Dynamic, Probabilistic, and Higher-Order Network Analysis


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Documentation for package ‘Nestimate’ version 0.9.24

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A B C D E F G H I L M N O 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.net_hypergraph_cluster Spectral clustering of hypergraph vertices
as.data.frame.net_hypergraph_transduction Transductive label spreading on a hypergraph
as.data.frame.state_freq Plot State Frequency Distributions
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_htna.net_mmm 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 Promote the Layers of an mcml to Networks
as_tna.default Promote the Layers of an mcml to Networks
as_tna.mcml Promote the Layers of an mcml to Networks

-- 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 descriptively
compare_networks Compare two or more networks
comparison_tables Tables of a network comparison
composites Cluster Scores From a Psychometric MCML Fit
composites.mcml_pc Cluster Scores From a Psychometric MCML Fit
convert_sequence_format Convert Sequence Data to Different Formats
cooccurrence Build a Co-occurrence Network

-- D --

distribution_plot State Distribution Plot Over Time

-- E --

edge_differences Tables of a network comparison
effects_table Effect Table of a Fitted Outcome Model
entropy_bayes Bayesian Transition Entropy
entropy_network Transition Entropy Network
entropy_trajectory Sliding-Window Transition Entropy Trajectory
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_pathways Cut an Event Log into Pathways
extract_transition_matrix Extract Transition Matrix from Model

-- F --

frequencies Build a Transition Frequency Matrix

-- G --

get_estimator Retrieve a Registered Estimator
global_differences Tables of a network comparison
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_cluster Spectral clustering of hypergraph vertices
hypergraph_laplacian Normalized hypergraph Laplacian
hypergraph_measures Structural measures for a hypergraph
hypergraph_transduction Transductive label spreading on a hypergraph

-- I --

item_loadings Item Diagnostics From a Psychometric MCML Fit
item_loadings.mcml_pc Item Diagnostics From a Psychometric MCML Fit

-- 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 --

macro_network Cluster-Level Network, With One Cluster Expanded
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_metrics Tables of a network comparison
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
node_differences Tables of a network comparison

-- O --

outcome_model Model Unit-Level Outcomes from Sequence or Network Predictors

-- 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
permutation_diagnostics Does Nesting Bias a Permutation Test?
persistence_landscape Persistence Landscape
persistent_homology Persistent Homology
plot.boot_glasso Bootstrap for Regularized Partial Correlation Networks
plot.chain_structure Qualitative structure of a discrete-time Markov chain
plot.cluster_choice Cluster Choice - sweep k, dissimilarity and method
plot.magnitude_difference Magnitude difference between the frequency and probability views
plot.mcml_pc Multi-Cluster Multi-Level Aggregation for Psychometric Networks
plot.mmm_compare Compare MMM fits across different k
plot.mosaic_analysis Two-variable mosaic analysis (chi-square test + flat mosaic)
plot.net_association_rules Discover Association Rules from Sequential or Transaction Data
plot.net_bayes Bayesian Dirichlet-Multinomial comparison of two transition networks
plot.net_casedrop_reliability Edge-weight Case-dropping Stability
plot.net_casedrop_reliability_group Edge-weight Case-dropping Stability
plot.net_centrality Compute Centrality Measures for a Network
plot.net_centrality_group Compute Centrality Measures for a Network
plot.net_clustering Cluster Sequences by Dissimilarity
plot.net_cluster_diagnostics Cluster Diagnostics
plot.net_comparison Compare two networks descriptively
plot.net_edge_betweenness Edge Betweenness Network
plot.net_entropy_bayes Bayesian Transition Entropy
plot.net_entropy_trajectory Sliding-Window Transition Entropy Trajectory
plot.net_honem Build HONEM Embeddings for Higher-Order Networks
plot.net_hypergraph_cluster Spectral clustering of hypergraph vertices
plot.net_hypergraph_transduction Transductive label spreading on a hypergraph
plot.net_markov_order Test the Markov order of a sequential process
plot.net_markov_stability Markov Stability Analysis
plot.net_mmm Fit a Mixed Markov Model
plot.net_mmm_clustering Fit a Mixed Markov Model
plot.net_mogen Build Multi-Order Generative Model (MOGen)
plot.net_mpt Mean First Passage Times
plot.net_network_comparison Compare two or more networks
plot.net_outcome_model Model Unit-Level Outcomes from Sequence or Network Predictors
plot.net_path_dependence Per-Context Path Dependence at Order k
plot.net_reliability Split-Half Reliability for Network Estimates
plot.net_sequence_comparison Compare Subsequence Patterns Between Groups
plot.net_stability Centrality Stability Coefficient (CS-coefficient)
plot.net_transition_entropy Transition Entropy of a Markov Chain
plot.net_vertex_bootstrap Vertex Bootstrap for Network-Level Statistics
plot.net_vertex_comparison Compare Network-Level Statistics of Two Networks
plot.pc_loading_stability Composite-Weight Stability Under Case Resampling
plot.persistence_landscape Persistence Landscape
plot.persistent_homology Persistent Homology
plot.q_analysis Q-Analysis
plot.simplicial_complex Build a Simplicial Complex
plot.state_freq Plot State Frequency Distributions
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 Bootstrap for Regularized Partial Correlation Networks
print.chain_structure Qualitative structure of a discrete-time Markov chain
print.chain_structure_group Qualitative structure of a discrete-time Markov chain
print.cluster_choice Cluster Choice - sweep k, dissimilarity and method
print.hypergraph_measures Structural measures for a hypergraph
print.magnitude_difference Magnitude difference between the frequency and probability views
print.mcml Build MCML from Raw Transition Data
print.mcml_layer Build MCML from Raw Transition Data
print.mcml_pc Multi-Cluster Multi-Level Aggregation for Psychometric Networks
print.mcml_sequence_plot Sequence Plot (heatmap, index, or distribution)
print.mmm_compare Compare MMM fits across different k
print.mosaic_analysis Two-variable mosaic analysis (chi-square test + flat mosaic)
print.nestimate_data Prepare Event Log Data for Network Estimation
print.nestimate_facet_list Plot State Frequency Distributions
print.nestimate_facet_plot Plot State Frequency Distributions
print.netdifference Subtract one network from another
print.netobject Build a Network
print.netobject_group Build a Network
print.netobject_ml Build a Network
print.net_association_rules Discover Association Rules from Sequential or Transaction Data
print.net_bayes Bayesian Dirichlet-Multinomial comparison of two transition networks
print.net_bayes_group Bayesian Dirichlet-Multinomial comparison of two transition networks
print.net_bootstrap Bootstrap a Network Estimate
print.net_bootstrap_group Bootstrap a Network Estimate
print.net_casedrop_reliability Edge-weight Case-dropping Stability
print.net_casedrop_reliability_group Edge-weight Case-dropping Stability
print.net_certainty Analytic certainty of network edges (Bayesian Dirichlet-Multinomial)
print.net_clustering Cluster Sequences by Dissimilarity
print.net_cluster_diagnostics Cluster Diagnostics
print.net_comparison Compare two networks descriptively
print.net_entropy_bayes Bayesian Transition Entropy
print.net_entropy_bayes_group Bayesian Transition Entropy
print.net_entropy_trajectory Sliding-Window Transition Entropy Trajectory
print.net_hon Build a Higher-Order Network (HON)
print.net_honem Build HONEM Embeddings for Higher-Order Networks
print.net_hypa Detect Path Anomalies via HYPA
print.net_hypergraph Higher-order hypergraph from a network's clique structure
print.net_hypergraph_cluster Spectral clustering of hypergraph vertices
print.net_hypergraph_transduction Transductive label spreading on a hypergraph
print.net_link_prediction Predict Missing or Future Links in a Network
print.net_markov_order Test the Markov order of a sequential process
print.net_markov_order_group Test the Markov order of a sequential process
print.net_markov_stability Markov Stability Analysis
print.net_markov_stability_group Markov Stability Analysis
print.net_mlvar Build a Multilevel Vector Autoregression (mlVAR) network
print.net_mmm Fit a Mixed Markov Model
print.net_mmm_clustering Fit a Mixed Markov Model
print.net_mogen Build Multi-Order Generative Model (MOGen)
print.net_mpt Mean First Passage Times
print.net_mpt_group Mean First Passage Times
print.net_nct Network Comparison Test
print.net_network_comparison Compare two or more networks
print.net_outcome_model Model Unit-Level Outcomes from Sequence or Network Predictors
print.net_path_dependence Per-Context Path Dependence at Order k
print.net_permutation Permutation Test for Network Comparison
print.net_permutation_group Permutation Test for Network Comparison
print.net_pruning_details Report Network Pruning Details
print.net_reliability Split-Half Reliability for Network Estimates
print.net_sequence_comparison Compare Subsequence Patterns Between Groups
print.net_stability Centrality Stability Coefficient (CS-coefficient)
print.net_stability_group Centrality Stability Coefficient (CS-coefficient)
print.net_table Tables of a network comparison
print.net_transition_entropy Transition Entropy of a Markov Chain
print.net_transition_entropy_group Transition Entropy of a Markov Chain
print.net_vertex_bootstrap Vertex Bootstrap for Network-Level Statistics
print.net_vertex_comparison Compare Network-Level Statistics of Two Networks
print.pc_loading_stability Composite-Weight Stability Under Case Resampling
print.persistence_landscape Persistence Landscape
print.persistent_homology Persistent Homology
print.q_analysis Q-Analysis
print.simplicial_complex Build a Simplicial Complex
print.state_freq Plot State Frequency Distributions
print.summary.netobject Build a Network
print.summary.netobject_group Build a Network
print.summary.net_casedrop_reliability_group Edge-weight Case-dropping Stability
print.summary.net_mpt Mean First Passage Times
print.summary.net_path_dependence Per-Context Path Dependence at Order k
print.summary.net_transition_entropy Transition Entropy of a Markov Chain
print.summary_chain_structure Qualitative structure of a discrete-time Markov chain
print.tidy_covariates Cluster Sequences by Dissimilarity
print.wtna_boot_mixed Bootstrap a Network Estimate
print.wtna_mixed Window-based Transition Network Analysis
print.wtna_perm_mixed Permutation Test for Network Comparison

-- 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)
session_ids The session behind each sequence
session_ids.default The session behind each sequence
session_ids.netobject The session behind each sequence
session_ids.net_clustering The session behind each sequence
session_ids.net_mmm The session behind each sequence
set_state_colors Set the state colours carried by a network object
set_state_colors.default Set the state colours carried by a network object
set_state_colors.htna Set the state colours carried by a network object
set_state_colors.mcml Set the state colours carried by a network object
set_state_colors.netobject Set the state colours carried by a network object
set_state_colors.netobject_group Set the state colours carried by a network object
simplicial_degree Simplicial Degree
simplicial_features Tidy Topological Features for One or Many Networks
srl_strategies Self-Regulated Learning Strategy Frequencies
state_colors The state colours an object will draw with
state_colors.default The state colours an object will draw with
state_colors.htna The state colours an object will draw with
state_colors.mcml The state colours an object will draw with
state_colors.netobject The state colours an object will draw with
state_colors.netobject_group The state colours an object will draw with
state_colors<- Set the state colours carried by a network object
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 Plot State Frequency Distributions
state_frequencies Compute State Frequencies from Trajectory Data
subtract_networks Subtract one network from another
summary.boot_glasso Bootstrap for Regularized Partial Correlation Networks
summary.chain_structure Qualitative structure of a discrete-time Markov chain
summary.chain_structure_group Qualitative structure of a discrete-time Markov chain
summary.cluster_choice Cluster Choice - sweep k, dissimilarity and method
summary.mcml Build MCML from Raw Transition Data
summary.mcml_pc Multi-Cluster Multi-Level Aggregation for Psychometric Networks
summary.mmm_compare Compare MMM fits across different k
summary.mosaic_analysis Two-variable mosaic analysis (chi-square test + flat mosaic)
summary.nest_initial_probs Extract Initial Probabilities from Model
summary.nest_transition_counts Build a Transition Frequency Matrix
summary.nest_transition_matrix Extract Transition Matrix from Model
summary.netobject Build a Network
summary.netobject_group Build a Network
summary.net_association_rules Discover Association Rules from Sequential or Transaction Data
summary.net_bayes Bayesian Dirichlet-Multinomial comparison of two transition networks
summary.net_bayes_group Bayesian Dirichlet-Multinomial comparison of two transition networks
summary.net_bootstrap Bootstrap a Network Estimate
summary.net_bootstrap_group Bootstrap a Network Estimate
summary.net_casedrop_reliability Edge-weight Case-dropping Stability
summary.net_casedrop_reliability_group Edge-weight Case-dropping Stability
summary.net_clustering Cluster Sequences by Dissimilarity
summary.net_entropy_bayes Bayesian Transition Entropy
summary.net_entropy_trajectory Sliding-Window Transition Entropy Trajectory
summary.net_hon Build a Higher-Order Network (HON)
summary.net_honem Build HONEM Embeddings for Higher-Order Networks
summary.net_hypa Detect Path Anomalies via HYPA
summary.net_hypergraph Higher-order hypergraph from a network's clique structure
summary.net_hypergraph_cluster Spectral clustering of hypergraph vertices
summary.net_hypergraph_transduction Transductive label spreading on a hypergraph
summary.net_link_prediction Predict Missing or Future Links in a Network
summary.net_markov_order Test the Markov order of a sequential process
summary.net_markov_stability Markov Stability Analysis
summary.net_mlvar Build a Multilevel Vector Autoregression (mlVAR) network
summary.net_mmm Fit a Mixed Markov Model
summary.net_mogen Build Multi-Order Generative Model (MOGen)
summary.net_mpt Mean First Passage Times
summary.net_nct Network Comparison Test
summary.net_network_comparison Tables of a network comparison
summary.net_outcome_model Model Unit-Level Outcomes from Sequence or Network Predictors
summary.net_path_dependence Per-Context Path Dependence at Order k
summary.net_permutation Permutation Test for Network Comparison
summary.net_permutation_group Permutation Test for Network Comparison
summary.net_reliability Split-Half Reliability for Network Estimates
summary.net_sequence_comparison Compare Subsequence Patterns Between Groups
summary.net_stability Centrality Stability Coefficient (CS-coefficient)
summary.net_stability_group Centrality Stability Coefficient (CS-coefficient)
summary.net_transition_entropy Transition Entropy of a Markov Chain
summary.net_vertex_bootstrap Vertex Bootstrap for Network-Level Statistics
summary.net_vertex_comparison Compare Network-Level Statistics of Two Networks
summary.wtna_boot_mixed Bootstrap a Network Estimate
summary.wtna_perm_mixed Permutation Test for Network Comparison

-- 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