adjacency               Extract Adjacency Matrix from Graph Objects
adjacency.neighbor_graph
                        Extract adjacency matrix from neighbor_graph
                        object
adjacency.nn_search     Create Adjacency Matrix from nnsearch Object
between_class_neighbors
                        Between-Class Neighbors
between_class_neighbors.class_graph
                        Between-Class Neighbors for class_graph Objects
bilateral_smoother      Bilateral Spatial Smoother
binary_label_matrix     Create a Binary Label Adjacency Matrix (All
                        Pairs)
class_graph             Construct a Class Graph
class_means             Class Means
class_means.class_graph
                        Class Means for class_graph Objects
commute_time_distance   Compute the commute-time distance between nodes
                        in a graph
compute_diffusion_kernel
                        Compute Markov diffusion kernel via eigen
                        decomposition
compute_diffusion_map   Diffusion map embedding and distance
convolve_matrix         Convolve a Data Matrix with a Kernel Matrix
cross_adjacency         Cross Adjacency
cross_spatial_adjacency
                        Cross Spatial Adjacency
cross_weighted_spatial_adjacency
                        Cross-adjacency matrix with feature weighting
design_kernel           Build a flexible design-similarity kernel
diagonal_label_matrix   Create a Diagonal Label Comparison Matrix
                        (Element-wise)
diagonal_label_matrix_na
                        Diagonal Label Comparison with NA Handling
difference_of_gauss     Compute the Difference of Gaussians for a
                        coordinate matrix
discriminating_distance
                        Compute Discriminating Distance for Similarity
                        Graph
discriminating_similarity
                        Compute Similarity Graph Weighted by Class
                        Structure
dist_to_sim             Convert Distance to Similarity
dist_to_sim.Matrix      Convert Distance to Similarity for Matrix
                        Objects
dist_to_sim.nn_search   Convert Distance to Similarity for nn_search
                        Objects
edges                   Edges for Graph-Like Objects
edges.neighbor_graph    Extract edges from neighbor_graph object
estimate_sigma          Estimate Bandwidth Parameter (Sigma) for the
                        Heat Kernel
example_kernel_5x5      Example 5x5 factorial kernel
expand_label_similarity
                        Expand Similarity Between Labels Based on a
                        Precomputed Similarity Matrix
factor_sim              Compute Similarity Matrix for Factors in a Data
                        Frame
feature_weighted_spatial_constraints
                        Construct Feature-Weighted Spatial Constraints
                        for Data Blocks
find_nn                 Find nearest neighbors
find_nn.nnsearcher      Find Nearest Neighbors Using nnsearcher
find_nn_among           Find nearest neighbors among a subset
find_nn_among.class_graph
                        Find Nearest Neighbors Among Classes
find_nn_among.nnsearcher
                        Find Nearest Neighbors Among Subset Using
                        nnsearcher
find_nn_between         Find nearest neighbors between two sets of data
                        points
find_nn_between.nnsearcher
                        Find Nearest Neighbors Between Two Sets Using
                        nnsearcher
graph_weights           Convert a Data Matrix to an Adjacency Graph
graph_weights_fast      Fast kNN Graph Weights
heat_kernel             Compute the Heat Kernel
helmert_contrasts       Build Helmert orthonormal contrasts
heterogeneous_neighbors
                        Heterogeneous Neighbors for class_graph Objects
homogeneous_neighbors   Homogeneous Neighbors for class_graph Objects
inverse_heat_kernel     inverse_heat_kernel
kernel_alignment        Kernel alignment score
kernel_roots            Square root and inverse square root of a PSD
                        kernel
laplacian               Compute Graph Laplacian of a Weight Matrix
laplacian.neighbor_graph
                        Compute Laplacian matrix for neighbor_graph
                        object
local_global_adjacency
                        Local + Global KNN Adjacency
make_doubly_stochastic
                        Compute the doubly stochastic matrix from a
                        given matrix
nclasses                Number of Classes
nclasses.class_graph    Number of Classes for class_graph Objects
neighbor_graph          Neighbor Graph
neighbor_graph.nnsearcher
                        Create Neighbor Graph from nnsearcher Object
neighbors               Neighbors of a Set of Nodes
neighbors.neighbor_graph
                        Get neighbors for neighbor_graph object
nnsearcher              Nearest Neighbor Searcher
node_density            Node Density
node_density.neighbor_graph
                        Compute node density for neighbor_graph object
non_neighbors           Get Indices of Non-neighbors of a Node
non_neighbors.neighbor_graph
                        Get non-neighbors for neighbor_graph object
normalize_adjacency     Normalize Adjacency Matrix
normalized_heat_kernel
                        normalized_heat_kernel
nvertices               Number of Vertices in Graph-like Objects
nvertices.neighbor_graph
                        Get number of vertices in neighbor_graph object
pairwise_adjacency      Compute a pairwise adjacency matrix for
                        multiple graphs
print.repulsion_graph   Print method for repulsion_graph objects
psparse                 Apply a Function to Non-Zero Elements in a
                        Sparse Matrix
repulsion_graph         Create a Repulsion Graph
search_result           Search result for nearest neighbor search
search_result.nnsearcher
                        Convert Search Results for nnsearcher Objects
spatial_adjacency       Compute the spatial adjacency matrix for a
                        coordinate matrix
spatial_autocor         Compute a spatial autocorrelation matrix
spatial_constraints     Construct a Sparse Matrix of Spatial
                        Constraints for Data Blocks
spatial_lap_of_gauss    Spatial Laplacian of Gaussian for coordinates
spatial_laplacian       Compute the spatial Laplacian matrix of a
                        coordinate matrix
spatial_smoother        Compute the spatial smoother matrix for a
                        coordinate matrix
sum_contrasts           Build sum-to-zero contrasts
temporal_adjacency      Compute the temporal adjacency matrix of a time
                        series
temporal_autocor        Compute the temporal autocorrelation of a
                        matrix
temporal_laplacian      Compute the temporal Laplacian matrix of a time
                        series
threshold_adjacency     Threshold Adjacency
weighted_factor_sim     Compute Weighted Similarity Matrix for Factors
                        in a Data Frame
weighted_knn            Weighted k-Nearest Neighbors
weighted_spatial_adjacency
                        Weighted Spatial Adjacency
within_class_neighbors
                        Within-Class Neighbors
within_class_neighbors.class_graph
                        Within-Class Neighbors for class_graph Objects
