API Overview - Incanter 1.4.1 (legacy)

Incanter is a Clojure-based, R-like statistical computing and graphics environment for the JVM.


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by David Edgar Liebke
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This is library provides functions for performing
basic Bayesian modeling and inference.
Contents: sample-model-params sample-multinomial-params sample-mvn-params sample-proportions


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  censored-mean-lower censored-mean-two-sided censored-mean-upper censored-variance-lower censored-variance-two-sided censored-variance-upper truncated-variance 


by David Edgar Liebke
Detailed API documentation
This is the core charting library for Incanter.
It provides basic scatter plots, histograms, box plots
xy plots, bar charts, line charts, as well as
specialized charts like trace plots and Bland-Altman

This library is built on the JFreeChart library
Contents: add-box-plot add-categories add-function add-histogram add-image add-lines add-parametric add-pointer add-points add-polygon add-subtitle add-text area-chart bar-chart bland-altman-plot box-plot clear-background dynamic-scatter-plot dynamic-xy-plot function-plot get-series heat-map histogram line-chart parametric-plot pie-chart qq-plot scatter-plot set-alpha set-background-alpha set-background-default set-stroke set-stroke-color set-theme set-theme-bw set-title set-x-label set-x-range set-y-label set-y-range slider sliders sliders* stacked-area-chart stacked-bar-chart time-series-plot trace-plot xy-plot


by David Edgar Liebke
Detailed API documentation
This is the core numerics library for Incanter.
It provides functions for vector- and matrix-based
mathematical operations and the core data manipulation
functions for Incanter.

This library is built on Parallel Colt
an extension of the Colt numerics library
Contents: $ $= $data $fn $group-by $join $map $order $rollup $where ->Dataset abs acos asin atan atan2 beta bind-columns bind-rows block-diag block-matrix categorical-var choose col-names condition conj-cols conj-rows copy cos cumulative-sum data-table dataset Dataset dataset? decomp-cholesky decomp-eigenvalue decomp-lu decomp-qr decomp-svd deshape det diag diagonal-blocks dim div exp factorial gamma get-categories grid-apply group-on half-vectorize head identity-matrix incomplete-beta kronecker length log log10 log2 make-unique map->Dataset matrix matrix-map matrix? minus mmult mult plus pow prod query-dataset query-to-pred quit rank regularized-beta save sel separate-blocks set-data sin solve solve-quadratic sq sqrt sum sum-of-squares symmetric-matrix tan to-dataset to-labels to-levels to-list to-map to-matrix to-vect trace trans transform-col vectorize view with-data


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by Mark M. Fredrickson and William Leung
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Probability functions (pdf, cdf, draw, etc.) for common distributions, and for collections, sets, and maps.
Contents: ->Beta-rec ->Binomial-rec ->ChiSquare-rec ->Combination ->DoubleUniform-rec ->Exponential-rec ->F ->Gamma-rec ->NegativeBinomial-rec ->Normal-rec ->Poisson-rec ->StudentT-rec ->UniformInt beta-distribution Beta-rec binomial-distribution Binomial-rec cdf chisq-distribution ChiSquare-rec Combination combination-distribution Distribution DoubleUniform-rec draw exponential-distribution Exponential-rec F f-distribution gamma-distribution Gamma-rec integer-distribution map->Beta-rec map->Binomial-rec map->ChiSquare-rec map->Combination map->DoubleUniform-rec map->Exponential-rec map->F map->Gamma-rec map->NegativeBinomial-rec map->Normal-rec map->Poisson-rec map->StudentT-rec map->UniformInt mean neg-binomial-distribution NegativeBinomial-rec normal-distribution Normal-rec pdf poisson-distribution Poisson-rec roulette-wheel StudentT-rec support t-distribution test-statistic-distribution uniform-distribution UniformInt variance


by David James Humphreys
Detailed API documentation
Excel module for reading and writing Incanter datasets.  Recognizes both old and new
Excel file formats (.xls and .xlsx).
Contents: read-xls save-xls

Variables and functions in excel.cells: get-cell-formula-value get-cell-value

Variables and functions in excel.workbook: get-workbook-sheet


by J. Bester
Detailed API documentation
Library for converting infix mathematical formula to prefix expressions
Contents: defop formula infix-to-prefix


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  hint is-matrix 


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Library for reading and writing Incanter datasets and matrices.
Contents: read-dataset


by David Edgar Liebke
Detailed API documentation
This library is used to render LaTex Math equations, based
on the jLateXMath library, and applying them incanter.charts as annotations
and subtitles.
Contents: add-latex add-latex-subtitle latex to-latex


by David Edgar Liebke
Detailed API documentation
A simple library that provides functions for persisting 
Incanter data structures using MongoDB.

Use incanter.mongodb in combination with the somnium.congomongo library. 
For usage examples, see the Congomongo README at http://github.com/somnium/congomongo, 
and the examples/blog/mongodb_datasets.clj file in the Incanter distribution. 

Here are Somnium's descriptions of Congomongo's functions:

  (mongo! & args) : Creates a Mongo object and sets the default database.
     Keyword arguments include:
     :host -> defaults to localhost
     :port -> defaults to 27017
     :db   -> defaults to nil (you'll have to set it anyway, might as well do it now.)

  (get-coll coll) : Returns a DBCollection object

  (fetch coll & options) : Fetches objects from a collection. Optional arguments include
   :where  -> takes a query map
   :only   -> takes an array of keys to retrieve
   :as     -> what to return, defaults to :clojure, can also be :json or :mongo
   :from   -> argument type, same options as above
   :one?   -> defaults to false, use fetch-one as a shortcut
   :count? -> defaults to false, use fetch-count as a shortcut

  (fetch-one coll & options) : same as (fetch collection :one? true)

  (fetch-count coll & options) : same as (fetch collection :count? true)

  (insert! coll obj & options) : Inserts a map into collection. Will not overwrite existing maps.
   Takes optional from and to keyword arguments. To insert
   as a side-effect only specify :to as nil.

  (mass-insert! coll objs & options) : Inserts a sequence of maps.

  (update! coll old new & options) : Alters/inserts a map in a collection. Overwrites existing objects.
   The shortcut forms need a map with valid :_id and :_ns fields or
   a collection and a map with a valid :_id field.

  (destroy! coll query-map) : Removes map from collection. Takes a collection name and
    a query map

  (add-index! coll fields & options) : Adds an index on the collection for the specified fields if it does not exist.
    Options include:
    :unique -> defaults to false
    :force  -> defaults to true

  (drop-index! coll fields) : Drops an index on the collection for the specified fields

  (drop-all-indexes! coll) : Drops all indexes from a collection

  (get-indexes coll & options) : Get index information on collection

  (drop-database title) : drops a database from the mongo server

  (set-database title) : atomically alters the current database

  (databases) : List databases on the mongo server

  (collections) : Returns the set of collections stored in the current database

  (drop-collection coll) : Permanently deletes a collection. Use with care.
Contents: fetch-dataset insert-dataset


Detailed API documentation

  derivative gradient hessian integrate non-linear-model 


Detailed API documentation
This library currently has only a single function, save-pdf, which saves
charts as a PDF file. To build this namespace make sure the you have the iText
library (http://itextpdf.com/) as a declared dependency in your pom.xml or
project.clj file:
[com.lowagie/itext "1.4"] 
Contents: save-pdf


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SQL module for interacting with databases.
Contents: read-dataset


by David Edgar Liebke and Bradford Cross
Detailed API documentation
This is the core statistical library for Incanter.
It provides probability functions (cdf, pdf, quantile),
random number generation, statistical tests, basic
modeling functions, similarity/association measures,
and more.

This library is built on Parallel Colt 
an extension of the Colt numerics library 
Contents: auto-correlation benford-test bootstrap category-col-summarizer cdf-beta cdf-binomial cdf-chisq cdf-empirical cdf-exp cdf-f cdf-gamma cdf-neg-binomial cdf-normal cdf-poisson cdf-t cdf-uniform cdf-weibull chebyshev-distance chisq-test choose-singletype-col-summarizer correlation correlation-linearity-test correlation-ratio cosine-similarity covariance cumulative-mean detabulate dice-coefficient dice-coefficient-str discordant-pairs euclidean-distance f-test gamma-coefficient hamming-distance indicator jaccard-distance jaccard-index kendalls-tau kendalls-w kurtosis lee-distance levenshtein-distance linear-model mahalanobis-distance manhattan-distance mean median minkowski-distance n-grams normalized-kendall-tau-distance numeric-col-summarizer odds-ratio pairings pairs pdf-beta pdf-binomial pdf-chisq pdf-exp pdf-f pdf-gamma pdf-neg-binomial pdf-normal pdf-poisson pdf-t pdf-uniform pdf-weibull permute predict principal-components product-marginal-test quantile quantile-normal quantile-t rank-index sample sample-beta sample-binomial sample-chisq sample-dirichlet sample-exp sample-gamma sample-inv-wishart sample-multinomial sample-mvn sample-neg-binomial sample-normal sample-permutations sample-poisson sample-t sample-uniform sample-weibull sample-wishart scalar-abs sd simple-ci simple-p-value simple-regression simple-t-test skewness sorensen-index spearmans-rho square-devs-from-mean sum-of-square-devs-from-mean sum-variance-test summarizable? summarizer-fn summary sweep t-test tabulate tanimoto-coefficient variance within


by Bryce Nyeggen, with modifications by David Edgar Liebke
Detailed API documentation
A library for performing symbolic math, a port from SICP (http://mitpress.mit.edu/sicp/).
Contents: deriv deriv* deriv-fn deriv-fn*


by David Edgar Liebke
Detailed API documentation
This is a port of Zoo from R in order to create the basis
of a library for time series data.

This library is built on Parallel Colt 
an extension of the Colt numerics library 
Contents: $$ aligned? coredata lag roll-apply roll-max roll-mean roll-median roll-min within-zoo? zoo zoo-apply zoo-row-map zoo-row-map- zoo-row-map-occupied
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