A major update of stagedtrees (v2.0.0) is available on CRAN.

The update will almost surely break any code written with v1.0.2. Functions naming and functions parameters have been updated to simplify user experience. Check the complete changelog for details.

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.