Package: gRbase 2.0.3

Søren Højsgaard

gRbase: A Package for Graphical Modelling in R

The 'gRbase' package provides graphical modelling features used by e.g. the packages 'gRain', 'gRim' and 'gRc'. 'gRbase' implements graph algorithms including (i) maximum cardinality search (for marked and unmarked graphs). (ii) moralization, (iii) triangulation, (iv) creation of junction tree. 'gRbase' facilitates array operations, 'gRbase' implements functions for testing for conditional independence. 'gRbase' illustrates how hierarchical log-linear models may be implemented and describes concept of graphical meta data. The facilities of the package are documented in the book by Højsgaard, Edwards and Lauritzen (2012, <doi:10.1007/978-1-4614-2299-0>) and in the paper by Dethlefsen and Højsgaard, (2005, <doi:10.18637/jss.v014.i17>). Please see 'citation("gRbase")' for citation details.

Authors:Søren Højsgaard [aut, cre]

gRbase_2.0.3.tar.gz
gRbase_2.0.3.tar.gz(r-4.5-noble)gRbase_2.0.3.tar.gz(r-4.4-noble)
gRbase_2.0.3.tgz(r-4.4-emscripten)gRbase_2.0.3.tgz(r-4.3-emscripten)
gRbase.pdf |gRbase.html
gRbase/json (API)
NEWS

# Install 'gRbase' in R:
install.packages('gRbase', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
Datasets:
  • BodyFat - Body Fat Data
  • Nutrimouse - The Nutrimouse Dataset
  • ashtrees - Crown dieback in ash trees
  • breastcancer - Gene expression signatures for p53 mutation status in 250 breast cancer samples
  • cad1 - Coronary artery disease data
  • cad2 - Coronary artery disease data
  • carcass - Lean meat contents of 344 pig carcasses
  • carcassall - Lean meat contents of 344 pig carcasses
  • chestSim1000 - Simulated data from the Chest Clinic example
  • chestSim10000 - Simulated data from the Chest Clinic example
  • chestSim100000 - Simulated data from the Chest Clinic example
  • chestSim500 - Simulated data from the Chest Clinic example
  • chestSim50000 - Simulated data from the Chest Clinic example
  • dietox - Growth curves of pigs in a 3x3 factorial experiment
  • dumping - Gastric Dumping
  • lizard - Lizard behaviour
  • lizardAGG - Lizard behaviour
  • lizardRAW - Lizard behaviour
  • math - Mathematics marks for students
  • mathmark - Mathematics marks for students
  • mildew - Mildew fungus
  • milkcomp - Milk composition data
  • milkcomp1 - Milk composition data
  • personality - Personality traits
  • prostate - Prostate Tumor Gene Expression Dataset
  • rats - Weightloss of rats
  • reinis - Risk factors for coronary heart disease.
  • wine - Chemical composition of wine

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

7.58 score 20 packages 209 scripts 3.4k downloads 3 mentions 240 exports 14 dependencies

Last updated 2 months agofrom:de2eeb409c. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 22 2024
R-4.5-linux-x86_64OKNov 22 2024

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Dependencies:clicpp11glueigraphlatticelifecyclemagrittrMatrixpkgconfigRcppRcppArmadilloRcppEigenrlangvctrs

Array operations with the gRbase package

Rendered fromarrays.rmdusingknitr::knitron Nov 22 2024.

Last update: 2024-10-22
Started: 2024-06-06

Graphs with the gRbase package

Rendered fromgraphs.rmdusingknitr::knitron Nov 22 2024.

Last update: 2024-06-06
Started: 2024-06-06

Readme and manuals

Help Manual

Help pageTopics
Create all possible pairsall_pairs names2pairs
Create all subsetsall_subsets all_subsets0
Array slicesapi_tabSlice tabSlice tabSlice2 tabSlice2Entries tabSliceMult tabSlicePrim
Array operations (2007)api-array-07 tableDiv tableGetSliceIndex tableMargin tableMult tableOp tableOp0 tableOp2 tablePerm tableSetSliceValue tableSlice tableSlicePrim
Check if object is arrayapi-array-properties dimnames_match is.named.array is_dimnames_ is_named_array_ is_number_vector_
Table cell operations.api-cell cell2entry cell2entry_perm entry2cell fact_grid next_cell next_cell2 next_cell_slice perm_cell_entries slice2entry
Low level table cell operations implemented in c++api-cell_ cell2entry_ cell2entry_perm_ entry2cell_ make_plevels_ next_cell2_ next_cell_ next_cell_slice_ perm_cell_entries_ slice2entry_
Representation of and operations on multidimensional arraysapi-parray as.parray data2parray makeDimNames parray
Array algebra%a*% %a+% %a-% %a/% %a/0% %a==% %aalign% %amarg% %aperm% %aslice% %aslice*% %a^% %a_% api-pct-operations
Marginalize and condition in multidimensional array.api-tabDist tabDist
Create multidimensional arraysapi-tabNew tabNew
Interface - operations on multidimensional arrays.api-tabX tabAdd tabAlign tabDiv tabDiv0 tabEqual tabExpand tabListAdd tabListMult tabMarg tabMult tabNormalize tabOp tabPerm tabProd tabSubt tabSum
Table operations implemented in c++api-tabX_ tab_add_ tab_align_ tab_div0_ tab_div_ tab_equal_ tab_expand_ tab_list_add_ tab_list_mult_ tab_marg_ tab_mult_ tab_op_ tab_perm_ tab_subt_
Simulate data from array.array-simulate simulate.array simulate.table simulate.xtabs simulateArray
Generic function for model comparisoncompareModels
Partial correlation (matrix)conc2pcor cov2pcor
Coronary artery disease datacad1 cad2 data_cad
Utilities for data handlingdata_handling nLevels nLevels.default valueLabels valueLabels.default varNames varNames.default
Crown dieback in ash treesashtrees data-ashtrees
Body Fat DataBodyFat data-BodyFat
Gene expression signatures for p53 mutation status in 250 breast cancer samplesbreastcancer data-breastcancer
Lean meat contents of 344 pig carcassescarcass carcassall data-carcass
Simulated data from the Chest Clinic examplechestSim1000 chestSim10000 chestSim100000 chestSim500 chestSim50000 data-chestSim
Growth curves of pigs in a 3x3 factorial experimentdata-dietox dietox
Gastric Dumpingdata-dumping dumping
Lizard behaviourdata-lizard lizard lizardAGG lizardRAW
Mathematics marks for studentsdata-mathmark math mathmark
Mildew fungusdata-mildew mildew
Milk composition datadata-milkcomp milkcomp milkcomp1
The Nutrimouse Datasetdata-Nutrimouse Nutrimouse
Personality traitsdata-personality personality
Weightloss of ratsdata-rats rats
Risk factors for coronary heart disease.data-reinis reinis
Chemical composition of winedata-wine wine
Downstream aliasesdownstream-aliases ell ellK
Coerce dag to edge matrixdag2edge_matrix edge_matrix edge_matrix2dag
Generate All Combinations of n Elements Taken m at a Timecombn_prim fastcombn
Functions from Graphical Modelling with R bookas.adjMAT gmwr_book
Coercion of graphs represented as listsgraph_coerce_list g_adl2dm_ g_adl2ig_ g_adl2M_ g_adl2sm_ g_adl2XX_ g_dagl2dm_ g_dagl2ig_ g_dagl2M_ g_dagl2sm_ g_dagl2XX_ g_M2adl_ g_M2dagl_ g_M2ugl_ g_ugl2dm_ g_ugl2ig_ g_ugl2M_ g_ugl2sm_ g_ugl2XX_
Function for plotting graphs using the 'igraph' package.graph_iplot iplot iplot.igraph
Check properties of graphs.graph_is is.adjMAT is.DAG is.DG is.TUG is.UG is_adjMAT is_dag is_dagMAT is_dg is_dgMAT is_tug is_tugMAT is_ug is_ugMAT
Query a graphaddEdge adj ancestors ancestralGraph ancestralSet children closure connComp edges edges_ graph_query is.complete is.decomposition is.simplicial is.triangulated nodes nodes,igraph-method nodes_ parents qgraph querygraph removeEdge separates simplicialNodes subGraph
Topological sort of vertices in directed acyclic graphgraph_topo_sort topoSort topoSortMAT topo_sort topo_sortMAT
List of vertices and their parents for graph.graph_vpar vchi vchiMAT vpar vparMAT
Get cliques of an undirected graphgetCliques get_cliques graph-clique maxClique maxCliqueMAT max_cliqueMAT
Graph coercioncoerceGraph graph-coerce graph_as
API for coercing graph representationsgraph-coerce-api g_dm2ig_ g_dm2sm_ g_ig2dm_ g_ig2sm_ g_sm2dm_ g_sm2ig_ g_xm2dm_ g_xm2ig_ g_xm2sm_ g_xm2xm_
Create undirected and directed graphsdag dagi dagList graph-create ug ugi ugList
Find edges in a graph and edges not in a graph.edgeList edgeListMAT graph-edgeList nonEdgeList nonEdgeListMAT
Properties of a generating class (for defining a graph).graph-gcproperties isDecomposable isDecomposable.default isGraphical isGraphical.default
Maximum cardinality search on undirected graph.graph-mcs mcs mcs.default mcsMAT mcs_marked mcs_marked.default mcs_markedMAT
Minimal triangulation of an undirected graphgraph-min-triangulate minimal_triang minimal_triangMAT
Moralize a directed acyclic graphgraph-moralize moralize moralize.default moralizeMAT
Maximal prime subgraph decompositiongraph-mpd mpd mpd.default mpdMAT
Random directed acyclic graphgraph-randomdag random_dag
Create RIP ordering of the cliques of an undirected graph; create junction tree.graph-rip jTree junctionTree junction_tree junction_tree.default junction_treeMAT rip rip.default ripMAT
Triangulation of an undirected graphgraph-triangulate triang triang.default triangulate triangulate.default triangulateMAT triang_elo triang_elo.default triang_eloMAT triang_eloMAT_ triang_mcwh triang_mcwh.default triang_mcwhMAT_
The package `gRbase': summary informationgRbase
Compile and propagate functionscompile fit grbase_generics propagate stepwise
gRbase utilitiescolmat2list colSumsPrim colwiseProd grbase-utilities lapplyI2V lapplyV2I list2rhsf list2rhsFormula listify_dots matrix2list pairs2num rhsf2list rhsf2vec rhsFormula2list rowmat2list rowSumsPrim which.arr.index which_matrix_index
Internal functions for the gRbase package%>% addEdge.gModel dropEdge.gModel extract.power ggm internal isGSD_glist MAT2ftM_ processFormula randomGraph selectOrder solveSPD symMAT2ftM_
Prostate Tumor Gene Expression Datasetprostate
Suite of set operationsfilter_maximal_vectors get_subset get_superset is.subsetof is_inset is_subsetof maximal_sets minimal_sets remove_redundant set-operations subsetof
Coerce between undirected and directed graphs when possibleug2dag