Changes in version 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.

                        Changes in version 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.

                        Changes in version 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.