# Network Estimation, Bootstrap, and Higher-Order Analysis

## Documentation for package ‘Nestimate’ version 0.4.3

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

## Help Pages

A B C D E G H L M N P Q R S T V W

## -- A --

action_to_onehot | Convert Action Column to One-Hot Encoding
ai_long | Human-AI Vibe Coding Interaction Data (Long Format)
association_rules | Discover Association Rules from Sequential or Transaction Data
as_tna | Convert cluster_summary to tna Objects
as_tna.default | Convert cluster_summary to tna Objects
as_tna.mcml | Convert cluster_summary to tna Objects

## -- B --

betti_numbers | Betti Numbers
bootstrap_network | Bootstrap a Network Estimate
boot_glasso | Bootstrap for Regularized Partial Correlation Networks
build_atna | Build an Attention-Weighted Transition Network (ATNA)
build_clusters | Cluster Sequences by Dissimilarity
build_cna | Build a Co-occurrence Network (CNA)
build_cor | Build a Correlation Network
build_ftna | Build a Frequency Transition Network (FTNA)
build_gimme | GIMME: Group Iterative Multiple Model Estimation
build_glasso | Build a Graphical Lasso Network (EBICglasso)
build_hon | Build a Higher-Order Network (HON)
build_honem | Build HONEM Embeddings for Higher-Order Networks
build_hypa | Detect Path Anomalies via HYPA
build_ising | Build an Ising Network
build_mcml | Build MCML from Raw Transition Data
build_mlvar | Build a Multilevel Vector Autoregression (mlVAR) network
build_mmm | Fit a Mixed Markov Model
build_mogen | Build Multi-Order Generative Model (MOGen)
build_network | Build a Network
build_pcor | Build a Partial Correlation Network
build_simplicial | Build a Simplicial Complex
build_tna | Build a Transition Network (TNA)

## -- C --

centrality_stability | Centrality Stability Coefficient (CS-coefficient)
chatgpt_srl | ChatGPT Self-Regulated Learning Scale Scores
cluster_mmm | Cluster sequences using Mixed Markov Models
cluster_network | Cluster data and build per-cluster networks in one step
cluster_summary | Cluster Summary Statistics
coefs | Tidy coefficients from a fitted mlvar model
coefs.default | Tidy coefficients from a fitted mlvar model
coefs.net_mlvar | Tidy coefficients from a fitted mlvar model
compare_mmm | Compare MMM fits across different k
convert_sequence_format | Convert Sequence Data to Different Formats
cooccurrence | Build a Co-occurrence Network

## -- D --

distribution_plot | State Distribution Plot Over Time

## -- E --

estimate_network | Estimate a Network (Deprecated)
euler_characteristic | Euler Characteristic
evaluate_links | Evaluate Link Predictions Against Known Edges
extract_edges | Extract Edge List with Weights
extract_initial_probs | Extract Initial Probabilities from Model
extract_transition_matrix | Extract Transition Matrix from Model

## -- G --

get_estimator | Retrieve a Registered Estimator
group_regulation_long | Group Regulation in Collaborative Learning (Long Format)

## -- H --

human_long | Human-AI Vibe Coding Interaction Data (Long Format)

## -- L --

learning_activities | Online Learning Activity Indicators
list_estimators | List All Registered Estimators
long-data | Human-AI Vibe Coding Interaction Data (Long Format)
long_to_wide | Convert Long Format to Wide Sequences

## -- M --

markov_stability | Markov Stability Analysis
mogen_transitions | Extract Transition Table from a MOGen Model

## -- N --

nct | Network Comparison Test
network_reliability | Split-Half Reliability for Network Estimates
net_aggregate_weights | Aggregate Edge Weights
net_centrality | Compute Centrality Measures for a Network

## -- P --

passage_time | Mean First Passage Times
pathways | Extract Pathways from Higher-Order Network Objects
pathways.netobject | Extract Pathways from Higher-Order Network Objects
pathways.net_association_rules | Extract Pathways from Higher-Order Network Objects
pathways.net_hon | Extract Pathways from Higher-Order Network Objects
pathways.net_hypa | Extract Pathways from Higher-Order Network Objects
pathways.net_link_prediction | Extract Pathways from Higher-Order Network Objects
pathways.net_mogen | Extract Pathways from Higher-Order Network Objects
path_counts | Count Path Frequencies in Trajectory Data
permutation | Permutation Test for Network Comparison
persistent_homology | Persistent Homology
plot.boot_glasso | Plot Method for boot_glasso
plot.mcml | Plot Method for mcml
plot.mmm_compare | Plot Method for mmm_compare
plot.net_association_rules | Plot Method for net_association_rules
plot.net_clustering | Plot Sequence Clustering Results
plot.net_gimme | Plot Method for net_gimme
plot.net_honem | Plot Method for net_honem
plot.net_link_prediction | Plot Method for net_link_prediction
plot.net_markov_stability | Markov Stability Analysis
plot.net_mmm | Plot Method for net_mmm
plot.net_mogen | Plot Method for net_mogen
plot.net_mpt | Mean First Passage Times
plot.net_reliability | Plot Method for net_reliability
plot.net_sequence_comparison | Plot Method for net_sequence_comparison
plot.net_stability | Plot Method for net_stability
plot.persistent_homology | Plot Persistent Homology
plot.q_analysis | Plot Q-Analysis
plot.simplicial_complex | Plot a Simplicial Complex
predictability | Compute Node Predictability
predictability.netobject | Compute Node Predictability
predictability.netobject_group | Compute Node Predictability
predictability.netobject_ml | Compute Node Predictability
predict_links | Predict Missing or Future Links in a Network
prepare | Prepare Event Log Data for Network Estimation
prepare_for_tna | Prepare Data for TNA Analysis
prepare_onehot | Import One-Hot Encoded Data into Sequence Format
print.boot_glasso | Print Method for boot_glasso
print.mcml | Print Method for mcml
print.mmm_compare | Print Method for mmm_compare
print.nestimate_data | Print Method for nestimate_data
print.netobject | Print Method for Network Object
print.netobject_group | Print Method for Group Network Object
print.netobject_ml | Print Method for Multilevel Network Object
print.net_association_rules | Print Method for net_association_rules
print.net_bootstrap | Print Method for net_bootstrap
print.net_bootstrap_group | Print Method for net_bootstrap_group
print.net_clustering | Print Method for net_clustering
print.net_gimme | Print Method for net_gimme
print.net_hon | Print Method for net_hon
print.net_honem | Print Method for net_honem
print.net_hypa | Print Method for net_hypa
print.net_link_prediction | Print Method for net_link_prediction
print.net_mlvar | Print method for net_mlvar
print.net_mmm | Print Method for net_mmm
print.net_mogen | Print Method for net_mogen
print.net_nct | Print Method for net_nct
print.net_permutation | Print Method for net_permutation
print.net_permutation_group | Print Method for net_permutation_group
print.net_reliability | Print Method for net_reliability
print.net_sequence_comparison | Print Method for net_sequence_comparison
print.net_stability | Print Method for net_stability
print.persistent_homology | Print persistent homology results
print.q_analysis | Print Q-analysis results
print.simplicial_complex | Print a simplicial complex
print.wtna_boot_mixed | Print Method for wtna_boot_mixed
print.wtna_mixed | Print Method for wtna_mixed

## -- Q --

q_analysis | Q-Analysis

## -- R --

register_estimator | Register a Network Estimator
remove_estimator | Remove a Registered Estimator

## -- S --

sequence_compare | Compare Subsequence Patterns Between Groups
sequence_plot | Sequence Plot (heatmap, index, or distribution)
simplicial_degree | Simplicial Degree
srl_strategies | Self-Regulated Learning Strategy Frequencies
state_frequencies | Compute State Frequencies from Trajectory Data
summary.boot_glasso | Summary Method for boot_glasso
summary.mcml | Summary Method for mcml
summary.net_association_rules | Summary Method for net_association_rules
summary.net_bootstrap | Summary Method for net_bootstrap
summary.net_bootstrap_group | Summary Method for net_bootstrap_group
summary.net_clustering | Summary Method for net_clustering
summary.net_gimme | Summary Method for net_gimme
summary.net_hon | Summary Method for net_hon
summary.net_honem | Summary Method for net_honem
summary.net_hypa | Summary Method for net_hypa
summary.net_link_prediction | Summary Method for net_link_prediction
summary.net_mlvar | Summary method for net_mlvar
summary.net_mmm | Summary Method for net_mmm
summary.net_mogen | Summary Method for net_mogen
summary.net_mpt | Mean First Passage Times
summary.net_permutation | Summary Method for net_permutation
summary.net_permutation_group | Summary Method for net_permutation_group
summary.net_sequence_comparison | Summary Method for net_sequence_comparison
summary.net_stability | Summary Method for net_stability
summary.wtna_boot_mixed | Summary Method for wtna_boot_mixed

## -- T --

trajectories | Student Engagement Trajectories

## -- V --

verify_simplicial | Verify Simplicial Complex Against igraph

## -- W --

wide_to_long | Convert Wide Sequences to Long Format
wtna | Window-based Transition Network Analysis