src/packages.lisp

   1 ;;; -*- mode: lisp -*-
   2
   3 ;;; Time-stamp: <2008-12-03 07:49:59 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
  81            iseq ordered-nneg-seq
  82            select split-list which
  83            difference rseq
  84            flatten-list ))
  85
  86 (defpackage :lisp-stat-macros
  87   (:use :common-lisp
  88         :lisp-stat-compound-data)
  89   (:export make-rv-function make-rv-function-1))
  90
  91 (defpackage :lisp-stat-basics
  92     (:use :common-lisp
  93           :lisp-stat-object-system
  94           :lisp-stat-types
  95           :lisp-stat-float
  96           :lisp-stat-macros
  97           :lisp-stat-compound-data)
  98   (:shadowing-import-from :lisp-stat-object-system
  99                           slot-value call-method call-next-method)
 100   (:export permute-array sum prod count-elements mean
 101            if-else sample))
 102
 103
 104
 105 (defpackage :lisp-stat-float
 106   (:use :common-lisp)
 107   (:export +stat-float-typing+ +stat-cfloat-typing+ +stat-float-template+
 108            machine-epsilon base-float makedouble
 109
 110            make-base-trans-fun-2 make-base-trans-fun
 111
 112            BASE-LOG BASE-EXP BASE-EXPT BASE-SQRT BASE-SIN BASE-COS
 113            BASE-TAN BASE-ASIN BASE-ACOS BASE-ATAN BASE-SINH
 114            BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
 115            BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
 116            BASE-FROUND BASE-SIGNUM BASE-CIS))
 117
 118 ;;;
 119
 120 (defpackage :lisp-stat-macros
 121   (:use :common-lisp
 122         :lisp-stat-compound-data)
 123   (:export make-rv-function make-rv-function-1))
 124
 125 ;;; NEW CLOS STRUCTURE
 126
 127 (defpackage :lisp-stat-data-clos
 128   (:use :common-lisp
 129         :lisp-matrix)
 130   (:export get-variable-matrix get-variable-vector
 131            ;; generic container class for data -- if small enough
 132            ;; could be value, otherwise might be reference.
 133            data-pointer))
 134
 135 #|
 136 (defpackage :lisp-stat-regression-linear-clos
 137   (:use :common-lisp
 138         :lisp-matrix
 139         :lisp-stat-data-clos)
 140   (:export regression-model))
 141 |#
 142
 143
 144 ;;; USER PACKAGES
 145
 146 (defpackage :lisp-stat-ffi-int
 147   (:use :common-lisp
 148         :cffi)
 149   (:export ccl-store-integer ccl-store-double ccl-store-ptr
 150            get-buf ))
 151
 152 (defpackage :lisp-stat-probability
 153   (:use :common-lisp
 154         :cffi
 155         :lisp-stat-ffi-int
 156         :lisp-stat-macros)
 157   (:export log-gamma set-seed
 158            uniform-rand
 159            normal-cdf normal-quant normal-dens normal-rand
 160            bivnorm-cdf
 161            cauchy-cdf cauchy-quant cauchy-dens cauchy-rand
 162            gamma-cdf gamma-quant gamma-dens gamma-rand
 163            chisq-cdf chisq-quant chisq-dens chisq-rand
 164            beta-cdf beta-quant beta-dens beta-rand
 165            t-cdf t-quant t-dens t-rand
 166            f-cdf f-quant f-dens f-rand
 167            poisson-cdf poisson-quant poisson-pmf poisson-rand
 168            binomial-cdf binomial-quant binomial-pmf binomial-rand))
 169
 170
 171
 172 (defpackage :lisp-stat-matrix
 173   (:use :common-lisp
 174         :cffi
 175         :lisp-stat-compound-data)
 176   (:export matrixp ;;  matrix -- conflicts!
 177            num-rows num-cols matmult identity-matrix diagonal
 178            row-list column-list inner-product outer-product
 179            cross-product transpose bind-columns bind-rows
 180            array-data-vector vector-to-array
 181
 182            check-matrix check-square-matrix
 183
 184            copy-array copy-vector
 185            ))
 186
 187 (defpackage :lisp-stat-linalg-data
 188   (:use :common-lisp
 189         :cffi
 190         :lisp-stat-ffi-int
 191         :lisp-stat-types
 192         :lisp-stat-compound-data
 193         :lisp-stat-matrix)
 194   (:export ;; more to add
 195       +mode-in+ +mode-re+ +mode-cx+ mode-of
 196
 197       la-data-mode la-allocate la-free
 198
 199       la-get-double la-put-double
 200       la-put-integer
 201
 202       la-matrix la-free-matrix la-matrix-to-data la-data-to-matrix
 203       la-vector la-free-vector la-vector-to-data la-data-to-vector ))
 204
 205
 206 (defpackage :lisp-stat-math
 207    (:use :common-lisp
 208          :lisp-stat-object-system
 209          :lisp-stat-macros
 210          :lisp-stat-compound-data
 211          :lisp-stat-float)
 212    (:shadowing-import-from :lisp-stat-object-system
 213                            slot-value call-method call-next-method)
 214    (:shadow expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 215            asin acos atan sinh cosh tanh asinh acosh atanh float random
 216            truncate floor ceiling round minusp zerop plusp evenp oddp
 217            < <= = /= >= > ;; complex
 218            conjugate realpart imagpart phase
 219            min max logand logior logxor lognot ffloor fceiling
 220            ftruncate fround signum cis)
 221    (:export ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 222            tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 223            truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 224            /= >= > ;; complex
 225            conjugate realpart imagpart phase min max
 226            logand logior logxor lognot ffloor fceiling ftruncate fround
 227            signum cis)
 228    (:documentation "Vectorization of numerical functions"))
 229
 230
 231 (defpackage :lisp-stat-linalg
 232   (:use :common-lisp
 233         :cffi
 234         :lisp-stat-ffi-int
 235         :lisp-stat-math
 236         :lisp-stat-types
 237         :lisp-stat-float
 238         :lisp-stat-compound-data
 239         :lisp-stat-linalg-data
 240         :lisp-stat-matrix)
 241   (:shadowing-import-from :lisp-stat-math
 242           expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 243           asin acos atan sinh cosh tanh asinh acosh atanh float random
 244           truncate floor ceiling round minusp zerop plusp evenp oddp
 245           < <= = /= >= > complex conjugate realpart imagpart phase
 246           min max logand logior logxor lognot ffloor fceiling
 247           ftruncate fround signum cis)
 248   (:export chol-decomp lu-decomp lu-solve determinant inverse
 249            sv-decomp qr-decomp rcondest make-rotation spline
 250            kernel-dens kernel-smooth
 251            fft make-sweep-matrix sweep-operator ax+y eigen
 252
 253            check-real ;; for optimize
 254
 255            covariance-matrix matrix print-matrix solve
 256            backsolve eigenvalues eigenvectors accumulate cumsum combine
 257            lowess))
 258
 259
 260
 261
 262 (defpackage :lisp-stat-data
 263   (:documentation "Data management, integration, I/O, and other data technologies.")
 264   (:nicknames :ls-data)
 265   (:use :common-lisp
 266         :lisp-stat-object-system
 267         :lisp-stat-config
 268         :lisp-stat-types
 269         :lisp-stat-compound-data)
 270   (:shadowing-import-from :lisp-stat-object-system
 271                           slot-value call-method call-next-method)
 272   (:export open-file-dialog read-data-file read-data-columns load-data
 273            load-example *variables* *ask-on-redefine*
 274            def variables savevar undef))
 275
 276 (defpackage :lisp-stat-descriptive-statistics
 277  (:use :common-lisp
 278        :lisp-stat-data
 279        :lisp-stat-math
 280        :lisp-stat-compound-data
 281        :lisp-matrix
 282        :lisp-stat-basics)
 283    (:shadowing-import-from :lisp-stat-math ;; life is a vector!
 284       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 285       asin acos atan sinh cosh tanh asinh acosh atanh float random
 286       truncate floor ceiling round minusp zerop plusp evenp oddp
 287       < <= = /= >= > ;; complex
 288       conjugate realpart imagpart phase
 289       min max logand logior logxor lognot ffloor fceiling
 290       ftruncate fround signum cis)
 291    (:export standard-deviation quantile median interquartile-range
 292             fivnum sample))
 293
 294
 295 (defpackage :lisp-stat-regression-linear
 296   (:use :common-lisp
 297         :lisp-stat-object-system
 298         :lisp-stat-basics
 299         :lisp-stat-compound-data
 300         :lisp-stat-math
 301         :lisp-matrix
 302         :lisp-stat-descriptive-statistics)
 303   (:shadowing-import-from :lisp-stat-object-system
 304                           slot-value call-method call-next-method)
 305   (:shadowing-import-from :lisp-stat-math
 306       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 307       asin acos atan sinh cosh tanh asinh acosh atanh float random
 308       truncate floor ceiling round minusp zerop plusp evenp oddp
 309       < <= = /= >= > ;; complex
 310       conjugate realpart imagpart phase
 311       min max logand logior logxor lognot ffloor fceiling
 312       ftruncate fround signum cis)
 313   (:export regression-model regression-model-proto x y intercept sweep-matrix
 314            basis weights included total-sum-of-squares residual-sum-of-squares
 315            predictor-names response-name case-labels))
 316
 317 (defpackage :lisp-stat
 318     (:documentation "Experimentation package for LispStat.  Serious
 319     work should be packaged up elsewhere for reproducibility.  By this
 320     I mean, creating a data/analytics/analysis package with the
 321     minimal set of objects required.")
 322   (:use :common-lisp
 323         :lisp-stat-object-system
 324         :lisp-stat-compound-data
 325         :lisp-stat-probability
 326         :lisp-stat-types
 327         :lisp-stat-float
 328         :lisp-stat-basics
 329         :lisp-stat-data
 330         :lisp-stat-math
 331         :lisp-matrix ;; conversion to a more robust linalg approach
 332         :lisp-stat-descriptive-statistics
 333         :lisp-stat-regression-linear)
 334   (:shadowing-import-from :lisp-stat-object-system
 335         slot-value call-method call-next-method)
 336   (:shadowing-import-from :lisp-stat-math
 337         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 338         asin acos atan sinh cosh tanh asinh acosh atanh float random
 339         truncate floor ceiling round minusp zerop plusp evenp oddp
 340         < <= = /= >= >
 341         ;;complex
 342         conjugate realpart imagpart phase
 343
 344         min max
 345         logand logior logxor lognot
 346         ffloor fceiling ftruncate fround
 347         signum cis)
 348   (:export
 349    ;; lsobjects :
 350    defproto defproto2
 351    defmeth send
 352
 353    ;; lstypes :
 354    fixnump check-nonneg-fixnum check-one-fixnum
 355    check-one-real check-one-number
 356
 357    ;; lsmacros:
 358
 359    ;; lsfloat :
 360    machine-epsilon
 361
 362    ;; compound :
 363    compound-data-p *compound-data-proto* compound-object-p
 364    compound-data-seq compound-data-length
 365    element-list element-seq
 366    sort-data order rank
 367    recursive-map-elements map-elements
 368    repeat
 369    check-sequence
 370    get-next-element make-next-element set-next-element
 371    ;; sequencep
 372    iseq
 373    ordered-nneg-seq
 374    select which
 375    difference rseq
 376
 377    ;; lsmath.lsp
 378    ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 379    tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 380    truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 381    /= >= > ;; complex
 382    conjugate realpart imagpart phase min max
 383    logand logior logxor lognot ffloor fceiling ftruncate fround
 384    signum cis
 385
 386 #|
 387    ;; The following need to be re-found in lisp-matrix...
 388    ;; matrices.lisp
 389    matrixp num-rows num-cols matmult identity-matrix diagonal row-list
 390    column-list inner-product outer-product cross-product transpose
 391    bind-columns bind-rows
 392
 393    ;; linalg.lisp
 394    chol-decomp lu-decomp lu-solve determinant inverse
 395    sv-decomp qr-decomp rcondest make-rotation spline
 396    kernel-dens kernel-smooth
 397    fft make-sweep-matrix sweep-operator ax+y eigen
 398    check-real
 399    covariance-matrix matrix print-matrix solve
 400    backsolve eigenvalues eigenvectors accumulate cumsum combine
 401    lowess
 402
 403    ;; in linalg.lisp, possibly not supported by matlisp
 404    spline kernel-dens kernel-smooth
 405
 406 |#
 407
 408    ;; optimize.lsp
 409    newtonmax nelmeadmax
 410
 411    ;; lispstat-macros
 412    make-rv-function make-rv-function-1
 413
 414    ;; data.lisp
 415    open-file-dialog read-data-file read-data-columns load-data
 416    load-example *variables* *ask-on-redefine*
 417    def variables savevar undef
 418
 419    ;; statistics.lsp  (descriptions, should probably be moved
 420    ;; later...?
 421    standard-deviation quantile median interquartile-range
 422    fivnum sample
 423
 424    ;; probability (dists.lisp)
 425    log-gamma set-seed
 426    uniform-rand normal-cdf normal-quant normal-dens
 427    normal-rand bivnorm-cdf cauchy-cdf cauchy-quant cauchy-dens
 428    cauchy-rand gamma-cdf gamma-quant gamma-dens gamma-rand
 429    chisq-cdf chisq-quant chisq-dens chisq-rand beta-cdf beta-quant
 430    beta-dens beta-rand t-cdf t-quant t-dens t-rand f-cdf f-quant
 431    f-dens f-rand poisson-cdf poisson-quant poisson-pmf poisson-rand
 432    binomial-cdf binomial-quant binomial-pmf binomial-rand
 433
 434    ;; Here is where we have a problem -- lispstat core should be core
 435    ;; data management and config problems, with packages providing
 436    ;; specialized extensions to LispStat, i.e. regression, nonlin
 437    ;; regression, bayesian regression via laplace approximation, etc.
 438
 439    ;; The following could be considered "recommended packages",
 440    ;; similar to the idea of the recommended packages in R.  Probably
 441    ;; we want them to do the exporting within that package, therefore
 442    ;; NOT being able to lock the "data-ish" package, but only the
 443    ;; subpackages prior to export.
 444
 445    ;; regression.lsp
 446    regression-model regression-model-proto x y intercept sweep-matrix
 447    basis weights included total-sum-of-squares residual-sum-of-squares
 448    predictor-names response-name case-labels
 449
 450    ;; nonlin.lsp
 451    nreg-model nreg-model-proto mean-function theta-hat epsilon
 452    count-limit verbose
 453
 454    ;; bayes.lsp
 455    bayes-model bayes-model-proto bayes-internals))
 456
 457
 458 ;;;; PACKAGES FOR USEABILITY
 459
 460 (defpackage :lisp-stat-data-examples
 461   (:documentation "Example data for unittests, examples, illustrations,")
 462   (:use :common-lisp
 463         :lisp-stat)
 464   (:shadowing-import-from :lisp-stat
 465       slot-value call-method call-next-method
 466
 467       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 468       asin acos atan sinh cosh tanh asinh acosh atanh float random
 469       truncate floor ceiling round minusp zerop plusp evenp oddp
 470       < <= = /= >= > > ;; complex
 471       conjugate realpart imagpart phase
 472       min max logand logior logxor lognot ffloor fceiling
 473       ftruncate fround signum cis
 474
 475       <= float imagpart)
 476   (:export iron aluminum absorbtion
 477            diabetes dlabs))
 478
 479
 480 (defpackage :lisp-stat-user
 481   (:documentation "Experimentation package for LispStat.
 482 Serious work should be placed in a similar package elsewhere for
 483 reproducibility.  But this should hint as to what needs to be
 484 done for a user- or analysis-package.")
 485   (:nicknames :ls-user)
 486   (:use :common-lisp
 487         :lisp-matrix
 488         :lisp-stat
 489         :lisp-stat-data-examples) ;; this last is to have 'things to play with'
 490   (:shadowing-import-from :lisp-stat
 491       slot-value call-method call-next-method
 492
 493       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 494       asin acos atan sinh cosh tanh asinh acosh atanh float random
 495       truncate floor ceiling round minusp zerop plusp evenp oddp
 496       < <= = /= >= > > ;; complex
 497       conjugate realpart imagpart phase
 498       min max logand logior logxor lognot ffloor fceiling
 499       ftruncate fround signum cis
 500
 501       <= float imagpart))
 502
 503 (defpackage :lisp-stat-unittests
 504   (:use :common-lisp :lift :lisp-stat :lisp-stat-data-examples)
 505   (:shadowing-import-from :lisp-stat
 506         slot-value call-method call-next-method ;; objects
 507         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan ;; lsmath
 508         asin acos atan sinh cosh tanh asinh acosh atanh float random
 509         truncate floor ceiling round minusp zerop plusp evenp oddp
 510         < <= = /= >= > ;; complex
 511         conjugate realpart imagpart phase
 512         min max logand logior logxor lognot ffloor fceiling
 513         ftruncate fround signum cis)
 514   (:export run-lisp-stat-tests run-lisp-stat-test scoreboard ; exec
 515            almost= almost=lists numerical=)) ; compare
 516
 517 (defpackage :lisp-stat-data-clos-example
 518   (:use :common-lisp
 519         :lift  :lisp-stat-unittests
 520         :lisp-stat-data-examples
 521         :lisp-stat-data-clos)
 522   (:export absorbtion aluminum iron))