src/packages.lisp

   1 ;;; -*- mode: lisp -*-
   2
   3 ;;; Time-stamp: <2008-11-04 07:53:06 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 ;;; This organization and structure is new to the 21st Century
  16 ;;; version.
  17
  18 (in-package :cl-user)
  19
  20 ;;; LispStat Basics
  21
  22 (in-package :cl-user)
  23
  24 (defpackage :lisp-stat-object-system
  25  (:nicknames :ls-objects :lsos)
  26  (:use :common-lisp)
  27  (:shadow :call-method :call-next-method :slot-value)
  28  (:export ls-object objectp *object* kind-of-p make-object
  29           *message-hook*
  30           *set-slot-hook* slot-value self
  31           send call-next-method call-method
  32           defmeth defproto instance-slots proto-name))
  33
  34
  35
  36
  37
  38 (defpackage :lisp-stat-types
  39   (:documentation "Provides some typeing for LispStat, but is clearly
  40                    a bit incomplete.")
  41   (:use :common-lisp)
  42   (:export fixnump
  43            check-nonneg-fixnum check-one-nonneg-fixnum
  44            check-one-fixnum check-one-real check-one-number))
  45
  46
  47 ;;; Package Setup
  48
  49 (in-package :cl-user)
  50
  51 (defpackage :lisp-stat-float
  52   (:use :common-lisp)
  53   (:export +stat-float-typing+ +stat-cfloat-typing+ +stat-float-template+
  54            machine-epsilon base-float makedouble
  55
  56            make-base-trans-fun-2 make-base-trans-fun
  57
  58            base-log base-exp base-expt base-sqrt base-sin base-cos
  59            base-tan base-asin base-acos base-atan base-sinh
  60            BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
  61            BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
  62            BASE-FROUND BASE-SIGNUM BASE-CIS))
  63
  64
  65 (defpackage :lisp-stat-compound-data
  66   (:use :common-lisp
  67         :lisp-stat-object-system
  68         :lisp-stat-types)
  69   (:shadowing-import-from :lisp-stat-object-system
  70                           slot-value
  71                           call-next-method call-method)
  72   (:export compound-data-p *compound-data-proto*
  73            compound-object-p
  74            compound-data-seq compound-data-length
  75            element-list element-seq
  76            sort-data order rank
  77            recursive-map-elements map-elements repeat
  78            check-sequence
  79            get-next-element make-next-element set-next-element
  80            sequencep iseq ordered-nneg-seq
  81            select split-list which
  82            difference rseq
  83            flatten-list ))
  84
  85 (defpackage :lisp-stat-macros
  86   (:use :common-lisp
  87         :lisp-stat-compound-data)
  88   (:export make-rv-function make-rv-function-1))
  89
  90 (defpackage :lisp-stat-basics
  91     (:use :common-lisp
  92           :lisp-stat-object-system
  93           :lisp-stat-types
  94           :lisp-stat-float
  95           :lisp-stat-macros
  96           :lisp-stat-compound-data)
  97   (:shadowing-import-from :lisp-stat-object-system
  98                           slot-value call-method call-next-method)
  99   (:export permute-array sum prod count-elements mean
 100            if-else sample))
 101
 102
 103 ;;;
 104
 105
 106
 107 (defpackage :lisp-stat-float
 108   (:use :common-lisp)
 109   (:export +stat-float-typing+ +stat-cfloat-typing+ +stat-float-template+
 110            machine-epsilon base-float makedouble
 111
 112            make-base-trans-fun-2 make-base-trans-fun
 113
 114            BASE-LOG BASE-EXP BASE-EXPT BASE-SQRT BASE-SIN BASE-COS
 115            BASE-TAN BASE-ASIN BASE-ACOS BASE-ATAN BASE-SINH
 116            BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
 117            BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
 118            BASE-FROUND BASE-SIGNUM BASE-CIS))
 119
 120 ;;;
 121
 122 (defpackage :lisp-stat-macros
 123   (:use :common-lisp
 124         :lisp-stat-compound-data)
 125   (:export make-rv-function make-rv-function-1))
 126
 127 ;;; NEW CLOS STRUCTURE
 128
 129 (defpackage :lisp-stat-data-clos
 130   (:use :common-lisp
 131         :lisp-matrix)
 132   (:export get-variable-matrix get-variable-vector
 133            ;; generic container class for data -- if small enough
 134            ;; could be value, otherwise might be reference.
 135            data-pointer))
 136
 137 (defpackage :lisp-stat-regression-linear-clos
 138   (:use :common-lisp
 139         :lisp-matrix
 140         :lisp-stat-data-clos)
 141   (:export regression-model))
 142
 143
 144
 145 ;;; USER PACKAGES
 146
 147 (defpackage :lisp-stat-ffi-int
 148   (:use :common-lisp
 149         :cffi)
 150   (:export ccl-store-integer ccl-store-double ccl-store-ptr
 151            get-buf ))
 152
 153 (defpackage :lisp-stat-probability
 154   (:use :common-lisp
 155         :cffi
 156         :lisp-stat-ffi-int
 157         :lisp-stat-macros)
 158   (:export log-gamma set-seed
 159            uniform-rand
 160            normal-cdf normal-quant normal-dens normal-rand
 161            bivnorm-cdf
 162            cauchy-cdf cauchy-quant cauchy-dens cauchy-rand
 163            gamma-cdf gamma-quant gamma-dens gamma-rand
 164            chisq-cdf chisq-quant chisq-dens chisq-rand
 165            beta-cdf beta-quant beta-dens beta-rand
 166            t-cdf t-quant t-dens t-rand
 167            f-cdf f-quant f-dens f-rand
 168            poisson-cdf poisson-quant poisson-pmf poisson-rand
 169            binomial-cdf binomial-quant binomial-pmf binomial-rand))
 170
 171
 172
 173 (defpackage :lisp-stat-matrix
 174   (:use :common-lisp
 175         :cffi
 176         :lisp-stat-compound-data)
 177   (:export matrixp ;;  matrix -- conflicts!
 178            num-rows num-cols matmult identity-matrix diagonal
 179            row-list column-list inner-product outer-product
 180            cross-product transpose bind-columns bind-rows
 181            array-data-vector vector-to-array
 182
 183            check-matrix check-square-matrix
 184
 185            copy-array copy-vector
 186            ))
 187
 188 (defpackage :lisp-stat-linalg-data
 189   (:use :common-lisp
 190         :cffi
 191         :lisp-stat-ffi-int
 192         :lisp-stat-types
 193         :lisp-stat-compound-data
 194         :lisp-stat-matrix)
 195   (:export ;; more to add
 196       +mode-in+ +mode-re+ +mode-cx+ mode-of
 197
 198       la-data-mode la-allocate la-free
 199
 200       la-get-double la-put-double
 201       la-put-integer
 202
 203       la-matrix la-free-matrix la-matrix-to-data la-data-to-matrix
 204       la-vector la-free-vector la-vector-to-data la-data-to-vector ))
 205
 206
 207 (defpackage :lisp-stat-math
 208    (:use :common-lisp
 209          :lisp-stat-object-system
 210          :lisp-stat-macros
 211          :lisp-stat-compound-data
 212          :lisp-stat-float)
 213    (:shadowing-import-from :lisp-stat-object-system
 214                            slot-value call-method call-next-method)
 215    (:shadow expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 216            asin acos atan sinh cosh tanh asinh acosh atanh float random
 217            truncate floor ceiling round minusp zerop plusp evenp oddp
 218            < <= = /= >= > ;; complex
 219            conjugate realpart imagpart phase
 220            min max logand logior logxor lognot ffloor fceiling
 221            ftruncate fround signum cis)
 222    (:export ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 223            tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 224            truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 225            /= >= > ;; complex
 226            conjugate realpart imagpart phase min max
 227            logand logior logxor lognot ffloor fceiling ftruncate fround
 228            signum cis)
 229    (:documentation "Vectorization of numerical functions"))
 230
 231
 232 (defpackage :lisp-stat-linalg
 233   (:use :common-lisp
 234         :cffi
 235         :lisp-stat-ffi-int
 236         :lisp-stat-math
 237         :lisp-stat-types
 238         :lisp-stat-float
 239         :lisp-stat-compound-data
 240         :lisp-stat-linalg-data
 241         :lisp-stat-matrix)
 242   (:shadowing-import-from :lisp-stat-math
 243           expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 244           asin acos atan sinh cosh tanh asinh acosh atanh float random
 245           truncate floor ceiling round minusp zerop plusp evenp oddp
 246           < <= = /= >= > complex conjugate realpart imagpart phase
 247           min max logand logior logxor lognot ffloor fceiling
 248           ftruncate fround signum cis)
 249   (:export chol-decomp lu-decomp lu-solve determinant inverse
 250            sv-decomp qr-decomp rcondest make-rotation spline
 251            kernel-dens kernel-smooth
 252            fft make-sweep-matrix sweep-operator ax+y eigen
 253
 254            check-real ;; for optimize
 255
 256            covariance-matrix matrix print-matrix solve
 257            backsolve eigenvalues eigenvectors accumulate cumsum combine
 258            lowess))
 259
 260
 261 (defpackage :lisp-stat-config
 262   (:use :common-lisp)
 263   (:export *default-path*
 264            *lsos-files* *basic-files* *ls-files*
 265            *lispstat-data-dir* *lispstat-examples-dir*))
 266
 267
 268 (defpackage :lisp-stat-data
 269   (:documentation "Data management, integration, I/O, and other data technologies.")
 270   (:nicknames :ls-data)
 271   (:use :common-lisp
 272         :lisp-stat-object-system
 273         :lisp-stat-config
 274         :lisp-stat-types
 275         :lisp-stat-compound-data)
 276   (:shadowing-import-from :lisp-stat-object-system
 277                           slot-value call-method call-next-method)
 278   (:export open-file-dialog read-data-file read-data-columns load-data
 279            load-example *variables* *ask-on-redefine*
 280            def variables savevar undef))
 281
 282 (defpackage :lisp-stat-descriptive-statistics
 283  (:use :common-lisp
 284        :lisp-stat-data
 285        :lisp-stat-math
 286        :lisp-stat-compound-data
 287        :lisp-stat-matrix
 288        :lisp-stat-linalg-data
 289        :lisp-stat-linalg
 290        :lisp-stat-basics)
 291    (:shadowing-import-from :lisp-stat-math ;; life is a vector!
 292       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 293       asin acos atan sinh cosh tanh asinh acosh atanh float random
 294       truncate floor ceiling round minusp zerop plusp evenp oddp
 295       < <= = /= >= > ;; complex
 296       conjugate realpart imagpart phase
 297       min max logand logior logxor lognot ffloor fceiling
 298       ftruncate fround signum cis)
 299    (:export standard-deviation quantile median interquartile-range
 300             fivnum sample))
 301
 302
 303 (defpackage :lisp-stat-regression-linear
 304   (:use :common-lisp
 305         :lisp-stat-object-system
 306         :lisp-stat-basics
 307         :lisp-stat-compound-data
 308         :lisp-stat-math
 309         :lisp-stat-matrix
 310         :lisp-stat-linalg
 311         :lisp-stat-descriptive-statistics)
 312   (:shadowing-import-from :lisp-stat-object-system
 313                           slot-value call-method call-next-method)
 314   (:shadowing-import-from :lisp-stat-math
 315       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 316       asin acos atan sinh cosh tanh asinh acosh atanh float random
 317       truncate floor ceiling round minusp zerop plusp evenp oddp
 318       < <= = /= >= > ;; complex
 319       conjugate realpart imagpart phase
 320       min max logand logior logxor lognot ffloor fceiling
 321       ftruncate fround signum cis)
 322   (:export regression-model regression-model-proto x y intercept sweep-matrix
 323            basis weights included total-sum-of-squares residual-sum-of-squares
 324            predictor-names response-name case-labels))
 325
 326
 327 (defpackage :lisp-stat
 328     (:documentation "Experimentation package for LispStat.  Serious
 329     work should be packaged up elsewhere for reproducibility.  By this
 330     I mean, creating a data/analytics/analysis package with the
 331     minimal set of objects required.")
 332   (:use :common-lisp
 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         :lisp-stat-math
 341         :lisp-stat-matrix
 342         :lisp-stat-linalg
 343         :lisp-stat-descriptive-statistics
 344         :lisp-stat-regression-linear)
 345   (:shadowing-import-from :lisp-stat-object-system
 346         slot-value call-method call-next-method)
 347   (:shadowing-import-from :lisp-stat-math
 348         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 349         asin acos atan sinh cosh tanh asinh acosh atanh float random
 350         truncate floor ceiling round minusp zerop plusp evenp oddp
 351         < <= = /= >= > ;;complex
 352         conjugate realpart imagpart phase
 353         min max logand logior logxor lognot ffloor fceiling
 354         ftruncate fround signum cis)
 355   (:export
 356    ;; lsobjects :
 357    defproto defproto2
 358    defmeth send
 359
 360    ;; lstypes :
 361    fixnump check-nonneg-fixnum check-one-fixnum
 362    check-one-real check-one-number
 363
 364    ;; lsmacros:
 365
 366    ;; lsfloat :
 367    machine-epsilon
 368
 369    ;; compound :
 370    compound-data-p *compound-data-proto* compound-object-p
 371    compound-data-seq compound-data-length
 372    element-list element-seq
 373    sort-data order rank
 374    recursive-map-elements map-elements
 375    repeat
 376    check-sequence
 377    get-next-element make-next-element set-next-element
 378    sequencep iseq
 379    ordered-nneg-seq
 380    select which
 381    difference rseq
 382
 383    ;; lsmath.lsp
 384    ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 385    tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 386    truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 387    /= >= > ;; complex
 388    conjugate realpart imagpart phase min max
 389    logand logior logxor lognot ffloor fceiling ftruncate fround
 390    signum cis
 391
 392    ;; matrices.lisp
 393    matrixp num-rows num-cols matmult identity-matrix diagonal row-list
 394    column-list inner-product outer-product cross-product transpose
 395    bind-columns bind-rows
 396
 397    ;; linalg.lisp
 398    chol-decomp lu-decomp lu-solve determinant inverse
 399    sv-decomp qr-decomp rcondest make-rotation spline
 400    kernel-dens kernel-smooth
 401    fft make-sweep-matrix sweep-operator ax+y eigen
 402    check-real
 403    covariance-matrix matrix print-matrix solve
 404    backsolve eigenvalues eigenvectors accumulate cumsum combine
 405    lowess
 406
 407    ;; in linalg.lisp, possibly not supported by matlisp
 408    spline kernel-dens kernel-smooth
 409
 410    ;; optimize.lsp
 411    newtonmax nelmeadmax
 412
 413    ;; lispstat-macros
 414    make-rv-function make-rv-function-1
 415
 416    ;; data.lisp
 417    open-file-dialog read-data-file read-data-columns load-data
 418    load-example *variables* *ask-on-redefine*
 419    def variables savevar undef
 420
 421    ;; statistics.lsp
 422    standard-deviation quantile median interquartile-range
 423    fivnum sample
 424
 425    ;; dists
 426    log-gamma set-seed
 427    uniform-rand normal-cdf normal-quant normal-dens
 428    normal-rand bivnorm-cdf cauchy-cdf cauchy-quant cauchy-dens
 429    cauchy-rand gamma-cdf gamma-quant gamma-dens gamma-rand
 430    chisq-cdf chisq-quant chisq-dens chisq-rand beta-cdf beta-quant
 431    beta-dens beta-rand t-cdf t-quant t-dens t-rand f-cdf f-quant
 432    f-dens f-rand poisson-cdf poisson-quant poisson-pmf poisson-rand
 433    binomial-cdf binomial-quant binomial-pmf binomial-rand
 434
 435 ;;; Here is where we have a problem -- lispstat core should be core
 436 ;;; data management and config problems, with packages providing
 437 ;;; specialized extensions to LispStat, i.e. regression, nonlin
 438 ;;; regression, bayesian regression via laplace approximation, etc.
 439
 440 ;;; The following could be considered "recommended packages", similar
 441 ;;; to the idea of the recommended packages in R.
 442
 443    ;; regression.lsp
 444    regression-model regression-model-proto x y intercept sweep-matrix
 445    basis weights included total-sum-of-squares residual-sum-of-squares
 446    predictor-names response-name case-labels
 447
 448    ;; nonlin.lsp
 449    nreg-model nreg-model-proto mean-function theta-hat epsilon
 450    count-limit verbose
 451
 452    ;; bayes.lsp
 453    bayes-model bayes-model-proto bayes-internals))
 454
 455
 456 (defpackage :lisp-stat-data-examples
 457   (:documentation "Example data used for unittests and illustrations,")
 458   (:use :common-lisp
 459         :lisp-stat)
 460   (:shadowing-import-from :lisp-stat
 461       slot-value call-method call-next-method
 462
 463       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 464       asin acos atan sinh cosh tanh asinh acosh atanh float random
 465       truncate floor ceiling round minusp zerop plusp evenp oddp
 466       < <= = /= >= > > ;; complex
 467       conjugate realpart imagpart phase
 468       min max logand logior logxor lognot ffloor fceiling
 469       ftruncate fround signum cis
 470
 471       <= float imagpart)
 472   (:export iron aluminum absorbtion
 473            diabetes dlabs))
 474
 475
 476 (defpackage :lisp-stat-user
 477   (:documentation "Experimentation package for LispStat.
 478 Serious work should be placed in a similar package elsewhere for
 479 reproducibility.  But this should hint as to what needs to be
 480 done for a user- or analysis-package.")
 481   (:nicknames :ls-user)
 482   (:use :common-lisp
 483         :lisp-stat
 484         :lisp-stat-data-examples) ;; this last is to have 'things to play with'
 485   (:shadowing-import-from :lisp-stat
 486       slot-value call-method call-next-method
 487
 488       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 489       asin acos atan sinh cosh tanh asinh acosh atanh float random
 490       truncate floor ceiling round minusp zerop plusp evenp oddp
 491       < <= = /= >= > > ;; complex
 492       conjugate realpart imagpart phase
 493       min max logand logior logxor lognot ffloor fceiling
 494       ftruncate fround signum cis
 495
 496       <= float imagpart))
 497
 498
 499
 500 ;;;
 501
 502 (defpackage :lisp-stat-unittests
 503   (:use :common-lisp :lift :lisp-stat)
 504   (:shadowing-import-from :lisp-stat
 505         slot-value call-method call-next-method ;; objects
 506         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan ;; lsmath
 507         asin acos atan sinh cosh tanh asinh acosh atanh float random
 508         truncate floor ceiling round minusp zerop plusp evenp oddp
 509         < <= = /= >= > ;; complex
 510         conjugate realpart imagpart phase
 511         min max logand logior logxor lognot ffloor fceiling
 512         ftruncate fround signum cis)
 513   (:export run-lisp-stat-tests run-lisp-stat-test scoreboard ; exec
 514            almost= almost=lists numerical=)) ; compare
 515
 516
 517 (defpackage :lisp-stat-data-clos-example
 518   (:use :common-lisp
 519         :lift  :lisp-stat-unittests
 520         :lisp-stat-data-clos))