Migrated findMutualNN() from batchelor.
Vendored the RcppAnnoy headers for greater reproducibility.
Added a distance="Cosine" option for all algorithms.
Allow memory-efficient retrieval of the distance to the furthest neighbors.
Added a warn.ties= argument to turn off tie-related warnings in the KMKNN and VP tree algorithms.
Return neighbor counts in rangeFind*() and rangeQuery*() functions when get.index=FALSE and get.distance=FALSE.
findNeighbors() and queryNeighbors() now accept a vector of point-specific thresholds.
Added an VP tree implemention in findVptree(), queryVptree(), buildVptree(). Supported dispatch to these methods in the generics.
Added a HNSW implementation in findHnsw(), queryHnsw(), buildHnsw(). Supported dispatch to these methods in the generics.
Renamed buildNNIndex() to buildIndex().
Converted findNeighbors() and queryNeighbors() into S4 methods. Created specific rangeFind*() and rangeQuery*() functions for KMKNN and VP tree algorithms.
Modified AnnoyIndex class to hold the original data matrix. Created bnorder(), bndata() generics to obtain (possibly reordered) input matrices for all indexes.
Supported Manhattan distance searching in all algorithms.
New package BiocNeighbors, for k-means-based k-nearest neighbor detection.