Constructing Adjacency Matrices Based on Spatial and Feature Similarity

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Documentation for package ‘adjoin’ version 0.1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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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
neighbors	Neighbors of a Set of Nodes
neighbors.neighbor_graph	Get neighbors for neighbor_graph object
neighbor_graph	Neighbor Graph
neighbor_graph.igraph	Neighbor Graph
neighbor_graph.Matrix	Neighbor Graph
neighbor_graph.matrix	Neighbor Graph
neighbor_graph.nnsearcher	Create Neighbor Graph from nnsearcher 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
normalized_heat_kernel	normalized_heat_kernel
normalize_adjacency	Normalize Adjacency Matrix
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_laplacian	Compute the spatial Laplacian matrix of a coordinate matrix
spatial_lap_of_gauss	Spatial Laplacian of Gaussian for coordinates
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