# Network Estimation, Bootstrap, and Higher-Order Analysis

## Documentation for package ‘Nestimate’ version 0.8.0

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

## Help Pages

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

## -- A --

action_to_onehot | Convert Action Column to One-Hot Encoding
actor_endpoints | Tidy per-actor endpoint summary of a wide-format sequence dataset
ai_long | Human-AI Vibe Coding Interaction Data (Long Format)
as.data.frame.net_cluster_diagnostics | Cluster Diagnostics
as.data.frame.state_freq | Print, Plot, and Convert a state_freq Object
association_rules | Discover Association Rules from Sequential or Transaction Data
as_htna | Build a grouped node-level network (htna) from data and a clustering
as_htna.default | Build a grouped node-level network (htna) from data and a clustering
as_htna.mcml | Build a grouped node-level network (htna) from data and a clustering
as_netdifference | Coerce an inferential comparison to a network difference
as_netdifference.default | Coerce an inferential comparison to a network difference
as_netdifference.netdifference | Coerce an inferential comparison to a network difference
as_netdifference.net_bayes | Coerce an inferential comparison to a network difference
as_netobject | Coerce a network object to a Nestimate netobject
as_netobject.cograph_network | Coerce a network object to a Nestimate netobject
as_netobject.default | Coerce a network object to a Nestimate netobject
as_netobject.netobject | Coerce a network object to a Nestimate netobject
as_netobject.psychnet | Coerce a network object to a Nestimate netobject
as_networks | Promote a psychometric MCML result to a network group
as_networks.default | Promote a psychometric MCML result to a network group
as_networks.mcml_pc | Promote a psychometric MCML result to a network group
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 --

bayes_compare | Bayesian Dirichlet-Multinomial comparison of two transition networks
betti_numbers | Betti Numbers
bipartite_groups | Hypergraph from bipartite group / event data
bootstrap_network | Bootstrap a Network Estimate
boot_glasso | Bootstrap for Regularized Partial Correlation Networks
bottleneck_distance | Bottleneck Distance Between Persistence Diagrams
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_hypergraph | Higher-order hypergraph from a network's clique structure
build_ising | Build an Ising Network
build_mcml | Build MCML from Raw Transition Data
build_mcml_pc | Multi-Cluster Multi-Level Aggregation for Psychometric Networks
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 --

casedrop_reliability | Edge-weight Case-dropping Stability
centrality_stability | Centrality Stability Coefficient (CS-coefficient)
certainty | Analytic certainty of network edges (Bayesian Dirichlet-Multinomial)
chain_structure | Qualitative structure of a discrete-time Markov chain
chatgpt_srl | ChatGPT Self-Regulated Learning Scale Scores
clique_expansion | Clique expansion of a hypergraph
cluster_choice | Cluster Choice - sweep k, dissimilarity and method
cluster_diagnostics | Cluster Diagnostics
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
compare_model | Compare two networks descriptively
compare_model.cograph_network | Compare two networks descriptively
compare_model.matrix | Compare two networks descriptively
compare_model.netobject | Compare two networks descriptively
compare_model.netobject_group | Compare two networks within a netobject_group
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

## -- F --

frequencies | Sequence Data Conversion Functions

## -- 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)
hypergraph_centrality | Hypergraph eigenvector centralities
hypergraph_measures | Structural measures for a hypergraph

## -- L --

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

## -- M --

magnitude_difference | Magnitude difference between the frequency and probability views
markov_order_test | Test the Markov order of a sequential process
markov_stability | Markov Stability Analysis
mark_first_state | Mark leading-NA cells with an explicit state label
mark_terminal_state | Mark terminal-NA cells with an explicit state label
mogen_transitions | Extract Transition Table from a MOGen Model
mosaic_analysis | Two-variable mosaic analysis (chi-square test + flat mosaic)
mosaic_plot | Mosaic Plot of a Network's Transition or Co-occurrence Counts
mosaic_plot.default | Mosaic Plot of a Network's Transition or Co-occurrence Counts
mosaic_plot.htna | Mosaic Plot of a Network's Transition or Co-occurrence Counts
mosaic_plot.matrix | Mosaic Plot of a Network's Transition or Co-occurrence Counts
mosaic_plot.mcml | Mosaic Plot of a Network's Transition or Co-occurrence Counts
mosaic_plot.netobject | Mosaic Plot of a Network's Transition or Co-occurrence Counts
mosaic_plot.netobject_group | Mosaic Plot of a Network's Transition or Co-occurrence Counts
mosaic_plot.table | Mosaic Plot of a Network's Transition or Co-occurrence Counts

## -- 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
net_deprune | Undo Network Pruning
net_deprune.default | Undo Network Pruning
net_deprune.netobject | Undo Network Pruning
net_deprune.netobject_group | Undo Network Pruning
net_edge_betweenness | Edge Betweenness Network
net_edge_betweenness.default | Edge Betweenness Network
net_edge_betweenness.netobject | Edge Betweenness Network
net_edge_betweenness.netobject_group | Edge Betweenness Network
net_prune | Prune a Network's Edges
net_prune.default | Prune a Network's Edges
net_prune.netobject | Prune a Network's Edges
net_prune.netobject_group | Prune a Network's Edges
net_pruning_details | Report Network Pruning Details
net_pruning_details.default | Report Network Pruning Details
net_pruning_details.netobject | Report Network Pruning Details
net_pruning_details.netobject_group | Report Network Pruning Details
net_reprune | Re-apply Network Pruning
net_reprune.default | Re-apply Network Pruning
net_reprune.netobject | Re-apply Network Pruning
net_reprune.netobject_group | Re-apply Network Pruning

## -- 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
path_dependence | Per-Context Path Dependence at Order k
permutation | Permutation Test for Network Comparison
persistence_landscape | Persistence Landscape
persistent_homology | Persistent Homology
plot.boot_glasso | Plot Method for boot_glasso
plot.chain_structure | Plot method for 'chain_structure'
plot.cluster_choice | Plot Method for cluster_choice
plot.magnitude_difference | Magnitude difference between the frequency and probability views
plot.mcml_pc | Plot an MCML-PC Object
plot.mmm_compare | Plot Method for mmm_compare
plot.mosaic_analysis | Plot method for mosaic_analysis objects
plot.net_association_rules | Plot Method for net_association_rules
plot.net_bayes | Plot method for net_bayes
plot.net_casedrop_reliability | Edge-weight Case-dropping Stability
plot.net_casedrop_reliability_group | Edge-weight Case-dropping Stability
plot.net_centrality | Plot centrality measures
plot.net_centrality_group | Plot grouped centrality measures
plot.net_clustering | Plot Sequence Clustering Results
plot.net_cluster_diagnostics | Plot Method for net_cluster_diagnostics
plot.net_comparison | Plot a network comparison
plot.net_edge_betweenness | Plot edge-betweenness scores
plot.net_gimme | Plot Method for net_gimme
plot.net_honem | Plot Method for net_honem
plot.net_markov_order | Plot Method for net_markov_order
plot.net_markov_stability | Markov Stability Analysis
plot.net_mmm | Plot Method for net_mmm
plot.net_mmm_clustering | Plot Method for MMM Clustering Attribute
plot.net_mogen | Plot Method for net_mogen
plot.net_mpt | Mean First Passage Times
plot.net_path_dependence | Plot method for 'net_path_dependence'
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.net_transition_entropy | Plot method for 'net_transition_entropy'
plot.net_vertex_bootstrap | Plot Vertex Bootstrap Distributions
plot.net_vertex_comparison | Plot a Two-Network Vertex-Bootstrap Comparison
plot.pc_loading_stability | Plot Composite-Weight Stability
plot.persistence_landscape | Plot Persistence Landscape
plot.persistent_homology | Plot Persistent Homology
plot.q_analysis | Plot Q-Analysis
plot.simplicial_complex | Plot a Simplicial Complex
plot.state_freq | Print, Plot, and Convert a state_freq Object
plot_mosaic | Draw a Marimekko / Mosaic Plot from a Tidy Data Frame
plot_state_frequencies | Plot State Frequency Distributions
plot_state_frequencies.default | Plot State Frequency Distributions
plot_state_frequencies.htna | Plot State Frequency Distributions
plot_state_frequencies.mcml | Plot State Frequency Distributions
plot_state_frequencies.netobject | Plot State Frequency Distributions
plot_state_frequencies.netobject_group | Plot State Frequency Distributions
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.chain_structure | Print method for 'chain_structure'
print.chain_structure_group | Print method for 'chain_structure_group'
print.cluster_choice | Print Method for cluster_choice
print.hypergraph_measures | Structural measures for a hypergraph
print.magnitude_difference | Magnitude difference between the frequency and probability views
print.mcml | Print Method for mcml
print.mcml_layer | Print Method for an mcml Layer
print.mcml_pc | Print an MCML-PC Object
print.mmm_compare | Print Method for mmm_compare
print.mosaic_analysis | Print method for mosaic_analysis objects
print.nestimate_data | Print Method for nestimate_data
print.netdifference | Subtract one network from another
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_bayes | Print method for net_bayes
print.net_bayes_group | Print method for net_bayes_group
print.net_bootstrap | Print Method for net_bootstrap
print.net_bootstrap_group | Print Method for net_bootstrap_group
print.net_casedrop_reliability | Edge-weight Case-dropping Stability
print.net_casedrop_reliability_group | Edge-weight Case-dropping Stability
print.net_certainty | Print Method for net_certainty
print.net_clustering | Print Method for net_clustering
print.net_cluster_diagnostics | Print Method for net_cluster_diagnostics
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_hypergraph | Higher-order hypergraph from a network's clique structure
print.net_link_prediction | Print Method for net_link_prediction
print.net_markov_order | Print Method for net_markov_order
print.net_markov_order_group | Print method for 'net_markov_order_group'
print.net_markov_stability_group | Print method for 'net_markov_stability_group'
print.net_mlvar | Print method for net_mlvar
print.net_mmm | Print Method for net_mmm
print.net_mmm_clustering | Print Method for MMM Clustering Attribute
print.net_mogen | Print Method for net_mogen
print.net_mpt_group | Print method for 'net_mpt_group'
print.net_nct | Print Method for net_nct
print.net_path_dependence | Print method for 'net_path_dependence'
print.net_permutation | Print Method for net_permutation
print.net_permutation_group | Print Method for net_permutation_group
print.net_pruning_details | Print method for pruning details
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.net_stability_group | Print Method for net_stability_group
print.net_transition_entropy | Print method for 'net_transition_entropy'
print.net_transition_entropy_group | Print method for 'net_transition_entropy_group'
print.net_vertex_bootstrap | Print a Vertex Bootstrap Result
print.net_vertex_comparison | Print a Two-Network Vertex-Bootstrap Comparison
print.pc_loading_stability | Print Composite-Weight Stability
print.persistence_landscape | Print Persistence Landscape
print.persistent_homology | Print persistent homology results
print.q_analysis | Print Q-analysis results
print.simplicial_complex | Print a simplicial complex
print.state_freq | Print, Plot, and Convert a state_freq Object
print.summary.net_casedrop_reliability_group | Edge-weight Case-dropping Stability
print.summary.net_path_dependence | Print method for 'summary.net_path_dependence'
print.summary.net_transition_entropy | Print method for 'summary.net_transition_entropy'
print.summary_chain_structure | Print method for 'summary.chain_structure'
print.tidy_covariates | Print method for tidy covariate output
print.wtna_boot_mixed | Print Method for wtna_boot_mixed
print.wtna_mixed | Print Method for wtna_mixed
print.wtna_perm_mixed | Print Method for wtna_perm_mixed

## -- Q --

q_analysis | Q-Analysis

## -- R --

register_estimator | Register a Network Estimator
remove_estimator | Remove a Registered Estimator
rename_models | Rename the models of a 'netobject_group'
rename_models.default | Rename the models of a 'netobject_group'
rename_models.netobject_group | Rename the models of a 'netobject_group'

## -- 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_distribution | Per-Class State Distribution as a Tidy Data Frame
state_distribution.default | Per-Class State Distribution as a Tidy Data Frame
state_distribution.htna | Per-Class State Distribution as a Tidy Data Frame
state_distribution.mcml | Per-Class State Distribution as a Tidy Data Frame
state_distribution.netobject | Per-Class State Distribution as a Tidy Data Frame
state_distribution.netobject_group | Per-Class State Distribution as a Tidy Data Frame
state_freq | Print, Plot, and Convert a state_freq Object
state_frequencies | Compute State Frequencies from Trajectory Data
subtract_networks | Subtract one network from another
summary.boot_glasso | Summary Method for boot_glasso
summary.chain_structure | Tidy per-state summary of a 'chain_structure'
summary.chain_structure_group | Cross-group comparison of 'chain_structure_group'
summary.cluster_choice | Summary Method for cluster_choice
summary.mcml | Summary Method for mcml
summary.mcml_pc | Summarize an MCML-PC Object
summary.mmm_compare | Summary Method for mmm_compare
summary.mosaic_analysis | Summary method for mosaic_analysis objects
summary.nest_initial_probs | Summary Method for Initial Probability Vectors
summary.nest_transition_counts | Summary Method for Transition Count Matrices
summary.nest_transition_matrix | Summary Method for Transition Matrices
summary.netobject | Network metrics for a netobject
summary.netobject_group | Network metrics for a netobject_group
summary.net_association_rules | Summary Method for net_association_rules
summary.net_bayes | Summary method for net_bayes
summary.net_bayes_group | Summary method for net_bayes_group
summary.net_bootstrap | Summary Method for net_bootstrap
summary.net_bootstrap_group | Summary Method for net_bootstrap_group
summary.net_casedrop_reliability | Edge-weight Case-dropping Stability
summary.net_casedrop_reliability_group | Edge-weight Case-dropping Stability
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_hypergraph | Higher-order hypergraph from a network's clique structure
summary.net_link_prediction | Summary Method for net_link_prediction
summary.net_markov_order | Summary Method for net_markov_order
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_nct | Summary Method for net_nct
summary.net_path_dependence | Summary method for 'net_path_dependence'
summary.net_permutation | Summary Method for net_permutation
summary.net_permutation_group | Summary Method for net_permutation_group
summary.net_reliability | Summary Method for net_reliability
summary.net_sequence_comparison | Summary Method for net_sequence_comparison
summary.net_stability | Summary Method for net_stability
summary.net_stability_group | Summary Method for net_stability_group
summary.net_transition_entropy | Summary method for 'net_transition_entropy'
summary.net_vertex_bootstrap | Summarize a Vertex Bootstrap Result
summary.net_vertex_comparison | Summarize a Two-Network Vertex-Bootstrap Comparison
summary.wtna_boot_mixed | Summary Method for wtna_boot_mixed
summary.wtna_perm_mixed | Summary Method for wtna_perm_mixed

## -- T --

trajectories | Student Engagement Trajectories
transition_entropy | Transition Entropy of a Markov Chain

## -- V --

validate_netobject | Validate a netobject / cograph_network against the shared schema
verify_simplicial | Verify Simplicial Complex Against igraph
vertex_bootstrap | Vertex Bootstrap for Network-Level Statistics
vertex_compare | Compare Network-Level Statistics of Two Networks

## -- W --

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