## Index of all namespaces

Utility 'tool belt' of functions for common tasks; trees; clustering; probability, stats, and information theory; et.al.

Various supplementary collection functions not included in the dstandard Clojure ecosystem. Mostly for seqs, but also for vectors, maps and sets.

VARS

D drop-until dropv dropv-until dropv-while

I in

M map->csv-map map-entry? merge-with* mkseq

P partitionv-all pos pos-any positions pxmap

R random-subset reduce-in-parallel reducem rotate rotations

S separate separatev sliding-take splitv-at subsets

T take-until take-until-nochange takev takev-until takev-while third transpose

V vfold

BK-trees: Metric trees over discrete spaces. Parameterizable with various (not necessarily discrete) metrics and arbitrary values.

Various graph algorithms, techniques, functions. Generally applicable, but typically used for sequence similarity, clustering, and path metrics of various sorts.

Tree branch/node oriented wrapper for zippers.

Various supplementary I/O functions and macros. Some new, some recapitulations of previous extremely useful functionality that is no longer included in the standard Clojure ecosystem.

VARS

A ->auioReader add-rdrwtr assemble-bindings auio-rdrs

D do-text-file do-text-to-text

G get-xform-body-bindings get-xform-rdrwrtr-bindings

L letio

O open-file open-streaming-gzip

R rdrwtrs-set rdrwtrs? read-lines read-stream reduce-file rwfl-syms

W with-in-reader with-out-append-writer with-out-writer write-lines write-stream

Various math functions that don't quite have enough totality to have their own home namespace just yet.

Various data clustering algorithms, techniques, functions. Generally applicable, but typically used for sequence clustering of various sorts.

VARS

C center-dist-expect center-distances centers cluster-distances cluster-stdev clusters

D davies-bouldin-index DBI-Rij DBI-Si density dist-matrix

F farthest farthest-pd find-clusters

I intercluster-density intra-dist-expect intra-distances ith-sum-sqr-err

K km++init kmeans kmeans++ knn knn-graph krnn-clust krnn-graph

S S-Dbw-index scatt split-krnn split-worst-cluster sum-sqr-err

X ||x||

Various supplementary math functions centering on combinatorics that are not supplied by clojure.math.combinatorics. Effectively an extension of that library.

Various Information Theory functions and measures rooted in Shannon Entropy measure and targetting a variety of sequence and string data.

VARS

C combin-joint-entropy cond-entropy conditional-mutual-information CREl

D dice-coeff diff-fn DLX||Y DX||Y

F freq-jaccard-index freq-xdict-dict

H hamming hamming-stgs HXY HX|Y hybrid-dictionary

I II information-capacity informativity interaction-information IXY IXY|Z

J jaccard-dist jaccard-index jensen-shannon joint-entropy

K KLD

L lambda-divergence levenshtein limit-entropy limit-informativity lod-score log-odds

M max-qdict-entropy mutual-information

N new-row ngram-compare ngram-vec normed-codepoints

R raw-lod-score reconstruct-dict relative-entropy

S seq-joint-entropy shannon-entropy

Various frequency, combinatorial, probability, statistical, measure, and metrics for a variety of sequence and string data.

VARS

A alphabet2 avg-std-deviation avg-variance

C cc-combins-freqn cc-combins-freqs-probs cc-freqn cc-freqs cc-freqs&probs cc-freqs-probs cc-tfreqn cc-tfreqs choose-k-freqn combin-count-reduction combins-freqn combins-freqs-probs cond-probability correlation covariance

F flatten-pair-coll freqm-probm freqn freqs&probs freqs-probs

G geometric-dist geometric-pdf

J joint-prob-x joint-probability JPSxy JPxy

K keysort

P p-value pair-coll? pdsum pearson-correlation poisson-cdf poisson-dist poisson-pdf poisson-sample probs pXY|y

V variance

Various data test and analysis performance scoring.

General utility functions and macros. Basically these resources are fairly general and intended to be usable on most any part of most any project

Various supplementary string functions not included in the standard Clojure ecosystem or some that are but which now have broken argument order in terms of threading. Most of this stuff really should be in clojure.string, but for unknown reasons isn't.