bacontrees 0.0.4

Changes

• plot.baConTree() has been redesigned to reflect the package’s focus on exact Bayesian inference. Node fill now encodes posteriorBranchingProbability (the posterior probability that the node has children in the true context tree). The previous version coloured nodes by prunePosteriorRatio, a quantity specific to the Metropolis-Hastings sampler with no direct probabilistic interpretation.

New features

• treeFromContexts() has been removed. Instead, ContextTree now exposes an $activateFromContexts(contexts) method that activates a specific tree on an existing ContextTree object. It accepts the same input format as the old function (a character vector of context paths, or a single brace-enclosed comma-separated string).

• baConTree nodes now store priorBranchingProbability and posteriorBranchingProbability in their extra list. These are computed during initialisation as prod(children sigmaPrior) / sigmaPrior (and the posterior analogue), representing the probability that the tree branches at that node rather than stopping.

• baConTree now exposes a $sampleTree(type) method for exact sampling from the prior (type = "prior") or posterior (type = "posterior") distribution over context trees. The method sets the active tree to the sampled tree and invisibly returns its tree code.

• baConTree now exposes a $activateMap() method that sets the active tree to the Maximum a Posteriori (MAP) tree — the context tree with the highest posterior probability. baConTree$new() also gains an initialTree argument ("map" or "root", defaulting to "map") to control which tree is active right after construction.

• baConTree now exposes a $getMarginalLikelihood(log = TRUE) method that returns the marginal likelihood of the data under the Bayesian context tree model (i.e. sigmaPosterior / sigmaPrior at the root, summed over all trees). Pass log = TRUE (default) for a plain R numeric on the log scale, or log = FALSE for the exact value as a brob object.

bacontrees 0.0.3

API changes

• The priorWeights argument in baConTree$new() and the context_weights argument in metropolis_vlmc() now expect a function that returns weights on the natural scale (i.e. non-log). The log() transformation is applied internally. The default for context_weights has changed from function(node) 0 to function(node) 1 to preserve the same uniform-prior behaviour.

• Each node’s extra list now stores both priorWeight (natural scale, as returned by the user-supplied function) and logPriorWeight (log scale, used internally for posterior computations).

• In the baConTree class, alpha and priorWeights are now required arguments in $new() and must be passed at initialization. The $setAlpha() and $setContextPriorWeights() methods have been removed.

• The active argument has been removed from ContextTree$new() (and therefore baConTree$new()). The tree is always initialized with the maximal active tree. To start from the root, call $activateRoot() after construction.

• The initial_root argument has been removed from metropolis_vlmc(). The chain always starts from the maximal tree.

Internal / encapsulation improvements

• ContextTree$nodes is now a read-only active binding. External code can still read nodes and mutate their attributes (e.g. $extra) via R6 reference semantics, but structural changes to the node list (adding or removing nodes) are rejected with an error.

• TreeNode$counts is now a private field exposed through a validated active binding. The public interface is unchanged, but non-numeric assignments now throw an error.

• TreeNode$setChildrenPaths() has been removed from the public API. Children paths are now set internally by ContextTree via direct private-environment access, as this operation is only meaningful during tree construction.

Bug fixes

• Fixed TreeNode computing the wrong parentPath for alphabet symbols longer than one character. The path was truncated by a fixed two-character offset (str_sub(..., end = -3)) instead of splitting on . and dropping the last segment.

• ContextTree$activateByCode() now correctly recomputes growableNodes and prunableNodes after restoring a tree from a code, so subsequent $growActive() and $pruneActive() calls behave correctly.

bacontrees 0.0.2

API changes

• ContextTree (and therefore) baConTree classes can now initialize with a data argument instead of using $setData() method in a posterior call. The Alphabet argument is not required if data is used, and the alphabet is inferred from the data. data is the first argument, so initialization based on past implementation with unnamed arguments will break.

• In the ContextTree class, the isLeaf attribute is now substituted by the private attribute isLeaf_. The public isLeaf() method is available to check if a node is a leaf.

• In the baConTree class, the $setAllDirichletPars() method was renamed to $setAlpha(). Node attributes set by this class are now named: marginalNodeLL, priorWeight, posteriorWeight, childrenPosteriorWeight, growPosteriorRatio and prunePosteriorRatio.

New features

• Added $igraph() method do ContextTree for converting it to an igraph object. This object can be used for plotting with ggraph and contains the main attributes and all extra attributes from nodes.

• Added S3 plot methods for both ContextTree and baConTree classes.