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Forward Trajectory Tree (Prefix Tree)

Source: R/plot_trajectories.R
plot_trajectories.Rd

Where plot.transitiontrees draws the fitted context tree backwards (each node is a suffix, the most-recent move), this draws the same prompts forwards: a prefix tree that starts at a common root and follows each sequence move by move in time. The one tree can be coloured two ways:

measure = "frequency"

node and edge colour and width encode how many sequences walk each path.

measure = "predictability"

colour encodes \(P(\text{move} \mid \text{history})\) from the model (tree); edge width still encodes flow.

Higher values are drawn darker.

Usage

plot_trajectories(
  tree,
  measure = c("frequency", "predictability"),
  min_count = 4L
)

Arguments

tree

A transitiontrees (pass a pruned tree to read predictability off the pruned model).

measure

One of "frequency" (default) or "predictability".

min_count

Integer. Keep only prefixes occurring at least this many times. Default 4.

Value

A ggplot object.

Details

The predictability of a node's last move is the model's conditional probability of that move given the preceding history, truncated to the tree's max_depth and read via query_pathway() (the empty history for a first move uses the root distribution). This is the forward-reading complement to the backward context tree; it is a visualisation, so it depends on ggforce (in Suggests) for the rounded node glyphs and errors with an install hint if it is missing.

See also

plot.transitiontrees for the backward context tree, plot_pruning for the suffix-chain view.

Examples

# \donttest{
seqs <- replicate(120, sample(c("A", "B", "C"), 8, replace = TRUE),
                  simplify = FALSE)
tree   <- context_tree(seqs, max_depth = 3L, min_count = 3L)
pruned <- prune_tree(tree)
if (requireNamespace("ggforce", quietly = TRUE)) {
  plot_trajectories(tree,   measure = "frequency")
  plot_trajectories(pruned, measure = "predictability")
}

# }