2.2.0

• plot.ceg new plotting functions using igraph 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 sevt and 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 without ctables.
• 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 and barplot.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 with col_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 the name_unobserved stages are ignored.
• plot.sevt adds variables names by default (var_names argument).
• fix in compare_stages: because of changes in plot.sevt we need to specify that the root is always considered identical.
• internal function stndnaming accepts now uniq, prefix and
  ignore arguments, which control how stage names are generated and
  if some stage names should be left untouched (default: the name_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 and stages_kmeans, to learn stage structure using hierarchical or
  k-means clustering.
• all model selection functions accept scope and ignore
  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 suggested seq_along in all code.
• distance names in stages_bj and stages_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 to staged_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 in predict.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 if newdata 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 in logLik, join_stages and thus in the model selection algorithms.
  
• Fix #41; nvar.sevt bug
• Fix #34; order of elements in positions list of ceg.sevt
• Fix #38 subtree and colors in plot bugs
• Fix #46; removed Trump dataset

0.9.1

• New functions: varnames.sevt and nvar.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