NEWS (original) (raw)

2.3.0

• Fix new package doc format.
• Carli et al. 2022 JSS citation added in DESCRIPTION.
• Added functions for random generation of staged trees:random_sevt and random_parentslist.
• Added new function depsubtree which build the dependency subtree.
• New functions to translate sevt and cegobjects to graphs (edge lists and igraph).
• Fix #98; fixed handling of NAs.
• fix bug on plot.sevt and on graph conversion methods when ignoring stage “1” which is assigned to root
• Fix #80; sevt_fit earns the scopeargument, it is now possible to do partial re-fit of staged tree models. Moreover, with the compute_logLik argument, the user can decide if the log-likelihood should be computed when fitting the model.
• stages_hclust can now search the best cut of the hierarchical cluster with respect to some score function to be maximized.
• various minor fixes in colors specification for visualization functions.
• stages_simplebhc implements a new stage structure search by iterative joining of positions, thus searching in the space of simple staged trees.
• sevt_simplify return the simplified staged tree, that is a stage tree where positions and stages are equivalent.
• fix problem with positions computation in ceg when model has less than two variables.
• Fix #113; use cli package for errors and warnings.
• improve arguments checks in various functions.
• improve specific checks for sevt objects.
• fix minor coding style problems (some argument names have changed).
• improve test coverage.
• new return value of stages function and new indexing of stages via a new dedicated class sevt.stgs.
• use faster and unsafe functions internally, speedup in various functions (up to 10x).
• implemented stages_csbhc, a new stages learning algorithm which iteratively add context specific independencies. Additionally functions ci_matrices andjoin_all have been added.

2.2.1

• inst/CITATION file added as requested by JSS.
• The DOI in the CITATION is for a new JSS publication that will be registered after publication on CRAN.
• broken badge url fixed in README.
• update documentation.

2.2.0

• plot.ceg new plotting functions usingigraph plotting.
• new util function make_stages_col which help computing stages colors for sevt and ceg plotting.
• sample_from now returns a data.frame of factors.
• prob earns a new argument conditional_on, that makes easier to compute conditional probabilities.
• confint.sevt, implement a method for confidence intervals for the parameters of a model of class sevt.
• lr_test new function, implementing likelihood-ratio test.
• functions to search optimal staged trees among different orders:search_best and search_greedy.
• cid function that implements context intervention discrepancy.
• more and better testing and documentation.

2.1.0

• implemented various conversion algorithms between sevtand DAG representations.
• improve implementation of as_sevt.bn.fit.
• use instead of for package names in documentation.
• fix find_stage.
• fix problems with single-variable staged trees.
• fix summary.sevt for objects withoutctables.
• fix bug in path_probability and prob for sevt objects with not ordered $prob.
• more tests.

2.0.1

fix color assignment consistency between plot.sevt andbarplot.sevt

2.0.0

This version introduces major changes, in functions capabilities and in functions naming. These changes are almost surely breaking any previous code using older versions of the package. In particular, all functions named *.sevt but class methods are now called differently. Moreover, various improvements and functionalities are added to better deal with unobserved situations and to improve computations. Additional model selection methods based on clustering are now available.

COMPLETE CHANGELOG:

• DESCRIPTION updated.
• documentation updated.
• improve code comments.
• reduced exported functions.
• removed the fit parameter from full,indep. Now full and indep always fit the model while sevt is just the basic constructor of the sevt class.
• in full and indep by default unobserved situations are joined using join_unobserved, and probabilities are fitted only after the unobserved situations are joined, improving speed. Moreover, the name of the unobserved stages are stored as name_unobserved in the staged tree object.
• update internal function new_label to improve speed.
• plot.sevt allows now to set edges color withcol_edges.
• In plot.sevt and barplot.sevt it is possible to specify stages that should be ignored and not plotted via the ignore argument, by default thename_unobserved stages are ignored.
• plot.sevt adds variables names by default (var_names argument).
• fix in compare_stages: because of changes inplot.sevt we need to specify that the root is always considered identical.
• internal function stndnaming accepts nowuniq, prefix and ignorearguments, which control how stage names are generated and if some stage names should be left untouched (default: thename_unobserved stages).
• in stages_bj (previously bj.sevt) distance is now passed with a character and no longer as a function.
• two new model selection function: stages_hclust andstages_kmeans, to learn stage structure using hierarchical or k-means clustering.
• all model selection functions accept scope andignore parameters that allow to specify among which variables run the algorithm and which stages should be left untouched (default: the name_unobserved stages).
• replace 1:length(x) with the suggestedseq_along in all code.
• distance names in stages_bj andstages_hclust are compatibles.
• fixed bug in some probability distance functions when 0 probabilities.
• Conversion generic function as.sevt, only implemented one method for bn.fit class from bnlearn package
• fix inclusions_stages and provide better output.

1.0.2

• fix bug in summary, stages were wrongly matched to probabilities
• new function barplot_stages to draw barplots of the floret probabilities. Implemented relative tests.
• new example in plot.sevt.
• now order can be passed tostaged_ev_tree.bn.fit
• join_zero alias for join_zero_counts
• more tests

1.0.1

• fix indep, probabilities should not be of class table (it was triggering a bug in summary)
• fix subtree, now removing unused probabilities (it was triggering a bug in summary)
• fixing testing without long double
• fixing some errors in testing
• update some tests with unquoted expression
• new functions get_stage and get_path and relative tests

1.0.0

• Minor doc fix and references added
• xor is renamed as noisy_xor
• test added for noisy_xor
• more util functions marked as internal
• fixed return problem with NaN log-probabilities inpredict.sevt
• summary.sevt function added
• subtree.sevt works now for fitted objects

0.9.5

• Add inclusion.stages function
• Fix #28; predict.sevt now returns conditional probabilities P(C|X)
• Fix #62; predict.sevt works also ifnewdata does not include the class

0.9.4

• Fix #40; compare.sevt works with three different methods.
• Fix #37; join_stages throws error with bad stages.
• Fix #51; tests for model selection functions.

0.9.3

• Fix #39; lambda = 0 does not induce errors inlogLik, join_stages and thus in the model selection algorithms.
• Fix #41; nvar.sevt bug
• Fix #34; order of elements in positions list ofceg.sevt
• Fix #38 subtree and colors in plot bugs
• Fix #46; removed Trump dataset

0.9.1

• New functions: varnames.sevt andnvar.sevt
• Improved codecov
• fit.sevt is replaced by sevt.fit(following the lm.fit naming). fit.sevt is still available but marked as (DEPRECATED) in doc.
• minor bug fixing
• Doc for compare.sevt is updated with info on the capabilities.

0.9.0

First released version of the package