Package: stagedtrees 2.3.0

Gherardo Varando

stagedtrees: Staged Event Trees

Creates and fits staged event tree probability models, which are probabilistic graphical models capable of representing asymmetric conditional independence statements for categorical variables. Includes functions to create, plot and fit staged event trees from data, as well as many efficient structure learning algorithms. References: Carli F, Leonelli M, Riccomagno E, Varando G (2022). <doi:10.18637/jss.v102.i06>. Collazo R. A., Görgen C. and Smith J. Q. (2018, ISBN:9781498729604). Görgen C., Bigatti A., Riccomagno E. and Smith J. Q. (2018) <arxiv:1705.09457>. Thwaites P. A., Smith, J. Q. (2017) <arxiv:1510.00186>. Barclay L. M., Hutton J. L. and Smith J. Q. (2013) <doi:10.1016/j.ijar.2013.05.006>. Smith J. Q. and Anderson P. E. (2008) <doi:10.1016/j.artint.2007.05.004>.

Authors:Gherardo Varando [aut, cre], Federico Carli [aut], Manuele Leonelli [aut], Eva Riccomagno [aut]

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stagedtrees.pdf |stagedtrees.html✨
stagedtrees/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/stagedtrees/stagedtrees/issues

Datasets:

On CRAN:

55 exports 8 stars 1.47 score 3 dependencies 4 scripts 257 downloads

Last updated 7 months agofrom:b2c58485fb. Checks:OK: 5 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 13 2024
R-4.5-winOKSep 13 2024
R-4.5-linuxOKSep 13 2024
R-4.4-winOKSep 13 2024
R-4.4-macOKSep 13 2024
R-4.3-winERRORSep 13 2024
R-4.3-macERRORSep 13 2024

Exports:as_adj_matrixas_bnas_igraphas_parentslistas_sevtcegci_matricescidcompare_stagesdepsubtreediff_stagesfullgenerate_linear_datasetgenerate_random_datasetgenerate_xor_datasetget_edgesget_pathget_stageget_verticeshamming_stagesinclusions_stagesindepjoin_positionsjoin_stagesjoin_unobservedlr_testmake_stages_colprobrandom_parentslistrandom_sevtrename_stagesample_fromsearch_bestsearch_greedysevtsevt_addsevt_dfsevt_fitsevt_nvarsevt_simplifysevt_varnamesstagesstages_bhcstages_bhcrstages_bjstages_csbhcstages_fbhcstages_hcstages_hcluststages_kmeansstages_simplebhcstages<-stndnamingsubtreewrite_tikz

Dependencies:climatrixStatsrlang

Readme and manuals

Help Manual

Help pageTopics
Convert to an adjacency matrixas_adj_matrix as_adj_matrix.ceg as_adj_matrix.parentslist
Convert to a 'bnlearn' objectas_bn as_bn.parentslist as_bn.sevt
Obtain the equivalent DAG as list of parentsas_parentslist as_parentslist.bn as_parentslist.bn.fit as_parentslist.sevt
Coerce to sevtas_sevt as_sevt.bn as_sevt.bn.fit as_sevt.parentslist
Print a parentslist objectas.character.parentslist print.parentslist
Asym datasetAsym
Bar plots of stage probabilitiesbarplot.sevt
Chain event graph (CEG)ceg
Conditional independences matrices of stagesci_matrices
Context specific interventional discrepancycid
Compare two staged event treecompare_stages diff_stages hamming_stages
Confidence intervals for staged event tree parametersconfint.sevt
Trajectories of hospitalized SARS-CoV-2 patientscovid_patients
Extract dependency subtreedepsubtree
Full and independent staged event treefull full.data.frame full.table full_indep indep indep.data.frame indep.table
Generate a random binary dataset for classificationgenerate_linear_dataset
Generate a random binary datasetgenerate_random_dataset
Generate a xor datasetgenerate_xor_dataset
Get stage or pathget_path get_stage
'igraph' conversionas_igraph as_igraph.ceg as_igraph.sevt get_edges get_edges.ceg get_edges.sevt get_vertices get_vertices.ceg get_vertices.sevt igraph-conversion
Inclusions of stagesinclusions_stages
join positions in a staged tree modeljoin_positions
Join situations with no observationsjoin_unobserved
Log-Likelihood of a staged event treelogLik.sevt
Likelihood Ratio Test for staged trees modelslr_test
PhD Students PublicationsPhDArticles
igraph's plotting for CEGplot.ceg
Plot method for staged event treesmake_stages_col plot.sevt
Pokemon Go UsersPokemon
Predict method for staged event treepredict.sevt
Print a staged event treeprint.sevt
Probabilities for a staged event treeprob
Generate a random 'parentslist' object (DAG)random_parentslist
Generate a random (fitted) sevtrandom_sevt random_sevt.list random_sevt.parentslist random_sevt.sevt
Rename stage(s) in staged event treerename_stage
Sample from a staged event treesample_from
Optimal Order Searchsearch_best
Greedy Order Searchsearch_greedy
Staged event tree (sevt) classsevt sevt.data.frame sevt.list sevt.table
Add a variable to a staged event treesevt_add
Number of parameters of a staged event treesevt_df
Fit a staged event treesevt_fit
Number of variablessevt_nvar
Simplify a staged tree modelsevt_simplify
Variable namessevt_varnames
Staged event trees.stagedtrees-package stagedtrees
The stages of a staged event treeprint.sevt.stgs stages stages.sevt stages<- [.sevt.stgs [<-.sevt.stgs [[.sevt.stgs [[<-.sevt.stgs
Backward hill-climbingstages_bhc
Backward random hill-climbingstages_bhcr
Backward joining of stagesstages_bj
Context-specific Backward hill-climbingstages_csbhc
Fast backward hill-climbingstages_fbhc
Hill-climbingstages_hc
Learn a staged tree with hierarchical clusteringstages_hclust
Learn a staged tree with k-means clusteringstages_kmeans
Backward hill-climbing for simple staged treesstages_simplebhc
Standard renaming of stagesstndnaming
Extract subtreesubtree
Summarizing staged event treesprint.summary.sevt summary.sevt
Add text to a staged event tree plottext.sevt
Hospital trajectoriestrajectories
Export the staged tree or CEG graph to tikzwrite_tikz write_tikz.sevt