# Network-Based Communities and Kernel Machine Methods

## Documentation for package ‘CommKern’ version 1.0.1

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

## Help Pages

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