src/packages.lisp

   1 ;;; -*- mode: lisp -*-
   2
   3 ;;; Time-stamp: <2009-07-12 13:01:09 tony>
   4 ;;; Creation:   <2008-03-11 19:18:34 user>
   5 ;;; File:       packages.lisp
   6 ;;; Author:     AJ Rossini <blindglobe@gmail.com>
   7 ;;; Copyright:  (c)2007--2008, AJ Rossini.  BSD, LLGPL, or GPLv2, depending
   8 ;;;             on how it arrives.
   9 ;;; Purpose:    package structure description for lispstat
  10
  11 ;;; What is this talk of 'release'? Klingons do not make software
  12 ;;; 'releases'.  Our software 'escapes', leaving a bloody trail of
  13 ;;; designers and quality assurance people in its wake.
  14
  15 (in-package :cl-user)
  16
  17 ;;; Basics
  18
  19
  20 (defpackage :lisp-stat-object-system
  21   (:nicknames :ls-objects :lsos)
  22   (:use :common-lisp)
  23   (:shadow :call-method :call-next-method)
  24   (:export ls-object objectp *object* kind-of-p make-object
  25            *message-hook*
  26            *set-slot-hook* proto-slot-value self
  27            send call-next-method call-method
  28            defmeth defproto instance-slots proto-name))
  29
  30 (defpackage :lisp-stat-types
  31   (:documentation "Provides some typeing for LispStat, but is clearly
  32   a bit incomplete.")
  33   (:use :common-lisp)
  34   (:export fixnump
  35            check-nonneg-fixnum check-one-nonneg-fixnum
  36            check-one-fixnum check-one-real check-one-number))
  37
  38 (defpackage :lisp-stat-float
  39   (:use :common-lisp)
  40   (:export +stat-float-typing+ +stat-cfloat-typing+ +stat-float-template+
  41            machine-epsilon base-float makedouble
  42
  43            make-base-trans-fun-2 make-base-trans-fun
  44
  45            base-log base-exp base-expt base-sqrt base-sin base-cos
  46            base-tan base-asin base-acos base-atan base-sinh
  47            BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
  48            BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
  49            BASE-FROUND BASE-SIGNUM BASE-CIS))
  50
  51 (defpackage :lisp-stat-compound-data
  52   (:use :common-lisp
  53         :lisp-stat-object-system
  54         :lisp-stat-types)
  55   (:shadowing-import-from :lisp-stat-object-system
  56                           call-next-method call-method)
  57   (:export compound-data-p *compound-data-proto*
  58            compound-object-p
  59            compound-data-seq compound-data-length
  60            element-list element-seq
  61            sort-data order rank
  62            recursive-map-elements map-elements repeat
  63            check-sequence
  64            get-next-element make-next-element set-next-element
  65            ;; sequencep
  66            iseq ordered-nneg-seq
  67            select split-list which
  68            difference rseq
  69            flatten-list))
  70
  71 (defpackage :lisp-stat-macros
  72   (:use :common-lisp
  73         :lisp-stat-compound-data)
  74   (:export make-rv-function make-rv-function-1))
  75
  76 (defpackage :lisp-stat-basics
  77     (:use :common-lisp
  78           :lisp-stat-object-system
  79           :lisp-stat-types
  80           :lisp-stat-float
  81           :lisp-stat-macros
  82           :lisp-stat-compound-data)
  83   (:shadowing-import-from :lisp-stat-object-system
  84                           call-method call-next-method)
  85   (:export permute-array sum prod count-elements mean
  86            if-else sample))
  87
  88 (defpackage :lisp-stat-float
  89   (:use :common-lisp)
  90   (:export +stat-float-typing+ +stat-cfloat-typing+ +stat-float-template+
  91            machine-epsilon base-float makedouble
  92
  93            make-base-trans-fun-2 make-base-trans-fun
  94
  95            BASE-LOG BASE-EXP BASE-EXPT BASE-SQRT BASE-SIN BASE-COS
  96            BASE-TAN BASE-ASIN BASE-ACOS BASE-ATAN BASE-SINH
  97            BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
  98            BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
  99            BASE-FROUND BASE-SIGNUM BASE-CIS))
 100
 101 (defpackage :lisp-stat-macros
 102   (:use :common-lisp
 103         :lisp-stat-compound-data)
 104   (:export make-rv-function make-rv-function-1))
 105
 106 ;;; NEW CLOS STRUCTURE
 107
 108
 109
 110 (defpackage :cls-dataframe
 111   (:use :common-lisp
 112         :lisp-matrix)
 113   (:export
 114    ;; generic container class for data -- if small enough
 115    ;; could be value, otherwise might be reference.
 116    dataframe-like
 117    dataframe-array
 118    make-dataframe
 119
 120    ;; accessors
 121    varlabels caselabels nrows ncols
 122    dataframe-dimension dataframe-dimensons
 123    dfref dfref-case dfref-var
 124    consistent-dataframe-p
 125
 126    dataset
 127    list-of-columns ;; list-of-variables
 128    list-of-rows ;; list-of-observations
 129    ))
 130
 131
 132 (defpackage :cls-data-listoflist
 133   (:use :common-lisp
 134         :lisp-matrix
 135         :cls-dataframe) ; for dataframe
 136   (:export lists-of-same-size
 137            equal-listoflist
 138            transpose-listoflist
 139            listoflist->dataframe
 140            listoflist->array
 141            listoflist->matrix-like))
 142
 143
 144 (defpackage :cls-dataimport
 145   (:documentation "Data I/O and similar import technologies.")
 146   (:use :common-lisp
 147         :lisp-stat-object-system
 148         :cls-dataframe
 149         :cls-data-listoflist
 150         :rsm.string)
 151   (:shadowing-import-from :lisp-stat-object-system
 152                           call-method call-next-method)
 153   (:export dsvstream->dataframe dsvstream->matrix dsvstream->listoflist))
 154
 155
 156 (defpackage :lisp-stat-model
 157   (:documentation "Model management for data analysis.")
 158   (:use :common-lisp
 159         :lisp-matrix)
 160   (:export
 161    ;; data structures for model and model/data combination
 162    model statistical-model analysis))
 163
 164 ;;; visualization
 165
 166 (defpackage :cls-visualize
 167   (:use :common-lisp
 168         :lisp-matrix
 169         :cls-dataframe))
 170
 171 #|
 172 (defpackage :cls-visualize-plplot
 173   (:use :common-lisp
 174         :lisp-matrix
 175         :cls-dataframe
 176         :cl-plplot-system)
 177   (:export
 178    ;; examples
 179    plot-ex contour-plot-ex fn-contour-plot-ex shade-plot-ex 3D-plot-ex))
 180 |#
 181
 182 ;;; USER PACKAGES
 183
 184 (defpackage :lisp-stat-ffi-int
 185   (:use :common-lisp
 186         :cffi)
 187   (:export ccl-store-integer ccl-store-double ccl-store-ptr
 188            get-buf ))
 189
 190 (defpackage :lisp-stat-probability
 191   (:use :common-lisp
 192         :cffi
 193         :lisp-stat-ffi-int
 194         :lisp-stat-macros)
 195   (:export log-gamma set-seed
 196            uniform-rand
 197            normal-cdf normal-quant normal-dens normal-rand
 198            bivnorm-cdf
 199            cauchy-cdf cauchy-quant cauchy-dens cauchy-rand
 200            gamma-cdf gamma-quant gamma-dens gamma-rand
 201            chisq-cdf chisq-quant chisq-dens chisq-rand
 202            beta-cdf beta-quant beta-dens beta-rand
 203            t-cdf t-quant t-dens t-rand
 204            f-cdf f-quant f-dens f-rand
 205            poisson-cdf poisson-quant poisson-pmf poisson-rand
 206            binomial-cdf binomial-quant binomial-pmf binomial-rand))
 207
 208
 209
 210 (defpackage :lisp-stat-math
 211    (:use :common-lisp
 212          :lisp-stat-object-system
 213          :lisp-stat-macros
 214          :lisp-stat-compound-data
 215          :lisp-stat-float)
 216    (:shadowing-import-from :lisp-stat-object-system
 217                            call-method call-next-method)
 218    (:shadow expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 219            asin acos atan sinh cosh tanh asinh acosh atanh float random
 220            truncate floor ceiling round minusp zerop plusp evenp oddp
 221            < <= = /= >= > ;; complex
 222            conjugate realpart imagpart phase
 223            min max logand logior logxor lognot ffloor fceiling
 224            ftruncate fround signum cis)
 225    (:export ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 226            tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 227            truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 228            /= >= > ;; complex
 229            conjugate realpart imagpart phase min max
 230            logand logior logxor lognot ffloor fceiling ftruncate fround
 231            signum cis)
 232    (:documentation "Vectorization of numerical functions"))
 233
 234
 235 #| ;; some of this goes back in, but not all of it?
 236 (defpackage :lisp-stat-linalg
 237   (:use :common-lisp
 238         :cffi
 239         :lisp-matrix
 240         :lisp-stat-math
 241         :lisp-stat-types
 242         :lisp-stat-float
 243         :lisp-stat-compound-data)
 244   (:shadowing-import-from :lisp-stat-math
 245           expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 246           asin acos atan sinh cosh tanh asinh acosh atanh float random
 247           truncate floor ceiling round minusp zerop plusp evenp oddp
 248           < <= = /= >= > complex conjugate realpart imagpart phase
 249           min max logand logior logxor lognot ffloor fceiling
 250           ftruncate fround signum cis)
 251   (:export chol-decomp lu-decomp lu-solve determinant inverse
 252            sv-decomp qr-decomp rcondest make-rotation spline
 253            kernel-dens kernel-smooth
 254            fft make-sweep-matrix sweep-operator ax+y eigen
 255
 256            check-real ;; for optimize
 257
 258            covariance-matrix matrix print-matrix solve
 259            backsolve eigenvalues eigenvectors accumulate cumsum combine
 260            lowess))
 261
 262 |#
 263
 264
 265
 266
 267 (defpackage :lisp-stat-data
 268   (:documentation "Data management, integration, I/O, and other data technologies.")
 269   (:nicknames :ls-data)
 270   (:use :common-lisp
 271         :lisp-stat-object-system
 272         :lisp-stat-config
 273         :lisp-stat-types
 274         :lisp-stat-compound-data)
 275   (:shadowing-import-from :lisp-stat-object-system
 276                           call-method call-next-method)
 277   (:export open-file-dialog read-data-file read-data-columns load-data
 278            load-example *variables* *ask-on-redefine*
 279            def variables savevar undef))
 280
 281 (defpackage :lisp-stat-descriptive-statistics
 282  (:use :common-lisp
 283        :lisp-stat-data
 284        :lisp-stat-math
 285        :lisp-stat-compound-data
 286        :lisp-matrix
 287        :lisp-stat-basics)
 288    (:shadowing-import-from :lisp-stat-math ;; life is a vector!
 289       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 290       asin acos atan sinh cosh tanh asinh acosh atanh float random
 291       truncate floor ceiling round minusp zerop plusp evenp oddp
 292       < <= = /= >= > ;; complex
 293       conjugate realpart imagpart phase
 294       min max logand logior logxor lognot ffloor fceiling
 295       ftruncate fround signum cis)
 296    (:export standard-deviation
 297             quantile median interquartile-range
 298             fivnum sample))
 299
 300
 301 (defpackage :lisp-stat-regression-linear
 302   (:use :common-lisp
 303         :lisp-matrix
 304         :lisp-stat-basics
 305         :lisp-stat-compound-data
 306         :lisp-stat-descriptive-statistics )
 307   (:shadowing-import-from :lisp-stat-object-system
 308                           call-method call-next-method)
 309   (:export regression-model fit-model
 310
 311            estimates covariance-matrix
 312            ;; functions for helpers
 313            lm xtxinv
 314            print-object ;; for method dispatch
 315            ))
 316
 317 (defpackage :common-lisp-statistics
 318   (:documentation "Experimentation package for LispStat.  Serious work
 319     should be packaged up elsewhere for reproducibility.  By this I
 320     mean, creating a data/analytics/analysis package with the minimal
 321     set of objects required.")
 322   (:nicknames :cls :common-lisp-statistics :lisp-stat)
 323   (:use :common-lisp
 324         :lisp-stat-config
 325         :lisp-stat-object-system
 326         :lisp-stat-compound-data
 327         :lisp-stat-probability
 328         :lisp-stat-types
 329         :lisp-stat-float
 330         :lisp-stat-basics
 331         :lisp-stat-data
 332         :cls-dataframe
 333         :cls-data-listoflist
 334         :lisp-stat-math
 335         :lisp-matrix ;; conversion to a more robust linalg approach
 336         :lisp-stat-descriptive-statistics
 337         :lisp-stat-regression-linear
 338         ;; :cybertiggyr-dsv
 339         :cls-visualize
 340         ;; :cls-visualize-plplot
 341         )
 342   (:shadowing-import-from :lisp-stat-object-system
 343                           call-method call-next-method)
 344   (:shadowing-import-from :lisp-stat-math
 345         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 346         asin acos atan sinh cosh tanh asinh acosh atanh float random
 347         truncate floor ceiling round minusp zerop plusp evenp oddp
 348         < <= = /= >= >
 349         ;;complex
 350         conjugate realpart imagpart phase
 351
 352         min max
 353         logand logior logxor lognot
 354         ffloor fceiling ftruncate fround
 355         signum cis)
 356   (:export
 357    ;; lisp-stat-config:
 358    *default-path* *lsos-files* *basic-files* *ls-files*
 359    *lispstat-home-dir* *lispstat-data-dir* *lispstat-examples-dir*
 360
 361    ;; lsobjects :
 362    defproto defproto2
 363    defmeth send proto-slot-value
 364
 365    ;; lstypes :
 366    fixnump check-nonneg-fixnum check-one-fixnum
 367    check-one-nonneg-fixnum
 368    check-one-real check-one-number
 369
 370    ;; lsmacros:
 371
 372    ;; lsfloat :
 373    machine-epsilon
 374
 375    ;; compound :
 376    compound-data-p *compound-data-proto* compound-object-p
 377    compound-data-seq compound-data-length
 378    element-list element-seq
 379    sort-data order rank
 380    recursive-map-elements map-elements
 381    repeat
 382    check-sequence
 383    get-next-element make-next-element set-next-element
 384    ;; sequencep
 385    iseq
 386    ordered-nneg-seq
 387    select which
 388    difference rseq
 389
 390    ;; lsmath.lsp
 391    ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 392    tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 393    truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 394    /= >= > ;; complex
 395    conjugate realpart imagpart phase min max
 396    logand logior logxor lognot ffloor fceiling ftruncate fround
 397    signum cis
 398
 399 #| ;; The following need to be re-found in lisp-matrix...
 400
 401    ;; matrices.lisp
 402    matrixp num-rows num-cols matmult identity-matrix diagonal row-list
 403    column-list inner-product outer-product cross-product transpose
 404    bind-columns bind-rows
 405
 406    ;; linalg.lisp
 407    chol-decomp lu-decomp lu-solve determinant inverse
 408    sv-decomp qr-decomp rcondest make-rotation spline
 409    kernel-dens kernel-smooth
 410    fft make-sweep-matrix sweep-operator ax+y eigen
 411    check-real
 412    covariance-matrix matrix print-matrix solve
 413    backsolve eigenvalues eigenvectors accumulate cumsum combine
 414    lowess
 415
 416    ;; in linalg.lisp, possibly not supported by matlisp
 417    spline kernel-dens kernel-smooth
 418
 419 |#
 420
 421    ;; optimize.lsp
 422    newtonmax nelmeadmax
 423
 424    ;; lispstat-macros
 425    make-rv-function make-rv-function-1
 426
 427    ;; xarray
 428    xref xtype xdims xdim xdims*
 429
 430    ;; data
 431    open-file-dialog read-data-file read-data-columns load-data
 432    load-example *variables* *ask-on-redefine*
 433    def variables savevar undef
 434
 435    ;; dataframe
 436    dataframe-like dataframe-array make-dataframe
 437    varlabels caselabels nrows ncols
 438    dataframe-dimension dataframe-dimensons
 439    dfref dfref-case dfref-var
 440    consistent-dataframe-p
 441    dataset
 442    list-of-columns list-of-rows
 443
 444
 445
 446    ;; listoflist
 447    lists-of-same-size equal-listoflist
 448    transpose-listoflist
 449    listoflist->dataframe listoflist->array listoflist->matrix-like
 450
 451    ;; statistics.lsp  (descriptions, should probably be moved
 452    ;; later...?
 453    standard-deviation quantile median interquartile-range
 454    fivnum sample
 455
 456    ;; probability (dists.lisp)
 457    log-gamma set-seed
 458    uniform-rand normal-cdf normal-quant normal-dens
 459    normal-rand bivnorm-cdf cauchy-cdf cauchy-quant cauchy-dens
 460    cauchy-rand gamma-cdf gamma-quant gamma-dens gamma-rand
 461    chisq-cdf chisq-quant chisq-dens chisq-rand beta-cdf beta-quant
 462    beta-dens beta-rand t-cdf t-quant t-dens t-rand f-cdf f-quant
 463    f-dens f-rand poisson-cdf poisson-quant poisson-pmf poisson-rand
 464    binomial-cdf binomial-quant binomial-pmf binomial-rand
 465
 466    ;; Here is where we have a problem -- lispstat core should be core
 467    ;; data management and config problems, with packages providing
 468    ;; specialized extensions to LispStat, i.e. regression, nonlin
 469    ;; regression, bayesian regression via laplace approximation, etc.
 470
 471    ;; The following could be considered "recommended packages",
 472    ;; similar to the idea of the recommended packages in R.  Probably
 473    ;; we want them to do the exporting within that package, therefore
 474    ;; NOT being able to lock the "data-ish" package, but only the
 475    ;; subpackages prior to export.
 476
 477    ;; regression.lsp
 478    ;; -- linear regressin models.
 479    regression-model fit-model
 480    estimates covariance-matrix
 481
 482    regression-model-proto x y intercept sweep-matrix
 483    basis weights included total-sum-of-squares residual-sum-of-squares
 484    predictor-names response-name case-labels
 485    lm xtxinv
 486
 487    ;; nonlin.lsp
 488    ;; -- nonlinear regression models
 489    nreg-model nreg-model-proto mean-function theta-hat epsilon
 490    count-limit verbose
 491    ;; we might need something like xtxinv here?  But should be
 492    ;; encapsulated, so we use the one in regression.lisp
 493
 494    ;; bayes.lsp
 495    bayes-model bayes-model-proto bayes-internals
 496
 497    ;; plots.lisp
 498    plot-ex
 499    contour-plot-ex
 500    fn-contour-plot-ex
 501    shade-plot-ex
 502    3D-plot-ex
 503
 504    ))
 505
 506
 507 ;;;; PACKAGES FOR USEABILITY
 508
 509 (defpackage :lisp-stat-data-examples
 510   (:documentation "Example data for unittests, examples, illustrations,")
 511   (:use :common-lisp
 512         :common-lisp-statistics)
 513   (:shadowing-import-from :lisp-stat
 514                           call-method call-next-method
 515
 516       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 517       asin acos atan sinh cosh tanh asinh acosh atanh float random
 518       truncate floor ceiling round minusp zerop plusp evenp oddp
 519       < <= = /= >= > > ;; complex
 520       conjugate realpart imagpart phase
 521       min max logand logior logxor lognot ffloor fceiling
 522       ftruncate fround signum cis
 523
 524       <= float imagpart)
 525   (:export iron aluminum absorbtion
 526            diabetes dlabs))
 527
 528
 529 (defpackage :lisp-stat-user
 530   (:documentation "Experimentation package for LispStat.  Serious work
 531     should be placed in a similar package elsewhere for
 532     reproducibility.  But this should hint as to what needs to be done
 533     for a user- or analysis-package.")
 534   (:nicknames :ls-user)
 535   (:use :common-lisp ; always needed for user playgrounds!
 536         :lisp-matrix
 537         :common-lisp-statistics
 538         :lisp-stat-data-examples) ;; this last is to have 'things to play with'
 539   (:shadowing-import-from :lisp-stat
 540                           call-method call-next-method
 541
 542       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 543       asin acos atan sinh cosh tanh asinh acosh atanh float random
 544       truncate floor ceiling round minusp zerop plusp evenp oddp
 545       < <= = /= >= > > ;; complex
 546       conjugate realpart imagpart phase
 547       min max logand logior logxor lognot ffloor fceiling
 548       ftruncate fround signum cis
 549
 550       <= float imagpart))
 551
 552 (defpackage :lisp-stat-unittests
 553   (:use :common-lisp
 554         :lift :lisp-matrix
 555         :lisp-stat :lisp-stat-data-examples)
 556   (:shadowing-import-from :lisp-stat
 557                           call-method call-next-method ;; objects
 558         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan ;; lsmath
 559         asin acos atan sinh cosh tanh asinh acosh atanh float random
 560         truncate floor ceiling round minusp zerop plusp evenp oddp
 561         < <= = /= >= > ;; complex
 562         conjugate realpart imagpart phase
 563         min max logand logior logxor lognot ffloor fceiling
 564         ftruncate fround signum cis)
 565   (:export run-lisp-stat-tests run-lisp-stat-test scoreboard ; exec
 566            almost= almost=lists numerical=)) ; compare
 567
 568 (defpackage :cls-dataframe-example
 569   (:use :common-lisp
 570         :lift  :lisp-stat-unittests
 571         :lisp-stat-data-examples
 572         :cls-dataframe)
 573   (:export absorbtion aluminum iron))
 574
 575
 576 (defpackage :lisp-stat-optimize
 577  (:use :common-lisp
 578        :cffi
 579        :lisp-matrix
 580        :lisp-stat-ffi-int
 581        :lisp-stat-object-system
 582        :lisp-stat-types
 583        :lisp-stat-compound-data
 584        :lisp-stat-math
 585        :lisp-stat-float
 586        :lisp-stat-basics
 587 #|
 588        :lisp-stat-matrix
 589        :lisp-stat-linalg-data
 590        :lisp-stat-linalg
 591 |#
 592        )
 593  (:shadowing-import-from :lisp-stat-object-system
 594                          call-method call-next-method)
 595  (:shadowing-import-from :lisp-stat-math
 596            expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 597            asin acos atan sinh cosh tanh asinh acosh atanh float random
 598            truncate floor ceiling round minusp zerop plusp evenp oddp
 599            < <= = /= >= > complex conjugate realpart imagpart phase
 600            min max logand logior logxor lognot ffloor fceiling
 601            ftruncate fround signum cis)
 602  (:export
 603      ;; derivatives
 604      numgrad numhess
 605
 606      ;; optimization
 607      newtonmax nelmeadmax))