src/packages.lisp

   1 ;;; -*- mode: lisp -*-
   2
   3 ;;; Time-stamp: <2009-07-11 14:17:46 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-object-system
 325         :lisp-stat-compound-data
 326         :lisp-stat-probability
 327         :lisp-stat-types
 328         :lisp-stat-float
 329         :lisp-stat-basics
 330         :lisp-stat-data
 331         :cls-dataframe
 332         :cls-data-listoflist
 333         :lisp-stat-math
 334         :lisp-matrix ;; conversion to a more robust linalg approach
 335         :lisp-stat-descriptive-statistics
 336         :lisp-stat-regression-linear
 337         :cybertiggyr-dsv
 338         :cls-visualize
 339         ;; :cls-visualize-plplot
 340         )
 341   (:shadowing-import-from :lisp-stat-object-system
 342                           call-method call-next-method)
 343   (:shadowing-import-from :lisp-stat-math
 344         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 345         asin acos atan sinh cosh tanh asinh acosh atanh float random
 346         truncate floor ceiling round minusp zerop plusp evenp oddp
 347         < <= = /= >= >
 348         ;;complex
 349         conjugate realpart imagpart phase
 350
 351         min max
 352         logand logior logxor lognot
 353         ffloor fceiling ftruncate fround
 354         signum cis)
 355   (:export
 356    ;; lsobjects :
 357    defproto defproto2
 358    defmeth send
 359    proto-slot-value
 360
 361    ;; lstypes :
 362    fixnump check-nonneg-fixnum check-one-fixnum
 363    check-one-nonneg-fixnum
 364    check-one-real check-one-number
 365
 366    ;; lsmacros:
 367
 368    ;; lsfloat :
 369    machine-epsilon
 370
 371    ;; compound :
 372    compound-data-p *compound-data-proto* compound-object-p
 373    compound-data-seq compound-data-length
 374    element-list element-seq
 375    sort-data order rank
 376    recursive-map-elements map-elements
 377    repeat
 378    check-sequence
 379    get-next-element make-next-element set-next-element
 380    ;; sequencep
 381    iseq
 382    ordered-nneg-seq
 383    select which
 384    difference rseq
 385
 386    ;; lsmath.lsp
 387    ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 388    tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 389    truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 390    /= >= > ;; complex
 391    conjugate realpart imagpart phase min max
 392    logand logior logxor lognot ffloor fceiling ftruncate fround
 393    signum cis
 394
 395 #| ;; The following need to be re-found in lisp-matrix...
 396
 397    ;; matrices.lisp
 398    matrixp num-rows num-cols matmult identity-matrix diagonal row-list
 399    column-list inner-product outer-product cross-product transpose
 400    bind-columns bind-rows
 401
 402    ;; linalg.lisp
 403    chol-decomp lu-decomp lu-solve determinant inverse
 404    sv-decomp qr-decomp rcondest make-rotation spline
 405    kernel-dens kernel-smooth
 406    fft make-sweep-matrix sweep-operator ax+y eigen
 407    check-real
 408    covariance-matrix matrix print-matrix solve
 409    backsolve eigenvalues eigenvectors accumulate cumsum combine
 410    lowess
 411
 412    ;; in linalg.lisp, possibly not supported by matlisp
 413    spline kernel-dens kernel-smooth
 414
 415 |#
 416
 417    ;; optimize.lsp
 418    newtonmax nelmeadmax
 419
 420    ;; lispstat-macros
 421    make-rv-function make-rv-function-1
 422
 423    ;; xarray
 424    xref xtype xdims xdim xdims*
 425
 426    ;; data
 427    open-file-dialog read-data-file read-data-columns load-data
 428    load-example *variables* *ask-on-redefine*
 429    def variables savevar undef
 430
 431    ;; dataframe
 432    dataframe-like dataframe-array make-dataframe
 433    varlabels caselabels nrows ncols
 434    dataframe-dimension dataframe-dimensons
 435    dfref dfref-case dfref-var
 436    consistent-dataframe-p
 437    dataset
 438    list-of-columns list-of-rows
 439
 440
 441
 442    ;; listoflist
 443    lists-of-same-size equal-listoflist
 444    transpose-listoflist
 445    listoflist->dataframe listoflist->array listoflist->matrix-like
 446
 447    ;; statistics.lsp  (descriptions, should probably be moved
 448    ;; later...?
 449    standard-deviation quantile median interquartile-range
 450    fivnum sample
 451
 452    ;; probability (dists.lisp)
 453    log-gamma set-seed
 454    uniform-rand normal-cdf normal-quant normal-dens
 455    normal-rand bivnorm-cdf cauchy-cdf cauchy-quant cauchy-dens
 456    cauchy-rand gamma-cdf gamma-quant gamma-dens gamma-rand
 457    chisq-cdf chisq-quant chisq-dens chisq-rand beta-cdf beta-quant
 458    beta-dens beta-rand t-cdf t-quant t-dens t-rand f-cdf f-quant
 459    f-dens f-rand poisson-cdf poisson-quant poisson-pmf poisson-rand
 460    binomial-cdf binomial-quant binomial-pmf binomial-rand
 461
 462    ;; Here is where we have a problem -- lispstat core should be core
 463    ;; data management and config problems, with packages providing
 464    ;; specialized extensions to LispStat, i.e. regression, nonlin
 465    ;; regression, bayesian regression via laplace approximation, etc.
 466
 467    ;; The following could be considered "recommended packages",
 468    ;; similar to the idea of the recommended packages in R.  Probably
 469    ;; we want them to do the exporting within that package, therefore
 470    ;; NOT being able to lock the "data-ish" package, but only the
 471    ;; subpackages prior to export.
 472
 473    ;; regression.lsp
 474    ;; -- linear regressin models.
 475    regression-model fit-model
 476    estimates covariance-matrix
 477
 478    regression-model-proto x y intercept sweep-matrix
 479    basis weights included total-sum-of-squares residual-sum-of-squares
 480    predictor-names response-name case-labels
 481    lm xtxinv
 482
 483    ;; nonlin.lsp
 484    ;; -- nonlinear regression models
 485    nreg-model nreg-model-proto mean-function theta-hat epsilon
 486    count-limit verbose
 487    ;; we might need something like xtxinv here?  But should be
 488    ;; encapsulated, so we use the one in regression.lisp
 489
 490    ;; bayes.lsp
 491    bayes-model bayes-model-proto bayes-internals
 492
 493    ;; plots.lisp
 494    plot-ex
 495    contour-plot-ex
 496    fn-contour-plot-ex
 497    shade-plot-ex
 498    3D-plot-ex
 499
 500    ))
 501
 502
 503 ;;;; PACKAGES FOR USEABILITY
 504
 505 (defpackage :lisp-stat-data-examples
 506   (:documentation "Example data for unittests, examples, illustrations,")
 507   (:use :common-lisp
 508         :common-lisp-statistics)
 509   (:shadowing-import-from :lisp-stat
 510                           call-method call-next-method
 511
 512       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 513       asin acos atan sinh cosh tanh asinh acosh atanh float random
 514       truncate floor ceiling round minusp zerop plusp evenp oddp
 515       < <= = /= >= > > ;; complex
 516       conjugate realpart imagpart phase
 517       min max logand logior logxor lognot ffloor fceiling
 518       ftruncate fround signum cis
 519
 520       <= float imagpart)
 521   (:export iron aluminum absorbtion
 522            diabetes dlabs))
 523
 524
 525 (defpackage :lisp-stat-user
 526   (:documentation "Experimentation package for LispStat.  Serious work
 527     should be placed in a similar package elsewhere for
 528     reproducibility.  But this should hint as to what needs to be done
 529     for a user- or analysis-package.")
 530   (:nicknames :ls-user)
 531   (:use :common-lisp ; always needed for user playgrounds!
 532         :lisp-matrix
 533         :common-lisp-statistics
 534         :lisp-stat-data-examples) ;; this last is to have 'things to play with'
 535   (:shadowing-import-from :lisp-stat
 536                           call-method call-next-method
 537
 538       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 539       asin acos atan sinh cosh tanh asinh acosh atanh float random
 540       truncate floor ceiling round minusp zerop plusp evenp oddp
 541       < <= = /= >= > > ;; complex
 542       conjugate realpart imagpart phase
 543       min max logand logior logxor lognot ffloor fceiling
 544       ftruncate fround signum cis
 545
 546       <= float imagpart))
 547
 548 (defpackage :lisp-stat-unittests
 549   (:use :common-lisp
 550         :lift :lisp-matrix
 551         :lisp-stat :lisp-stat-data-examples)
 552   (:shadowing-import-from :lisp-stat
 553                           call-method call-next-method ;; objects
 554         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan ;; lsmath
 555         asin acos atan sinh cosh tanh asinh acosh atanh float random
 556         truncate floor ceiling round minusp zerop plusp evenp oddp
 557         < <= = /= >= > ;; complex
 558         conjugate realpart imagpart phase
 559         min max logand logior logxor lognot ffloor fceiling
 560         ftruncate fround signum cis)
 561   (:export run-lisp-stat-tests run-lisp-stat-test scoreboard ; exec
 562            almost= almost=lists numerical=)) ; compare
 563
 564 (defpackage :cls-dataframe-example
 565   (:use :common-lisp
 566         :lift  :lisp-stat-unittests
 567         :lisp-stat-data-examples
 568         :cls-dataframe)
 569   (:export absorbtion aluminum iron))
 570
 571
 572 (defpackage :lisp-stat-optimize
 573  (:use :common-lisp
 574        :cffi
 575        :lisp-matrix
 576        :lisp-stat-ffi-int
 577        :lisp-stat-object-system
 578        :lisp-stat-types
 579        :lisp-stat-compound-data
 580        :lisp-stat-math
 581        :lisp-stat-float
 582        :lisp-stat-basics
 583 #|
 584        :lisp-stat-matrix
 585        :lisp-stat-linalg-data
 586        :lisp-stat-linalg
 587 |#
 588        )
 589  (:shadowing-import-from :lisp-stat-object-system
 590                          call-method call-next-method)
 591  (:shadowing-import-from :lisp-stat-math
 592            expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 593            asin acos atan sinh cosh tanh asinh acosh atanh float random
 594            truncate floor ceiling round minusp zerop plusp evenp oddp
 595            < <= = /= >= > complex conjugate realpart imagpart phase
 596            min max logand logior logxor lognot ffloor fceiling
 597            ftruncate fround signum cis)
 598  (:export
 599      ;; derivatives
 600      numgrad numhess
 601
 602      ;; optimization
 603      newtonmax nelmeadmax))