{ "_id": "6a103460acfb0bcc41c98fdf", "Package": "bnstruct", "Description": "Bayesian Network Structure Learning from Data with Missing\nValues. The package implements the Silander-Myllymaki complete\nsearch, the Max-Min Parents-and-Children, the Hill-Climbing,\nthe Max-Min Hill-climbing heuristic searches, and the\nStructural Expectation-Maximization algorithm. Available\nscoring functions are BDeu, AIC, BIC. The package also\nimplements methods for generating and using bootstrap samples,\nimputed data, inference.", "Type": "Package", "Title": "Bayesian Network Structure Learning from Data with Missing\nValues", "Version": "1.0.15", "Date": "2024-01-09", "Authors@R": "c(person(\"Francesco\", \"Sambo\", role=c(\"aut\"),\nemail=\"magodellepercussioni@gmail.com\"), person(\"Alberto\", \"Franzin\", role=c(\"aut\",\"cre\"),\nemail=\"afranzin@ulb.ac.be\"))", "License": "GPL (>= 2) | file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "VignetteBuilder": "knitr", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-12 07:46:11 UTC", "User": "root" }, "Author": "Francesco Sambo [aut], Alberto Franzin [aut, cre]", "Maintainer": "Alberto Franzin ", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://albertofranzin.r-universe.dev", "Date/Publication": "2024-01-10 02:40:55 UTC", "RemoteUrl": "https://github.com/cran/bnstruct", "RemoteRef": "HEAD", "RemoteSha": 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], "_owner": "cran", "_selfowned": true, "_usedby": 3, "_updates": [], "_tags": [], "_stars": 1, "_contributors": [ { "user": "albertofranzin", "count": 12, "uuid": 1533069 } ], "_userbio": { "uuid": 1533069, "type": "user", "name": "Alberto Franzin" }, "_downloads": { "count": 495, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bnstruct" }, "_mentions": 5, "_searchresults": 110, "_rbuild": "4.6.0", "_assets": [ "extra/bnstruct.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "albertofranzin", "_cranurl": false, "_releases": [ { "version": "1.0", "date": "2015-07-30" }, { "version": "1.0.1", "date": "2016-11-10" }, { "version": "1.0.2", "date": "2016-12-13" }, { "version": "1.0.4", "date": "2018-08-31" }, { "version": "1.0.5", "date": "2019-07-02" }, { "version": "1.0.6", "date": "2019-07-09" }, { "version": "1.0.7", "date": "2020-05-09" }, { "version": "1.0.8", "date": "2020-05-22" }, { "version": "1.0.9", "date": "2021-03-09" }, { "version": "1.0.10", "date": "2021-05-06" }, { "version": "1.0.11", "date": "2021-05-19" }, { "version": "1.0.12", "date": "2022-01-09" }, { "version": "1.0.13", "date": "2022-10-20" }, { "version": "1.0.14", "date": "2022-11-30" }, { "version": "1.0.15", "date": "2024-01-10" } ], "_exports": [ "add.observations<-", "asia", "asia_2_layers", "belief.propagation", "bn", "BN", "bn<-", "BNDataset", "boot", "boots", "boots<-", "bootstrap", "build.junction.tree", "child", "complete", "cpts", "cpts<-", "dag", "dag.to.cpdag", "dag<-", "data.file", "data.file<-", "discreteness", "discreteness<-", "edge.dir.wpdag", "em", "get.most.probable.values", "has.boots", "has.imputed.boots", "has.imputed.data", "has.raw.data", "header.file", "header.file<-", "imp.boots", "imp.boots<-", "impute", "imputed.data", "imputed.data<-", "InferenceEngine", "interventions", 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"table": false, "tojson": false }, { "name": "asia_2_layers", "title": "load a two-layers dataset derived from the 'Asia' dataset.", "object": "asia_2_layers", "file": "asia_2_layers.rda", "class": [ "BNDataset" ], "fields": [], "table": false, "tojson": false }, { "name": "child_NA_5000", "title": "'Child' dataset.", "object": "child_NA_5000", "file": "child_NA_5000.rda", "class": [ "BNDataset" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "add.observations-set", "title": "add further evidence to an existing list of observations of an 'InferenceEngine'.", "topics": [ "add.observations<-", "add.observations<-,InferenceEngine-method" ] }, { "page": "asia", "title": "load 'Asia' dataset.", "topics": [ "asia" ] }, { "page": "asia_10000", "title": "'Asia' dataset.", "topics": [ "asia_10000" ] }, { "page": "asia_2_layers", "title": "load a two-layers dataset derived from the 'Asia' dataset.", "topics": [ "asia_2_layers" ] }, { "page": "belief.propagation", "title": "perform belief propagation.", "topics": [ "belief.propagation", "belief.propagation,InferenceEngine", "belief.propagation,InferenceEngine-method" ] }, { "page": "bn-method", "title": "get the 'BN' object contained in an 'InferenceEngine'.", "topics": [ "bn", "bn,InferenceEngine", "bn,InferenceEngine-method" ] }, { "page": "BN-class", "title": "BN class definition.", "topics": [ "BN", "BN,BN-class", "BN-class", "initialize,BN-method" ] }, { "page": "bn-set", "title": "set the original 'BN' object contained in an 'InferenceEngine'.", "topics": [ "bn<-", "bn<-,InferenceEngine-method" ] }, { "page": "BNDataset-class", "title": "BNDataset class.", "topics": [ "BNDataset", "BNDataset,BNDataset-class", "BNDataset-class", "initialize,BNDataset-method" ] }, { "page": "boot", "title": "get selected element of bootstrap list.", "topics": [ "boot", "boot,BNDataset", "boot,BNDataset,numeric-method" ] }, { "page": "boots", "title": "get list of bootstrap samples of a 'BNDataset'.", "topics": [ "boots", "boots,BNDataset", "boots,BNDataset-method" ] }, { "page": "boots-set", "title": "set list of bootstrap samples of a 'BNDataset'.", "topics": [ "boots<-", "boots<-,BNDataset-method" ] }, { "page": "bootstrap", "title": "Perform bootstrap.", "topics": [ "bootstrap", "bootstrap,BNDataset", "bootstrap,BNDataset-method" ] }, { "page": "build.junction.tree", "title": "build a JunctionTree.", "topics": [ "build.junction.tree", "build.junction.tree,InferenceEngine", "build.junction.tree,InferenceEngine-method" ] }, { "page": "child", "title": "load 'Child' dataset.", "topics": [ "child" ] }, { "page": "child_NA_5000", "title": "'Child' dataset.", "topics": [ "child_NA_5000" ] }, { "page": "complete", "title": "Subset a 'BNDataset' to get only complete cases.", "topics": [ "complete", "complete,BNDataset", "complete,BNDataset-method" ] }, { "page": "cpts", "title": "get the list of conditional probability tables of a 'BN'.", "topics": [ "cpts", "cpts,BN", "cpts,BN-method" ] }, { "page": "cpts-set", "title": "set the list of conditional probability tables of a network.", "topics": [ "cpts<-", "cpts<-,BN-method" ] }, { "page": "dag", "title": "get adjacency matrix of a network.", "topics": [ "dag", "dag,BN", "dag,BN-method" ] }, { "page": "dag.to.cpdag", "title": "convert a DAG to a CPDAG", "topics": [ "dag.to.cpdag" ] }, { "page": "dag-set", "title": "set adjacency matrix of an object.", "topics": [ "dag<-", "dag<-,BN-method" ] }, { "page": "data.file", "title": "get data file of a 'BNDataset'.", "topics": [ "data.file", "data.file,BNDataset", "data.file,BNDataset-method" ] }, { "page": "data.file-set", "title": "set data file of a 'BNDataset'.", "topics": [ "data.file<-", "data.file<-,BNDataset-method" ] }, { "page": "discreteness", "title": "get status (discrete or continuous) of the variables of an object.", "topics": [ "discreteness", "discreteness,BN", "discreteness,BN-method", "discreteness,BNDataset", "discreteness,BNDataset-method" ] }, { "page": "discreteness-set", "title": "set status (discrete or continuous) of the variables of an object.", "topics": [ "discreteness<-", "discreteness<-,BN-method", "discreteness<-,BNDataset-method" ] }, { "page": "edge.dir.wpdag", "title": "counts the edges in a WPDAG with their directionality", "topics": [ "edge.dir.wpdag" ] }, { "page": "em", "title": "expectation-maximization algorithm.", "topics": [ "em", "em,InferenceEngine,BNDataset", "em,InferenceEngine,BNDataset-method" ] }, { "page": "get.most.probable.values", "title": "compute the most probable values to be observed.", "topics": [ "get.most.probable.values", "get.most.probable.values,BN", "get.most.probable.values,BN-method", "get.most.probable.values,InferenceEngine", "get.most.probable.values,InferenceEngine-method" ] }, { "page": "has.boots", "title": "check whether a 'BNDataset' has bootstrap samples or not.", "topics": [ "has.boots", "has.boots,BNDataset", "has.boots,BNDataset-method" ] }, { "page": "has.imputed.boots", "title": "check whether a 'BNDataset' has bootstrap samples from imputed data or not.", "topics": [ "has.imputed.boots", "has.imputed.boots,BNDataset", "has.imputed.boots,BNDataset-method" ] }, { "page": "has.imputed.data", "title": "check if a BNDataset contains impited data.", "topics": [ "has.imputed.data", "has.imputed.data,BNDataset", "has.imputed.data,BNDataset-method" ] }, { "page": "has.raw.data", "title": "check if a BNDataset contains raw data.", "topics": [ "has.raw.data", "has.raw.data,BNDataset", "has.raw.data,BNDataset-method" ] }, { "page": "header.file", "title": "get header file of a 'BNDataset'.", "topics": [ "header.file", "header.file,BNDataset", "header.file,BNDataset-method" ] }, { "page": "header.file-set", "title": "set header file of a 'BNDataset'.", "topics": [ "header.file<-", "header.file<-,BNDataset-method" ] }, { "page": "imp.boots", "title": "get list of bootstrap samples from imputed data of a 'BNDataset'.", "topics": [ "imp.boots", "imp.boots,BNDataset", "imp.boots,BNDataset-method" ] }, { "page": "imp.boots-set", "title": "set list of bootstrap samples from imputed data of a 'BNDataset'.", "topics": [ "imp.boots<-", "imp.boots<-,BNDataset-method" ] }, { "page": "impute", "title": "Impute a 'BNDataset' raw data with missing values.", "topics": [ "impute", "impute,BNDataset", "impute,BNDataset-method" ] }, { "page": "imputed.data", "title": "get imputed data of a BNDataset.", "topics": [ "imputed.data", "imputed.data,BNDataset", "imputed.data,BNDataset-method" ] }, { "page": "imputed.data-set", "title": "add imputed data.", "topics": [ "imputed.data<-", "imputed.data<-,BNDataset-method" ] }, { "page": "InferenceEngine-class", "title": "InferenceEngine class.", "topics": [ "InferenceEngine", "InferenceEngine,InferenceEngine-class", "InferenceEngine-class", "initialize,InferenceEngine-method" ] }, { "page": "interventions", "title": "get the list of interventions of an 'InferenceEngine'.", "topics": [ "interventions", "interventions,InferenceEngine", "interventions,InferenceEngine-method" ] }, { "page": "interventions-set", "title": "set the list of interventions for an 'InferenceEngine'.", "topics": [ "interventions<-", "interventions<-,InferenceEngine-method" ] }, { "page": "jpts", "title": "get the list of joint probability tables compiled by an 'InferenceEngine'.", "topics": [ "jpts", "jpts,InferenceEngine", "jpts,InferenceEngine-method" ] }, { "page": "jpts-set", "title": "set the list of joint probability tables compiled by an 'InferenceEngine'.", "topics": [ "jpts<-", "jpts<-,InferenceEngine-method" ] }, { "page": "jt.cliques", "title": "get the list of cliques of the junction tree of an 'InferenceEngine'.", "topics": [ "jt.cliques", "jt.cliques,InferenceEngine", "jt.cliques,InferenceEngine-method" ] }, { "page": "jt.cliques-set", "title": "set the list of cliques of the junction tree of an 'InferenceEngine'.", "topics": [ "jt.cliques<-", "jt.cliques<-,InferenceEngine-method" ] }, { "page": "junction.tree", "title": "get the junction tree of an 'InferenceEngine'.", "topics": [ "junction.tree", "junction.tree,InferenceEngine", "junction.tree,InferenceEngine-method" ] }, { "page": "junction.tree-set", "title": "set the junction tree of an 'InferenceEngine'.", "topics": [ "junction.tree<-", "junction.tree<-,InferenceEngine-method" ] }, { "page": "knn.impute", "title": "Perform imputation of a data frame using k-NN.", "topics": [ "knn.impute" ] }, { "page": "layering", "title": "return the layering of the nodes.", "topics": [ "layering", "layering,BN", "layering,BN-method" ] }, { "page": "learn.dynamic.network", "title": "learn a dynamic network (structure and parameters) of a BN from a BNDataset.", "topics": [ "learn.dynamic.network", "learn.dynamic.network,BN", "learn.dynamic.network,BN-method", "learn.dynamic.network,BNDataset", "learn.dynamic.network,BNDataset-method" ] }, { "page": "learn.network", "title": "learn a network (structure and parameters) of a BN from a BNDataset.", "topics": [ "learn.network", "learn.network,BN", "learn.network,BN-method", "learn.network,BNDataset", "learn.network,BNDataset-method" ] }, { "page": "learn.params", "title": "learn the parameters of a BN.", "topics": [ "learn.params", "learn.params,BN,BNDataset", "learn.params,BN,BNDataset-method" ] }, { "page": "learn.structure", "title": "learn the structure of a network.", "topics": [ "learn.structure", "learn.structure,BN,BNDataset", "learn.structure,BN,BNDataset-method" ] }, { "page": "marginals", "title": "compute the list of inferred marginals of a BN.", "topics": [ "marginals", "marginals,InferenceEngine", "marginals,InferenceEngine-method" ] }, { "page": "name", "title": "get name of an object.", "topics": [ "name", "name,BN", "name,BN-method", "name,BNDataset", "name,BNDataset-method" ] }, { "page": "name-set", "title": "set name of an object.", "topics": [ "name<-", "name<-,BN-method", "name<-,BNDataset-method" ] }, { "page": "node.sizes", "title": "get size of the variables of an object.", "topics": [ "node.sizes", "node.sizes,BN", "node.sizes,BN-method", "node.sizes,BNDataset", "node.sizes,BNDataset-method" ] }, { "page": "node.sizes-set", "title": "set the size of variables of an object.", "topics": [ "node.sizes<-", "node.sizes<-,BN-method", "node.sizes<-,BNDataset-method" ] }, { "page": "num.boots", "title": "get number of bootstrap samples of a 'BNDataset'.", "topics": [ "num.boots", "num.boots,BNDataset", "num.boots,BNDataset-method" ] }, { "page": "num.boots-set", "title": "set number of bootstrap samples of a 'BNDataset'.", "topics": [ "num.boots<-", "num.boots<-,BNDataset-method" ] }, { "page": "num.items", "title": "get number of items of a 'BNDataset'.", "topics": [ "num.items", "num.items,BNDataset", "num.items,BNDataset-method" ] }, { "page": "num.items-set", "title": "set number of items of a 'BNDataset'.", "topics": [ "num.items<-", "num.items<-,BNDataset-method" ] }, { "page": "num.nodes", "title": "get number of nodes of an object.", "topics": [ "num.nodes", "num.nodes,BN", "num.nodes,BN-method", "num.nodes,InferenceEngine", "num.nodes,InferenceEngine-method" ] }, { "page": "num.nodes-set", "title": "set number of nodes of an object.", "topics": [ "num.nodes<-", "num.nodes<-,BN-method", "num.nodes<-,InferenceEngine-method" ] }, { "page": "num.time.steps", "title": "get number of time steps observed in a 'BN' or a 'BNDataset'.", "topics": [ "num.time.steps", "num.time.steps,BN", "num.time.steps,BN-method", "num.time.steps,BNDataset", "num.time.steps,BNDataset-method" ] }, { "page": "num.time.steps-set", "title": "set number of time steps of a 'BN' or a 'BNDataset'.", "topics": [ "num.time.steps<-", "num.time.steps<-,BN-method", "num.time.steps<-,BNDataset-method" ] }, { "page": "num.variables", "title": "get number of variables of a 'BNDataset'.", "topics": [ "num.variables", "num.variables,BNDataset", "num.variables,BNDataset-method" ] }, { "page": "num.variables-set", "title": "set number of variables of a 'BNDataset'.", "topics": [ "num.variables<-", "num.variables<-,BNDataset-method" ] }, { "page": "observations", "title": "get the list of observations of an 'InferenceEngine'.", "topics": [ "observations", "observations,InferenceEngine", "observations,InferenceEngine-method" ] }, { "page": "observations-set", "title": "set the list of observations of an 'InferenceEngine'.", "topics": [ "observations<-", "observations<-,InferenceEngine-method" ] }, { "page": "plot", "title": "plot a 'BN' as a picture.", "topics": [ "plot", "plot,BN", "plot.BN", "plot.BN,BN" ] }, { "page": "print", "title": "print a 'BN', 'BNDataset' or 'InferenceEngine' to 'stdout'.", "topics": [ "print", "print,BN", "print,BNDataset", "print,InferenceEngine", "print.BN", "print.BN,BN", "print.BNDataset", "print.BNDataset,BNDataset", "print.InferenceEngine", "print.InferenceEngine,InferenceEngine" ] }, { "page": "quantiles", "title": "get the list of quantiles of an object.", "topics": [ "quantiles", "quantiles,BN", "quantiles,BN-method", "quantiles,BNDataset", "quantiles,BNDataset-method" ] }, { "page": "quantiles-set", "title": "set the list of quantiles of an object.", "topics": [ "quantiles<-", "quantiles<-,BN-method", "quantiles<-,BNDataset-method" ] }, { "page": "raw.data", "title": "get raw data of a BNDataset.", "topics": [ "raw.data", "raw.data,BNDataset", "raw.data,BNDataset-method" ] }, { "page": "raw.data-set", "title": "add raw data.", "topics": [ "raw.data<-", "raw.data<-,BNDataset-method" ] }, { "page": "read.bif", "title": "Read a network from a '.bif' file.", "topics": [ "read.bif", "read.bif,character", "read.bif,character-method" ] }, { "page": "read.dataset", "title": "Read a dataset from file.", "topics": [ "read.dataset", "read.dataset,BNDataset,character,character", "read.dataset,BNDataset,character,character-method" ] }, { "page": "read.dsc", "title": "Read a network from a '.dsc' file.", "topics": [ "read.dsc", "read.dsc,character", "read.dsc,character-method" ] }, { "page": "read.net", "title": "Read a network from a '.net' file.", "topics": [ "read.net", "read.net,character", "read.net,character-method" ] }, { "page": "sample.dataset", "title": "sample a 'BNDataset' from a network of an inference engine.", "topics": [ "sample.dataset", "sample.dataset,BN", "sample.dataset,BN-method", "sample.dataset,InferenceEngine", "sample.dataset,InferenceEngine-method" ] }, { "page": "sample.row", "title": "sample a row vector of values for a network.", "topics": [ "sample.row", "sample.row,BN", "sample.row,BN-method" ] }, { "page": "save.to.eps", "title": "save a 'BN' picture as '.eps' file.", "topics": [ "save.to.eps", "save.to.eps,BN,character", "save.to.eps,BN,character-method" ] }, { "page": "scoring.func", "title": "Read the scoring function used to learn the structure of a network.", "topics": [ "scoring.func", "scoring.func,BN", "scoring.func,BN-method" ] }, { "page": "scoring.func-set", "title": "Set the scoring function used to learn the structure of a network.", "topics": [ "scoring.func<-", "scoring.func<-,BN-method" ] }, { "page": "shd", "title": "compute the Structural Hamming Distance between two adjacency matrices.", "topics": [ "shd" ] }, { "page": "show", "title": "Show method for objects.", "topics": [ "show", "show,AllTheClasses-method", "show,BN-method", "show,BNDataset-method", "show,InferenceEngine-method" ] }, { "page": "struct.algo", "title": "Read the algorithm used to learn the structure of a network.", "topics": [ "struct.algo", "struct.algo,BN", "struct.algo,BN-method" ] }, { "page": "struct.algo-set", "title": "Set the algorithm used to learn the structure of a network.", "topics": [ "struct.algo<-", "struct.algo<-,BN-method" ] }, { "page": "test.updated.bn", "title": "check if an updated 'BN' is present in an 'InferenceEngine'.", "topics": [ "test.updated.bn", "test.updated.bn,InferenceEngine", "test.updated.bn,InferenceEngine-method" ] }, { "page": "tune.knn.impute", "title": "tune the parameter k of the knn algorithm used in imputation.", "topics": [ "tune.knn.impute" ] }, { "page": "updated.bn-method", "title": "get the updated 'BN' object contained in an 'InferenceEngine'.", "topics": [ "updated.bn", "updated.bn,InferenceEngine", "updated.bn,InferenceEngine-method" ] }, { "page": "updated.bn-set", "title": "set the updated 'BN' object contained in an 'InferenceEngine'.", "topics": [ "updated.bn<-", "updated.bn<-,InferenceEngine-method" ] }, { "page": "variables", "title": "get variables of an object.", "topics": [ "variables", "variables,BN", "variables,BN-method", "variables,BNDataset", "variables,BNDataset-method" ] }, { "page": "variables-set", "title": "set variables of an object.", "topics": [ "variables<-", "variables<-,BN-method", "variables<-,BNDataset-method" ] }, { "page": "wpdag", "title": "get the WPDAG of an object.", "topics": [ "wpdag", "wpdag,BN", "wpdag,BN-method" ] }, { "page": "wpdag.from.dag", "title": "Initialize a WPDAG from a DAG.", "topics": [ "wpdag.from.dag", "wpdag.from.dag,BN", "wpdag.from.dag,BN-method" ] }, { "page": "wpdag-set", "title": "set WPDAG of the object.", "topics": [ "wpdag<-", "wpdag<-,BN-method" ] }, { "page": "write_xgmml", "title": "Write a network saving it in an 'XGMML' file.", "topics": [ "write_xgmml", "write_xgmml,BN", "write_xgmml,BN-method" ] }, { "page": "write.dsc", "title": "Write a network saving it in a '.dsc' file.", "topics": [ "write.dsc", "write.dsc,BN", "write.dsc,BN-method" ] } ], "_readme": "https://github.com/cran/bnstruct/raw/HEAD/README.md", "_rundeps": [ "bitops", "cli", "cpp11", "glue", "igraph", "lattice", "lifecycle", "magrittr", "Matrix", "pkgconfig", "rlang", "vctrs" ], "_vignettes": [ { "source": "bnstruct.Rnw", "filename": "bnstruct.pdf", "title": "\\texttt{bnstruct}: an R package for Bayesian Network Structure Learning", "engine": "utils::Sweave", "headings": [], "created": "2016-11-10 13:43:16", "modified": "2022-11-30 13:10:02", "commits": 8 } ], 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