Network Estimation, Bootstrap, and Higher-Order Analysis
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Documentation for package ‘Nestimate’ version 0.8.0
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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 |