Support for more connectivity similarity metrics#11
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- prepare_cosine_matrix -> prepare_similarity_matrix (old name kept as alias) - cosine_heatmap -> connectivity_heatmap (old name kept as alias) - Add distfun parameter to connectivity_heatmap for pluggable distance
- Add methods to Imports (needed for as() in similarity code) - Add samples/ to .gitignore and .Rbuildignore - Add Jaccard, binarised etc to spelling wordlist
- jaccard_sim() with weighted parameter for binary and weighted Jaccard - connectivity_similarity() as generic dispatcher (cosine/jaccard/weighted_jaccard) - Binary Jaccard uses sparse crossprod with in-place slot transformation - Weighted Jaccard uses threshold decomposition (sum of sparse crossprods) - Comprehensive tests including hand-computed values and naive reference
A form of weighted jaccard but potentially faster to compute
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idea is to have a plugin architecture for coconatfly clustrering to use a range of unctions besides cosine_sim