Calculates the ratio of two likelihoods in a structure move.", "topics": [ "CalculateLikelihoodRatio" ] }, { "page": "CalculatePriorRatio", "title": "Calculates the network prior ratio.", "topics": [ "CalculatePriorRatio" ] }, { "page": "CollectNetworkInfo", "title": "Collects all the network information in one list.", "topics": [ "CollectNetworkInfo" ] }, { "page": "computePx", "title": "Compute projection matrix.", "topics": [ "computePx" ] }, { "page": "computeRho4", "title": "Calculate proposal frequencies for changepoint moves.", "topics": [ "computeRho4" ] }, { "page": "convert_nets", "title": "Convert internal representation of networks.", "topics": [ "convert_nets" ] }, { "page": "cp.birth", "title": "Make changepoint birth move.", "topics": [ "cp.birth" ] }, { "page": "cp.death", "title": "Make changepoint death move.", "topics": [ "cp.death" ] }, { "page": "cp.shift", "title": "Makes a changepoint shift move.", "topics": [ "cp.shift" ] }, { "page": "defaultOptions", "title": "Set the default options for the MCMC simulation.", "topics": [ "defaultOptions" ] }, { "page": "dinvgamma", "title": "Calculate inverse gamma distribution.", "topics": [ "dinvgamma" ] }, { "page": "EDISON.run", "title": "Wrapper function for starting an MCMC simulation", "topics": [ "EDISON.run" ] }, { "page": "ExpHyperMove", "title": "Makes an exponential hyperparameter move.", "topics": [ "ExpHyperMove" ] }, { "page": "ExpHyperRatioTarget", "title": "Calculates the ratio of an exponential hyperparameter move.", "topics": [ "ExpHyperRatioTarget" ] }, { "page": "fix_eigenvalues", "title": "Modify network to ensure stationarity.", "topics": [ "fix_eigenvalues" ] }, { "page": "generateNetwork", "title": "Generate a random network.", "topics": [ "generateNetwork" ] }, { "page": "HyperparameterMove", "title": "Make a hyperparameter move.", "topics": [ "HyperparameterMove" ] }, { "page": "HyperParms", "title": "Sets up initial values of hyperparameters.", "topics": [ "HyperParms" ] }, { "page": "init", "title": "Initialise the MCMC simulation.", "topics": [ "init" ] }, { "page": "main", "title": "Main function of the MCMC simulation.", "topics": [ "main" ] }, { "page": "make_structure_move", "title": "Makes a structure move.", "topics": [ "make_structure_move" ] }, { "page": "NetworkProbBino", "title": "Calculates the prior probability of the network segments under the binomial prior.", "topics": [ "NetworkProbBino" ] }, { "page": "NetworkProbExp", "title": "Calculates the prior probability of the network using the exponential prior.", "topics": [ "NetworkProbExp" ] }, { "page": "NetworkRatioBino", "title": "Calculates the ratio of binomial prior probabilites.", "topics": [ "NetworkRatioBino" ] }, { "page": "NetworkRatioExp", "title": "Calculates the ratio of exponential network prior probabilities.", "topics": [ "NetworkRatioExp" ] }, { "page": "output", "title": "Collects and saves output.", "topics": [ "output" ] }, { "page": "phase.update", "title": "Make a network structure or hyperparameter move.", "topics": [ "phase.update" ] }, { "page": "PriorRatioPoisson", "title": "Calculate network prior ratio with Poisson prior.", "topics": [ "PriorRatioPoisson" ] }, { "page": "proposalTuning", "title": "Tune the proposal width for betas.", "topics": [ "proposalTuning" ] }, { "page": "proposeContinuous", "title": "Propose a new real hyperparameter value.", "topics": [ "proposeContinuous" ] }, { "page": "ProposeDiscrete", "title": "Propose a new discrete value.", "topics": [ "ProposeDiscrete" ] }, { "page": "psrf", "title": "Calculates the potential scale reduction factor.", "topics": [ "psrf" ] }, { "page": "psrf_check", "title": "Check the potential scale reduction factors for all parameters (edges).", "topics": [ "psrf_check" ] }, { "page": "psrf_check_hyper", "title": "Checks the potential scale reduction factor for the hyperparameters.", "topics": [ "psrf_check_hyper" ] }, { "page": "readDataTS", "title": "Read target data.", "topics": [ "readDataTS" ] }, { "page": "rinvgamma", "title": "Samples from the inverse gamma distribution.", "topics": [ "rinvgamma" ] }, { "page": "runDBN", "title": "Setup and run the MCMC simulation.", "topics": [ "runDBN" ] }, { "page": "sampleBinit", "title": "Sample initial regression coefficients.", "topics": [ "sampleBinit" ] }, { "page": "sampleBxy", "title": "Sample regression coefficients.", "topics": [ "sampleBxy" ] }, { "page": "sampleDelta2", "title": "Sample delta squared.", "topics": [ "sampleDelta2" ] }, { "page": "sampleK", "title": "Sample initial number of changepoints.", "topics": [ "sampleK" ] }, { "page": "sampleParms", "title": "Sample initial parameters for the MCMC simulation.", "topics": [ "sampleParms" ] }, { "page": "sampleSig2", "title": "Sample initial sigma squared.", "topics": [ "sampleSig2" ] }, { "page": "simulateNetwork", "title": "Generate network and simulate data.", "topics": [ "simulateNetwork" ] }, { "page": "updateSigMulti", "title": "Update sigma squared variances.", "topics": [ "updateSigMulti" ] }, { "page": "updateSigSolo", "title": "Sample new values for sigma squared.", "topics": [ "updateSigSolo" ] } ], "_rundeps": [ "corpcor", "MASS" ], "_score": 2.7993405494535817, "_indexed": true, "_nocasepkg": "edison", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.2", "date": "2026-05-20T08:12:44.000Z", "distro": "noble", "commit": "ec3764e535addeda937b46b748088e7849f90578", "fileid": "05c7e8fb02cdc8ed66d0103160dec1f157ea1551ccbea0ec0573e711e51e421f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26149854075" }, { "r": "4.6.0", "os": "linux", "version": "1.1.2", "date": "2026-05-20T08:13:00.000Z", "distro": "noble", "commit": "ec3764e535addeda937b46b748088e7849f90578", "fileid": "d740658f209ac410f86ad793d3c680edfe82c937db644b212b36d40cc883c5da", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/26149854075" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.2", "date": "2026-06-02T13:41:31.000Z", "commit": "ec3764e535addeda937b46b748088e7849f90578", "fileid": "b54564bac29eb880efb6a83bc638cdbe5fb01d1a342e40a543affb125bbc6dc2", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/26149854075" } ] }