# Transition Trajectories and Dynamics of Variable-Length Pathways or Sequences

## Documentation for package ‘transitiontrees’ version 0.1.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

ai_long | AI-collaboration messages (long format)
as.data.frame.transitiontrees | Coerce a context tree to a Tidy Data Frame
as.data.frame.transitiontrees_bootstrap | Coerce a context tree Bootstrap to a Tidy Data Frame
as.data.frame.transitiontrees_comparison | Coerce a context tree Comparison to a Tidy Data Frame
as.data.frame.transitiontrees_group | Coerce a Group of Trees to One Tidy Data Frame
as.data.frame.transitiontrees_group_comparison | Coerce a Group Comparison to a Tidy Data Frame
bootstrap_pathways | Bootstrap Pathway Stability and Informativeness
common_pathways | Most Common Pathways in a Fitted Tree
compare_groups | Compare Groups of Sequences for Structural Differences
compare_pruning | Compare Pruning Criteria on One Tree
compare_smoothing | Compare Smoothing Schemes on One Dataset
compare_trees | Compare Two context trees by Symmetric Divergence with Permutation Test
context_tree | Fit a Prediction Suffix Tree from Categorical Sequence Data
divergent_pathways | Most Predictively Divergent Pathways
engagement | Student engagement state sequences (wide format)
generate_sequences | Sample Sequences from a Fitted Context Tree
group_regulation_long | Collaborative-regulation events (long format)
impute_sequences | Impute Missing States in Sequences
logLik.transitiontrees | Log-Likelihood of a context tree
mine_contexts | Mine Contexts by Next-State Probability
mine_sequences | Mine Sequences by Predictive Surprise
model_fit | Model-Fit Scalars in One Call
nobs.transitiontrees | Number of Observations Used to Fit a context tree
n_nodes | Number of Contexts (Nodes) in a Tree
pathway_exists | Test Whether a Pathway Exists in the Tree
perplexity | Perplexity of a context tree
plot.transitiontrees | Plot a Context Tree
plot.transitiontrees_bootstrap | Plot a context tree Bootstrap
plot.transitiontrees_comparison | Plot a context tree Comparison
plot.transitiontrees_group | Plot Each Tree in a context tree Group
plot.transitiontrees_group_comparison | Plot a Group Comparison
plot.transitiontrees_tune | Plot a context tree CV Grid
plot_difference | Difference (Subtraction) Map Between Two Groups
plot_distributions | Per-Context Next-State Distributions
plot_divergence | Lollipop Chart of Pathway Divergence
plot_pathways | Plot Pathways as a Probability Heatmap
plot_pathway_resamples | Plot Bootstrap Resample Distributions per Pathway
plot_predictive | Predictive Diagnostics for Held-Out Scoring
plot_pruning | Illustrate Pruning Along a Pathway's Suffix Chain
plot_trajectories | Forward Trajectory Tree (Prefix Tree)
predict.transitiontrees | Predict Next-State Probabilities from a Context Tree
prepare_input | Reshape Long Event Data into a Wide Sequence Frame
print.summary.transitiontrees | Print a Context-Tree Summary
print.transitiontrees | Print a Context Tree
print.transitiontrees_bootstrap | Print a context tree Bootstrap
print.transitiontrees_comparison | Print a context tree Comparison
print.transitiontrees_group | Print a Group of Context Trees
print.transitiontrees_group_comparison | Print a Group Comparison
print.transitiontrees_tune | Print a context tree Tuning Grid
prune_tree | Prune a Context Tree
query_pathway | Query the Probability of a Specific Pathway -> Next State
score_positions | Per-Position Scoring
score_sequences | Per-Sequence Scoring
sharp_pathways | Sharpest Pathways
simulate.transitiontrees | Simulate Sequences from a Fitted context tree
smooth_tree | Re-Smooth a Fitted context tree
subtree | Extract the Subtree Rooted at a Pathway
summary.transitiontrees | Summary of a Context Tree
summary.transitiontrees_bootstrap | Summarise a context tree Bootstrap
summary.transitiontrees_group_comparison | Summarise a Group Comparison
trajectories | Student engagement trajectories
tree_dependence | Per-Context Path Dependence of a Context Tree
tree_distance | Symmetric KL Distance Between Two context trees
tree_pathways | Pathways from a Fitted Tree
tune_tree | Cross-Validated Hyperparameter Tuning for context trees