Network-Based Communities and Kernel Machine Methods

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Documentation for package ‘CommKern’ version 1.0.1

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adj_RI Adjusted Rand Index (ARI)
CommKern CommKern
community_allegiance Community Allegiance
community_plot Communities by layer plot
compute_modularity_matrix Compute modularity matrix
compute_multimodal_mod Compute multimodal modularity matrix
consensus_similarity Consensus Similarity
count_pairs Count pairs
degree Node degree calculation
entropy Entropy
ext_distance Extrinsic evaluation distance matrix creation
find_start_temp Starting temperature
get_weights Simulated network edge weights
group_adj_perturb Group adjacency matrices
group_network_perturb Simulated group networks
ham_distance Hamiltonian distance matrix creation
heatbath_multimodal Multimodal heatbath algorithm
hms Hierarchical multimodal spinglass algorithm
kernel Distance-based kernel
matrix_plot Functional and Structural Matrix Plot
matrix_to_df Convert matrices to dataframe list for network
NMI Normalized mutual information (NMI)
purity Purity
SBM_net Simulated functional and structural connectivity with nested hierarchical community structure
score_cont_nonparam Nonparametric score function for distance-based kernel and continuous outcome.
score_cont_semiparam Semiparametric score function for distance-based kernel and continuous outcome.
score_log_nonparam Nonparametric score function for distance-based kernel and binary outcome
score_log_semiparam Semiparametric score function for distance-based kernel
simasd_array Simulated Array
simasd_comm_df Simulated partitions of nodes to communities from HMS algorithm
simasd_covars Simulated demographics dataset modeled of a subset of the preprocessed ABIDE database
simasd_hamil_df Simulated Hamiltonian values from HMS algorithm
simnet_df_perturb Simulated network data frame
sort_pairs Sort pairs
subset_matrix_to_df Convert matrices to list of data frames for subnetworks
tr Trace
up_low Bounds of grid search function
zrand Rand z-score