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:
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')) |
- 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.
Last updated 1 months agofrom:de2eeb409c. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 22 2024 |
| R-4.5-linux-x86_64 | OK | Nov 22 2024 |
Exports:%a_%%a-%%a*%%a/%%a/0%%a^%%a+%%a==%%aalign%%amarg%%aperm%%aslice*%%aslice%addEdgeadjall_pairsall_subsetsall_subsets0ancestorsancestralGraphancestralSetas.adjMATas.parraycell2entrycell2entry_permchildrenclosurecoerceGraphcolmat2listcolSumsPrimcolwiseProdcombn_primcompareModelscompileconc2pcorconnCompcov2pcordagdag2edge_matrixdagidagListdata2parraydimnames_matchedge_matrix2dagedgeListedgeListMATedgesedges_ellellKentry2cellfact_gridfastcombnfilter_maximal_vectorsfitg_adl2dm_g_adl2ig_g_adl2M_g_adl2sm_g_adl2XX_g_dagl2dm_g_dagl2ig_g_dagl2M_g_dagl2sm_g_dagl2XX_g_dm2ig_g_dm2sm_g_ig2dm_g_ig2sm_g_M2adl_g_M2dagl_g_M2ugl_g_sm2dm_g_sm2ig_g_ugl2dm_g_ugl2ig_g_ugl2M_g_ugl2sm_g_ugl2XX_g_xm2dm_g_xm2ig_g_xm2sm_g_xm2xm_get_cliquesget_subsetget_supersetgetCliquesgraph_asiplotis_adjMATis_dagis_dagMATis_dgis_dgMATis_dimnames_is_insetis_named_array_is_number_vector_is_subsetofis_tugis_tugMATis_ugis_ugMATis.adjMATis.completeis.DAGis.decompositionis.DGis.named.arrayis.simplicialis.subsetofis.triangulatedis.TUGis.UGisDecomposableisDecomposable.defaultisGraphicalisGraphical.defaultisGSD_glistjTreejunction_treejunction_treeMATjunctionTreelapplyI2VlapplyV2Ilist2rhsflist2rhsFormulalistify_dotsmakeDimNamesMAT2ftM_matrix2listmax_cliqueMATmaxCliquemaxCliqueMATmaximal_setsmcsmcs_markedmcs_markedMATmcsMATminimal_setsminimal_triangminimal_triangMATmoralizemoralizeMATmpdmpdMATnames2pairsnext_cellnext_cell_slicenext_cell2nLevelsnodesnodes_nonEdgeListnonEdgeListMATpairs2numparentsparrayperm_cell_entriesplotpropagateqgraphquerygraphrandom_dagremove_redundantremoveEdgerhsf2listrhsf2vecrhsFormula2listripripMATrowmat2listrowSumsPrimseparatessimplicialNodessimulateArrayslice2entrysolveSPDstepwisesubGraphsubsetofsymMAT2ftM_tabAddtabAligntabDisttabDivtabDiv0tabEqualtabExpandtableDivtableGetSliceIndextableMargintableMulttableOptableOp0tableOp2tablePermtableSetSliceValuetableSlicetableSlicePrimtabListAddtabListMulttabMargtabMulttabNewtabNormalizetabOptabPermtabProdtabSlicetabSlice2tabSlice2EntriestabSliceMulttabSlicePrimtabSubttabSumtopo_sorttopo_sortMATtopoSorttopoSortMATtriangtriang_elotriang_eloMATtriang_eloMAT_triang_mcwhtriang_mcwhMAT_triangulatetriangulateMATugug2dagugiugListvalueLabelsvarNamesvchivchiMATvparvparMATwhich_matrix_indexwhich.arr.index
Dependencies:clicpp11glueigraphlatticelifecyclemagrittrMatrixpkgconfigRcppRcppArmadilloRcppEigenrlangvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Create all possible pairs | all_pairs names2pairs |
| Create all subsets | all_subsets all_subsets0 |
| Array slices | api_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 array | api-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 arrays | api-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 arrays | api-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 comparison | compareModels |
| Partial correlation (matrix) | conc2pcor cov2pcor |
| Coronary artery disease data | cad1 cad2 data_cad |
| Utilities for data handling | data_handling nLevels nLevels.default valueLabels valueLabels.default varNames varNames.default |
| Crown dieback in ash trees | ashtrees data-ashtrees |
| Body Fat Data | BodyFat data-BodyFat |
| Gene expression signatures for p53 mutation status in 250 breast cancer samples | breastcancer data-breastcancer |
| Lean meat contents of 344 pig carcasses | carcass carcassall data-carcass |
| Simulated data from the Chest Clinic example | chestSim1000 chestSim10000 chestSim100000 chestSim500 chestSim50000 data-chestSim |
| Growth curves of pigs in a 3x3 factorial experiment | data-dietox dietox |
| Gastric Dumping | data-dumping dumping |
| Lizard behaviour | data-lizard lizard lizardAGG lizardRAW |
| Mathematics marks for students | data-mathmark math mathmark |
| Mildew fungus | data-mildew mildew |
| Milk composition data | data-milkcomp milkcomp milkcomp1 |
| The Nutrimouse Dataset | data-Nutrimouse Nutrimouse |
| Personality traits | data-personality personality |
| Weightloss of rats | data-rats rats |
| Risk factors for coronary heart disease. | data-reinis reinis |
| Chemical composition of wine | data-wine wine |
| Downstream aliases | downstream-aliases ell ellK |
| Coerce dag to edge matrix | dag2edge_matrix edge_matrix edge_matrix2dag |
| Generate All Combinations of n Elements Taken m at a Time | combn_prim fastcombn |
| Functions from Graphical Modelling with R book | as.adjMAT gmwr_book |
| Coercion of graphs represented as lists | graph_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 graph | addEdge 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 graph | graph_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 graph | getCliques get_cliques graph-clique maxClique maxCliqueMAT max_cliqueMAT |
| Graph coercion | coerceGraph graph-coerce graph_as |
| API for coercing graph representations | graph-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 graphs | dag 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 graph | graph-min-triangulate minimal_triang minimal_triangMAT |
| Moralize a directed acyclic graph | graph-moralize moralize moralize.default moralizeMAT |
| Maximal prime subgraph decomposition | graph-mpd mpd mpd.default mpdMAT |
| Random directed acyclic graph | graph-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 graph | graph-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 information | gRbase |
| Compile and propagate functions | compile fit grbase_generics propagate stepwise |
| gRbase utilities | colmat2list 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 Dataset | prostate |
| Suite of set operations | filter_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 possible | ug2dag |
