src/packages.lisp

   1 ;;; -*- mode: lisp -*-
   2
   3 ;;; Time-stamp: <2009-07-14 19:17:52 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 ;;; -types and -float probably ought to be moved into a -numerics
  31 ;;; package.
  32
  33 (defpackage :lisp-stat-types
  34   (:documentation "Provides some typeing for LispStat, but is clearly
  35   a bit incomplete.")
  36   (:use :common-lisp)
  37   (:export fixnump
  38            check-nonneg-fixnum check-one-nonneg-fixnum
  39            check-one-fixnum check-one-real check-one-number))
  40
  41 (defpackage :lisp-stat-float
  42   (:use :common-lisp)
  43   (:export +stat-float-typing+ +stat-cfloat-typing+ +stat-float-template+
  44            machine-epsilon base-float makedouble
  45
  46            make-base-trans-fun-2 make-base-trans-fun
  47
  48            base-log base-exp base-expt base-sqrt base-sin base-cos
  49            base-tan base-asin base-acos base-atan base-sinh
  50            BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
  51            BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
  52            BASE-FROUND BASE-SIGNUM BASE-CIS))
  53
  54 ;;; Probably should move into cls-data package.
  55
  56 (defpackage :lisp-stat-compound-data
  57   (:use :common-lisp
  58         :lisp-stat-object-system
  59         :lisp-stat-types)
  60   (:shadowing-import-from :lisp-stat-object-system
  61                           call-next-method call-method)
  62   (:export compound-data-p *compound-data-proto*
  63            compound-object-p
  64            compound-data-seq compound-data-length
  65            element-list element-seq
  66            sort-data order rank
  67            recursive-map-elements map-elements repeat
  68            check-sequence
  69            get-next-element make-next-element set-next-element
  70            ;; sequencep
  71            iseq ordered-nneg-seq
  72            select split-list which
  73            difference rseq
  74            flatten-list))
  75
  76 (defpackage :lisp-stat-macros
  77   (:use :common-lisp
  78         :lisp-stat-compound-data)
  79   (:export make-rv-function make-rv-function-1))
  80
  81 (defpackage :lisp-stat-basics
  82     (:use :common-lisp
  83           :lisp-stat-object-system
  84           :lisp-stat-types
  85           :lisp-stat-float
  86           :lisp-stat-macros
  87           :lisp-stat-compound-data)
  88   (:shadowing-import-from :lisp-stat-object-system
  89                           call-method call-next-method)
  90   (:export permute-array sum prod count-elements mean
  91            if-else sample))
  92
  93 (defpackage :lisp-stat-float
  94   (:use :common-lisp)
  95   (:export +stat-float-typing+ +stat-cfloat-typing+ +stat-float-template+
  96            machine-epsilon base-float makedouble
  97
  98            make-base-trans-fun-2 make-base-trans-fun
  99
 100            BASE-LOG BASE-EXP BASE-EXPT BASE-SQRT BASE-SIN BASE-COS
 101            BASE-TAN BASE-ASIN BASE-ACOS BASE-ATAN BASE-SINH
 102            BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
 103            BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
 104            BASE-FROUND BASE-SIGNUM BASE-CIS))
 105
 106 (defpackage :lisp-stat-macros
 107   (:use :common-lisp
 108         :lisp-stat-compound-data)
 109   (:export make-rv-function make-rv-function-1))
 110
 111 ;;; NEW CLOS STRUCTURE
 112
 113 ;;; cls-data... in dataframe, though.
 114 (defpackage :cls-dataframe
 115   (:use :common-lisp
 116         :xarray
 117         :lisp-matrix)
 118   (:export
 119    ;; generic container class for data -- if small enough
 120    ;; could be value, otherwise might be reference.
 121    dataframe-like
 122    dataframe-array
 123    make-dataframe
 124
 125    ;; accessors
 126    varlabels caselabels  nrows ncols
 127    dataframe-dimension dataframe-dimensons
 128    xref xtype xdims xdim xrank slice take carray
 129 #|
 130    dfref dfref-case dfref-var
 131    consistent-dataframe-p
 132 |#
 133
 134    dataset
 135    list-of-columns ;; list-of-variables
 136    list-of-rows ;; list-of-observations
 137    ))
 138
 139 ;; move to cls-data -- but in listoflist.lisp
 140 (defpackage :cls-data-listoflist
 141   (:use :common-lisp
 142         :lisp-matrix
 143         :cls-dataframe) ; for dataframe
 144   (:export lists-of-same-size
 145            equal-listoflist
 146            transpose-listoflist
 147            listoflist->dataframe
 148            listoflist->array
 149            listoflist->matrix-like))
 150
 151
 152 (defpackage :cls-dataimport
 153   (:documentation "Data I/O and similar import technologies.")
 154   (:use :common-lisp
 155         :lisp-stat-object-system
 156         :cls-dataframe
 157         :cls-data-listoflist
 158         :rsm.string)
 159   (:shadowing-import-from :lisp-stat-object-system
 160                           call-method call-next-method)
 161   (:export dsvstream->dataframe dsvstream->matrix dsvstream->listoflist))
 162
 163
 164 (defpackage :lisp-stat-model
 165   (:documentation "Model management for data analysis.")
 166   (:use :common-lisp
 167         :lisp-matrix)
 168   (:export
 169    ;; data structures for model and model/data combination
 170    model statistical-model analysis))
 171
 172 ;;; visualization
 173
 174 (defpackage :cls-visualize
 175   (:use :common-lisp
 176         :lisp-matrix
 177         :cls-dataframe))
 178
 179 #|
 180 (defpackage :cls-visualize-plplot
 181   (:use :common-lisp
 182         :lisp-matrix
 183         :cls-dataframe
 184         :cl-plplot-system)
 185   (:export
 186    ;; examples
 187    plot-ex contour-plot-ex fn-contour-plot-ex shade-plot-ex 3D-plot-ex))
 188 |#
 189
 190 ;;; USER PACKAGES
 191
 192 (defpackage :lisp-stat-ffi-int
 193   (:use :common-lisp
 194         :cffi)
 195   (:export ccl-store-integer ccl-store-double ccl-store-ptr
 196            get-buf ))
 197
 198 (defpackage :lisp-stat-probability
 199   (:use :common-lisp
 200         :cffi
 201         :lisp-stat-ffi-int
 202         :lisp-stat-macros)
 203   (:export log-gamma set-seed
 204            uniform-rand
 205            normal-cdf normal-quant normal-dens normal-rand
 206            bivnorm-cdf
 207            cauchy-cdf cauchy-quant cauchy-dens cauchy-rand
 208            gamma-cdf gamma-quant gamma-dens gamma-rand
 209            chisq-cdf chisq-quant chisq-dens chisq-rand
 210            beta-cdf beta-quant beta-dens beta-rand
 211            t-cdf t-quant t-dens t-rand
 212            f-cdf f-quant f-dens f-rand
 213            poisson-cdf poisson-quant poisson-pmf poisson-rand
 214            binomial-cdf binomial-quant binomial-pmf binomial-rand))
 215
 216
 217
 218 (defpackage :lisp-stat-math
 219    (:use :common-lisp
 220          :lisp-stat-object-system
 221          :lisp-stat-macros
 222          :lisp-stat-compound-data
 223          :lisp-stat-float)
 224    (:shadowing-import-from :lisp-stat-object-system
 225                            call-method call-next-method)
 226    (:shadow expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 227            asin acos atan sinh cosh tanh asinh acosh atanh float random
 228            truncate floor ceiling round minusp zerop plusp evenp oddp
 229            < <= = /= >= > ;; complex
 230            conjugate realpart imagpart phase
 231            min max logand logior logxor lognot ffloor fceiling
 232            ftruncate fround signum cis)
 233    (:export ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 234            tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 235            truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 236            /= >= > ;; complex
 237            conjugate realpart imagpart phase min max
 238            logand logior logxor lognot ffloor fceiling ftruncate fround
 239            signum cis)
 240    (:documentation "Vectorization of numerical functions"))
 241
 242
 243 #| ;; some of this goes back in, but not all of it?
 244 (defpackage :lisp-stat-linalg
 245   (:use :common-lisp
 246         :cffi
 247         :lisp-matrix
 248         :lisp-stat-math
 249         :lisp-stat-types
 250         :lisp-stat-float
 251         :lisp-stat-compound-data)
 252   (:shadowing-import-from :lisp-stat-math
 253           expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 254           asin acos atan sinh cosh tanh asinh acosh atanh float random
 255           truncate floor ceiling round minusp zerop plusp evenp oddp
 256           < <= = /= >= > complex conjugate realpart imagpart phase
 257           min max logand logior logxor lognot ffloor fceiling
 258           ftruncate fround signum cis)
 259   (:export chol-decomp lu-decomp lu-solve determinant inverse
 260            sv-decomp qr-decomp rcondest make-rotation spline
 261            kernel-dens kernel-smooth
 262            fft make-sweep-matrix sweep-operator ax+y eigen
 263
 264            check-real ;; for optimize
 265
 266            covariance-matrix matrix print-matrix solve
 267            backsolve eigenvalues eigenvectors accumulate cumsum combine
 268            lowess))
 269
 270 |#
 271
 272
 273
 274
 275 (defpackage :lisp-stat-data
 276   (:documentation "Data management, integration, I/O, and other data technologies.")
 277   (:nicknames :ls-data)
 278   (:use :common-lisp
 279         :lisp-stat-object-system
 280         :lisp-stat-config
 281         :lisp-stat-types
 282         :lisp-stat-compound-data)
 283   (:shadowing-import-from :lisp-stat-object-system
 284                           call-method call-next-method)
 285   (:export open-file-dialog read-data-file read-data-columns load-data
 286            load-example *variables* *ask-on-redefine*
 287            def variables savevar undef))
 288
 289 (defpackage :lisp-stat-descriptive-statistics
 290  (:use :common-lisp
 291        :lisp-stat-data
 292        :lisp-stat-math
 293        :lisp-stat-compound-data
 294        :lisp-matrix
 295        :lisp-stat-basics)
 296    (:shadowing-import-from :lisp-stat-math ;; life is a vector!
 297       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 298       asin acos atan sinh cosh tanh asinh acosh atanh float random
 299       truncate floor ceiling round minusp zerop plusp evenp oddp
 300       < <= = /= >= > ;; complex
 301       conjugate realpart imagpart phase
 302       min max logand logior logxor lognot ffloor fceiling
 303       ftruncate fround signum cis)
 304    (:export standard-deviation
 305             quantile median interquartile-range
 306             fivnum sample))
 307
 308
 309 (defpackage :lisp-stat-regression-linear
 310   (:use :common-lisp
 311         :lisp-matrix
 312         :lisp-stat-basics
 313         :lisp-stat-compound-data
 314         :lisp-stat-descriptive-statistics )
 315   (:shadowing-import-from :lisp-stat-object-system
 316                           call-method call-next-method)
 317   (:export regression-model fit-model
 318
 319            estimates covariance-matrix
 320            ;; functions for helpers
 321            lm xtxinv
 322            print-object ;; for method dispatch
 323            ))
 324
 325 (defpackage :common-lisp-statistics
 326   (:documentation "Experimentation package for LispStat.  Serious work
 327     should be packaged up elsewhere for reproducibility.  By this I
 328     mean, creating a data/analytics/analysis package with the minimal
 329     set of objects required.")
 330   (:nicknames :cls :common-lisp-statistics :lisp-stat)
 331   (:use :common-lisp
 332         :lisp-stat-config
 333         :lisp-stat-object-system
 334         :lisp-stat-compound-data
 335         :lisp-stat-probability
 336         :lisp-stat-types
 337         :lisp-stat-float
 338         :lisp-stat-basics
 339         :lisp-stat-data
 340         :cls-dataframe
 341         :cls-data-listoflist
 342         :lisp-stat-math
 343         :lisp-matrix ;; conversion to a more robust linalg approach
 344         :lisp-stat-descriptive-statistics
 345         :lisp-stat-regression-linear
 346         ;; :cybertiggyr-dsv
 347         :cls-visualize
 348         ;; :cls-visualize-plplot
 349         )
 350   (:shadowing-import-from :lisp-stat-object-system
 351                           call-method call-next-method)
 352   (:shadowing-import-from :lisp-stat-math
 353         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 354         asin acos atan sinh cosh tanh asinh acosh atanh float random
 355         truncate floor ceiling round minusp zerop plusp evenp oddp
 356         < <= = /= >= >
 357         ;;complex
 358         conjugate realpart imagpart phase
 359
 360         min max
 361         logand logior logxor lognot
 362         ffloor fceiling ftruncate fround
 363         signum cis)
 364   (:export
 365    ;; lisp-stat-config:
 366    *default-path* *lsos-files* *basic-files* *ls-files*
 367    *lispstat-home-dir* *lispstat-data-dir* *lispstat-examples-dir*
 368
 369    ;; lsobjects :
 370    defproto defproto2
 371    defmeth send proto-slot-value
 372
 373    ;; lstypes :
 374    fixnump check-nonneg-fixnum check-one-fixnum
 375    check-one-nonneg-fixnum
 376    check-one-real check-one-number
 377
 378    ;; lsmacros:
 379
 380    ;; lsfloat :
 381    machine-epsilon
 382
 383    ;; compound :
 384    compound-data-p *compound-data-proto* compound-object-p
 385    compound-data-seq compound-data-length
 386    element-list element-seq
 387    sort-data order rank
 388    recursive-map-elements map-elements
 389    repeat
 390    check-sequence
 391    get-next-element make-next-element set-next-element
 392    ;; sequencep
 393    iseq
 394    ordered-nneg-seq
 395    select which
 396    difference rseq
 397
 398    ;; lsmath.lsp
 399    ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 400    tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 401    truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 402    /= >= > ;; complex
 403    conjugate realpart imagpart phase min max
 404    logand logior logxor lognot ffloor fceiling ftruncate fround
 405    signum cis
 406
 407 #| ;; The following need to be re-found in lisp-matrix...
 408
 409    ;; matrices.lisp
 410    matrixp num-rows num-cols matmult identity-matrix diagonal row-list
 411    column-list inner-product outer-product cross-product transpose
 412    bind-columns bind-rows
 413
 414    ;; linalg.lisp
 415    chol-decomp lu-decomp lu-solve determinant inverse
 416    sv-decomp qr-decomp rcondest make-rotation spline
 417    kernel-dens kernel-smooth
 418    fft make-sweep-matrix sweep-operator ax+y eigen
 419    check-real
 420    covariance-matrix matrix print-matrix solve
 421    backsolve eigenvalues eigenvectors accumulate cumsum combine
 422    lowess
 423
 424    ;; in linalg.lisp, possibly not supported by matlisp
 425    spline kernel-dens kernel-smooth
 426
 427 |#
 428
 429    ;; optimize.lsp
 430    newtonmax nelmeadmax
 431
 432    ;; lispstat-macros
 433    make-rv-function make-rv-function-1
 434
 435    ;; xarray
 436    xref xtype xdims xdim xdims*
 437
 438    ;; data
 439    open-file-dialog read-data-file read-data-columns load-data
 440    load-example *variables* *ask-on-redefine*
 441    def variables savevar undef
 442
 443    ;; dataframe
 444    dataframe-like dataframe-array make-dataframe
 445    varlabels caselabels nrows ncols
 446    dataframe-dimension dataframe-dimensons
 447    dfref dfref-case dfref-var
 448    consistent-dataframe-p
 449    dataset list-of-columns list-of-rows
 450
 451    ;; listoflist
 452    lists-of-same-size equal-listoflist
 453    transpose-listoflist
 454    listoflist->dataframe listoflist->array listoflist->matrix-like
 455
 456    ;; statistics.lsp  (descriptions, should probably be moved
 457    ;; later...?
 458    standard-deviation quantile median interquartile-range
 459    fivnum sample
 460
 461    ;; probability (dists.lisp)
 462    log-gamma set-seed
 463    uniform-rand normal-cdf normal-quant normal-dens
 464    normal-rand bivnorm-cdf cauchy-cdf cauchy-quant cauchy-dens
 465    cauchy-rand gamma-cdf gamma-quant gamma-dens gamma-rand
 466    chisq-cdf chisq-quant chisq-dens chisq-rand beta-cdf beta-quant
 467    beta-dens beta-rand t-cdf t-quant t-dens t-rand f-cdf f-quant
 468    f-dens f-rand poisson-cdf poisson-quant poisson-pmf poisson-rand
 469    binomial-cdf binomial-quant binomial-pmf binomial-rand
 470
 471    ;; Here is where we have a problem -- lispstat core should be core
 472    ;; data management and config problems, with packages providing
 473    ;; specialized extensions to LispStat, i.e. regression, nonlin
 474    ;; regression, bayesian regression via laplace approximation, etc.
 475
 476    ;; The following could be considered "recommended packages",
 477    ;; similar to the idea of the recommended packages in R.  Probably
 478    ;; we want them to do the exporting within that package, therefore
 479    ;; NOT being able to lock the "data-ish" package, but only the
 480    ;; subpackages prior to export.
 481
 482    ;; regression.lsp
 483    ;; -- linear regressin models.
 484    regression-model fit-model
 485    estimates covariance-matrix
 486
 487    regression-model-proto x y intercept sweep-matrix
 488    basis weights included total-sum-of-squares residual-sum-of-squares
 489    predictor-names response-name case-labels
 490    lm xtxinv
 491
 492    ;; nonlin.lsp
 493    ;; -- nonlinear regression models
 494    nreg-model nreg-model-proto mean-function theta-hat epsilon
 495    count-limit verbose
 496    ;; we might need something like xtxinv here?  But should be
 497    ;; encapsulated, so we use the one in regression.lisp
 498
 499    ;; bayes.lsp
 500    bayes-model bayes-model-proto bayes-internals
 501
 502    ;; plots.lisp
 503    plot-ex
 504    contour-plot-ex
 505    fn-contour-plot-ex
 506    shade-plot-ex
 507    3D-plot-ex
 508
 509    ))
 510
 511
 512 ;;;; PACKAGES FOR USEABILITY
 513
 514 (defpackage :lisp-stat-data-examples
 515   (:documentation "Example data for unittests, examples, illustrations,")
 516   (:use :common-lisp
 517         :common-lisp-statistics)
 518   (:shadowing-import-from :lisp-stat
 519                           call-method call-next-method
 520
 521       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 522       asin acos atan sinh cosh tanh asinh acosh atanh float random
 523       truncate floor ceiling round minusp zerop plusp evenp oddp
 524       < <= = /= >= > > ;; complex
 525       conjugate realpart imagpart phase
 526       min max logand logior logxor lognot ffloor fceiling
 527       ftruncate fround signum cis
 528
 529       <= float imagpart)
 530   (:export iron aluminum absorbtion
 531            diabetes dlabs))
 532
 533
 534 (defpackage :lisp-stat-user
 535   (:documentation "Experimentation package for LispStat.  Serious work
 536     should be placed in a similar package elsewhere for
 537     reproducibility.  But this should hint as to what needs to be done
 538     for a user- or analysis-package.")
 539   (:nicknames :ls-user)
 540   (:use :common-lisp ; always needed for user playgrounds!
 541         :lisp-matrix
 542         :common-lisp-statistics
 543         :lisp-stat-data-examples) ;; this last is to have 'things to play with'
 544   (:shadowing-import-from :lisp-stat
 545                           call-method call-next-method
 546
 547       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 548       asin acos atan sinh cosh tanh asinh acosh atanh float random
 549       truncate floor ceiling round minusp zerop plusp evenp oddp
 550       < <= = /= >= > > ;; complex
 551       conjugate realpart imagpart phase
 552       min max logand logior logxor lognot ffloor fceiling
 553       ftruncate fround signum cis
 554
 555       <= float imagpart))
 556
 557 (defpackage :lisp-stat-unittests
 558   (:use :common-lisp
 559         :lift :lisp-matrix
 560         :lisp-stat :lisp-stat-data-examples)
 561   (:shadowing-import-from :lisp-stat
 562                           call-method call-next-method ;; objects
 563         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan ;; lsmath
 564         asin acos atan sinh cosh tanh asinh acosh atanh float random
 565         truncate floor ceiling round minusp zerop plusp evenp oddp
 566         < <= = /= >= > ;; complex
 567         conjugate realpart imagpart phase
 568         min max logand logior logxor lognot ffloor fceiling
 569         ftruncate fround signum cis)
 570   (:export run-lisp-stat-tests run-lisp-stat-test scoreboard ; exec
 571            almost= almost=lists numerical=)) ; compare
 572
 573 (defpackage :cls-dataframe-example
 574   (:use :common-lisp
 575         :lift  :lisp-stat-unittests
 576         :lisp-stat-data-examples
 577         :cls-dataframe)
 578   (:export absorbtion aluminum iron))
 579
 580
 581 (defpackage :lisp-stat-optimize
 582  (:use :common-lisp
 583        :cffi
 584        :lisp-matrix
 585        :lisp-stat-ffi-int
 586        :lisp-stat-object-system
 587        :lisp-stat-types
 588        :lisp-stat-compound-data
 589        :lisp-stat-math
 590        :lisp-stat-float
 591        :lisp-stat-basics
 592 #|
 593        :lisp-stat-matrix
 594        :lisp-stat-linalg-data
 595        :lisp-stat-linalg
 596 |#
 597        )
 598  (:shadowing-import-from :lisp-stat-object-system
 599                          call-method call-next-method)
 600  (:shadowing-import-from :lisp-stat-math
 601            expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 602            asin acos atan sinh cosh tanh asinh acosh atanh float random
 603            truncate floor ceiling round minusp zerop plusp evenp oddp
 604            < <= = /= >= > complex conjugate realpart imagpart phase
 605            min max logand logior logxor lognot ffloor fceiling
 606            ftruncate fround signum cis)
 607  (:export
 608      ;; derivatives
 609      numgrad numhess
 610
 611      ;; optimization
 612      newtonmax nelmeadmax))