src/packages.lisp

   1 ;;; -*- mode: lisp -*-
   2
   3 ;;; Time-stamp: <2008-11-10 14:52:43 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 (defpackage :lisp-stat-float
 105   (:use :common-lisp)
 106   (:export +stat-float-typing+ +stat-cfloat-typing+ +stat-float-template+
 107            machine-epsilon base-float makedouble
 108
 109            make-base-trans-fun-2 make-base-trans-fun
 110
 111            BASE-LOG BASE-EXP BASE-EXPT BASE-SQRT BASE-SIN BASE-COS
 112            BASE-TAN BASE-ASIN BASE-ACOS BASE-ATAN BASE-SINH
 113            BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
 114            BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
 115            BASE-FROUND BASE-SIGNUM BASE-CIS))
 116
 117 ;;;
 118
 119 (defpackage :lisp-stat-macros
 120   (:use :common-lisp
 121         :lisp-stat-compound-data)
 122   (:export make-rv-function make-rv-function-1))
 123
 124 ;;; NEW CLOS STRUCTURE
 125
 126 (defpackage :lisp-stat-data-clos
 127   (:use :common-lisp
 128         :lisp-matrix)
 129   (:export get-variable-matrix get-variable-vector
 130            ;; generic container class for data -- if small enough
 131            ;; could be value, otherwise might be reference.
 132            data-pointer))
 133
 134 (defpackage :lisp-stat-regression-linear-clos
 135   (:use :common-lisp
 136         :lisp-matrix
 137         :lisp-stat-data-clos)
 138   (:export regression-model))
 139
 140
 141
 142 ;;; USER PACKAGES
 143
 144 (defpackage :lisp-stat-ffi-int
 145   (:use :common-lisp
 146         :cffi)
 147   (:export ccl-store-integer ccl-store-double ccl-store-ptr
 148            get-buf ))
 149
 150 (defpackage :lisp-stat-probability
 151   (:use :common-lisp
 152         :cffi
 153         :lisp-stat-ffi-int
 154         :lisp-stat-macros)
 155   (:export log-gamma set-seed
 156            uniform-rand
 157            normal-cdf normal-quant normal-dens normal-rand
 158            bivnorm-cdf
 159            cauchy-cdf cauchy-quant cauchy-dens cauchy-rand
 160            gamma-cdf gamma-quant gamma-dens gamma-rand
 161            chisq-cdf chisq-quant chisq-dens chisq-rand
 162            beta-cdf beta-quant beta-dens beta-rand
 163            t-cdf t-quant t-dens t-rand
 164            f-cdf f-quant f-dens f-rand
 165            poisson-cdf poisson-quant poisson-pmf poisson-rand
 166            binomial-cdf binomial-quant binomial-pmf binomial-rand))
 167
 168
 169
 170 (defpackage :lisp-stat-matrix
 171   (:use :common-lisp
 172         :cffi
 173         :lisp-stat-compound-data)
 174   (:export matrixp ;;  matrix -- conflicts!
 175            num-rows num-cols matmult identity-matrix diagonal
 176            row-list column-list inner-product outer-product
 177            cross-product transpose bind-columns bind-rows
 178            array-data-vector vector-to-array
 179
 180            check-matrix check-square-matrix
 181
 182            copy-array copy-vector
 183            ))
 184
 185 (defpackage :lisp-stat-linalg-data
 186   (:use :common-lisp
 187         :cffi
 188         :lisp-stat-ffi-int
 189         :lisp-stat-types
 190         :lisp-stat-compound-data
 191         :lisp-stat-matrix)
 192   (:export ;; more to add
 193       +mode-in+ +mode-re+ +mode-cx+ mode-of
 194
 195       la-data-mode la-allocate la-free
 196
 197       la-get-double la-put-double
 198       la-put-integer
 199
 200       la-matrix la-free-matrix la-matrix-to-data la-data-to-matrix
 201       la-vector la-free-vector la-vector-to-data la-data-to-vector ))
 202
 203
 204 (defpackage :lisp-stat-math
 205    (:use :common-lisp
 206          :lisp-stat-object-system
 207          :lisp-stat-macros
 208          :lisp-stat-compound-data
 209          :lisp-stat-float)
 210    (:shadowing-import-from :lisp-stat-object-system
 211                            slot-value call-method call-next-method)
 212    (:shadow expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 213            asin acos atan sinh cosh tanh asinh acosh atanh float random
 214            truncate floor ceiling round minusp zerop plusp evenp oddp
 215            < <= = /= >= > ;; complex
 216            conjugate realpart imagpart phase
 217            min max logand logior logxor lognot ffloor fceiling
 218            ftruncate fround signum cis)
 219    (:export ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 220            tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 221            truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 222            /= >= > ;; complex
 223            conjugate realpart imagpart phase min max
 224            logand logior logxor lognot ffloor fceiling ftruncate fround
 225            signum cis)
 226    (:documentation "Vectorization of numerical functions"))
 227
 228
 229 (defpackage :lisp-stat-linalg
 230   (:use :common-lisp
 231         :cffi
 232         :lisp-stat-ffi-int
 233         :lisp-stat-math
 234         :lisp-stat-types
 235         :lisp-stat-float
 236         :lisp-stat-compound-data
 237         :lisp-stat-linalg-data
 238         :lisp-stat-matrix)
 239   (:shadowing-import-from :lisp-stat-math
 240           expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 241           asin acos atan sinh cosh tanh asinh acosh atanh float random
 242           truncate floor ceiling round minusp zerop plusp evenp oddp
 243           < <= = /= >= > complex conjugate realpart imagpart phase
 244           min max logand logior logxor lognot ffloor fceiling
 245           ftruncate fround signum cis)
 246   (:export chol-decomp lu-decomp lu-solve determinant inverse
 247            sv-decomp qr-decomp rcondest make-rotation spline
 248            kernel-dens kernel-smooth
 249            fft make-sweep-matrix sweep-operator ax+y eigen
 250
 251            check-real ;; for optimize
 252
 253            covariance-matrix matrix print-matrix solve
 254            backsolve eigenvalues eigenvectors accumulate cumsum combine
 255            lowess))
 256
 257
 258 (defpackage :lisp-stat-config
 259   (:use :common-lisp)
 260   (:export *default-path*
 261            *lsos-files* *basic-files* *ls-files*
 262            *lispstat-data-dir* *lispstat-examples-dir*))
 263
 264
 265 (defpackage :lisp-stat-data
 266   (:documentation "Data management, integration, I/O, and other data technologies.")
 267   (:nicknames :ls-data)
 268   (:use :common-lisp
 269         :lisp-stat-object-system
 270         :lisp-stat-config
 271         :lisp-stat-types
 272         :lisp-stat-compound-data)
 273   (:shadowing-import-from :lisp-stat-object-system
 274                           slot-value call-method call-next-method)
 275   (:export open-file-dialog read-data-file read-data-columns load-data
 276            load-example *variables* *ask-on-redefine*
 277            def variables savevar undef))
 278
 279 (defpackage :lisp-stat-descriptive-statistics
 280  (:use :common-lisp
 281        :lisp-stat-data
 282        :lisp-stat-math
 283        :lisp-stat-compound-data
 284        :lisp-stat-matrix
 285        :lisp-stat-linalg-data
 286        :lisp-stat-linalg
 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 quantile median interquartile-range
 297             fivnum sample))
 298
 299
 300 (defpackage :lisp-stat-regression-linear
 301   (:use :common-lisp
 302         :lisp-stat-object-system
 303         :lisp-stat-basics
 304         :lisp-stat-compound-data
 305         :lisp-stat-math
 306         :lisp-stat-matrix
 307         :lisp-stat-linalg
 308         :lisp-stat-descriptive-statistics)
 309   (:shadowing-import-from :lisp-stat-object-system
 310                           slot-value call-method call-next-method)
 311   (:shadowing-import-from :lisp-stat-math
 312       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 313       asin acos atan sinh cosh tanh asinh acosh atanh float random
 314       truncate floor ceiling round minusp zerop plusp evenp oddp
 315       < <= = /= >= > ;; complex
 316       conjugate realpart imagpart phase
 317       min max logand logior logxor lognot ffloor fceiling
 318       ftruncate fround signum cis)
 319   (:export regression-model regression-model-proto x y intercept sweep-matrix
 320            basis weights included total-sum-of-squares residual-sum-of-squares
 321            predictor-names response-name case-labels))
 322
 323 (defpackage :lisp-stat
 324     (:documentation "Experimentation package for LispStat.  Serious
 325     work should be packaged up elsewhere for reproducibility.  By this
 326     I mean, creating a data/analytics/analysis package with the
 327     minimal set of objects required.")
 328   (:use :common-lisp
 329         :lisp-stat-object-system
 330         :lisp-stat-compound-data
 331         :lisp-stat-probability
 332         :lisp-stat-types
 333         :lisp-stat-float
 334         :lisp-stat-basics
 335         :lisp-stat-data
 336         :lisp-stat-math
 337         :lisp-stat-matrix
 338         :lisp-stat-linalg
 339         :lisp-stat-descriptive-statistics
 340         :lisp-stat-regression-linear)
 341   (:shadowing-import-from :lisp-stat-object-system
 342         slot-value 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         < <= = /= >= > ;;complex
 348         conjugate realpart imagpart phase
 349         min max logand logior logxor lognot ffloor fceiling
 350         ftruncate fround signum cis)
 351   (:export
 352    ;; lsobjects :
 353    defproto defproto2
 354    defmeth send
 355
 356    ;; lstypes :
 357    fixnump check-nonneg-fixnum check-one-fixnum
 358    check-one-real check-one-number
 359
 360    ;; lsmacros:
 361
 362    ;; lsfloat :
 363    machine-epsilon
 364
 365    ;; compound :
 366    compound-data-p *compound-data-proto* compound-object-p
 367    compound-data-seq compound-data-length
 368    element-list element-seq
 369    sort-data order rank
 370    recursive-map-elements map-elements
 371    repeat
 372    check-sequence
 373    get-next-element make-next-element set-next-element
 374    sequencep iseq
 375    ordered-nneg-seq
 376    select which
 377    difference rseq
 378
 379    ;; lsmath.lsp
 380    ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 381    tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 382    truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 383    /= >= > ;; complex
 384    conjugate realpart imagpart phase min max
 385    logand logior logxor lognot ffloor fceiling ftruncate fround
 386    signum cis
 387
 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    ;; optimize.lsp
 407    newtonmax nelmeadmax
 408
 409    ;; lispstat-macros
 410    make-rv-function make-rv-function-1
 411
 412    ;; data.lisp
 413    open-file-dialog read-data-file read-data-columns load-data
 414    load-example *variables* *ask-on-redefine*
 415    def variables savevar undef
 416
 417    ;; statistics.lsp
 418    standard-deviation quantile median interquartile-range
 419    fivnum sample
 420
 421    ;; dists
 422    log-gamma set-seed
 423    uniform-rand normal-cdf normal-quant normal-dens
 424    normal-rand bivnorm-cdf cauchy-cdf cauchy-quant cauchy-dens
 425    cauchy-rand gamma-cdf gamma-quant gamma-dens gamma-rand
 426    chisq-cdf chisq-quant chisq-dens chisq-rand beta-cdf beta-quant
 427    beta-dens beta-rand t-cdf t-quant t-dens t-rand f-cdf f-quant
 428    f-dens f-rand poisson-cdf poisson-quant poisson-pmf poisson-rand
 429    binomial-cdf binomial-quant binomial-pmf binomial-rand
 430
 431 ;;; Here is where we have a problem -- lispstat core should be core
 432 ;;; data management and config problems, with packages providing
 433 ;;; specialized extensions to LispStat, i.e. regression, nonlin
 434 ;;; regression, bayesian regression via laplace approximation, etc.
 435
 436 ;;; The following could be considered "recommended packages", similar
 437 ;;; to the idea of the recommended packages in R.
 438
 439    ;; regression.lsp
 440    regression-model regression-model-proto x y intercept sweep-matrix
 441    basis weights included total-sum-of-squares residual-sum-of-squares
 442    predictor-names response-name case-labels
 443
 444    ;; nonlin.lsp
 445    nreg-model nreg-model-proto mean-function theta-hat epsilon
 446    count-limit verbose
 447
 448    ;; bayes.lsp
 449    bayes-model bayes-model-proto bayes-internals))
 450
 451
 452 ;;;; PACKAGES FOR USEABILITY
 453
 454 (defpackage :lisp-stat-data-examples
 455   (:documentation "Example data for unittests, examples, illustrations,")
 456   (:use :common-lisp
 457         :lisp-stat)
 458   (:shadowing-import-from :lisp-stat
 459       slot-value call-method call-next-method
 460
 461       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 462       asin acos atan sinh cosh tanh asinh acosh atanh float random
 463       truncate floor ceiling round minusp zerop plusp evenp oddp
 464       < <= = /= >= > > ;; complex
 465       conjugate realpart imagpart phase
 466       min max logand logior logxor lognot ffloor fceiling
 467       ftruncate fround signum cis
 468
 469       <= float imagpart)
 470   (:export iron aluminum absorbtion
 471            diabetes dlabs))
 472
 473
 474 (defpackage :lisp-stat-user
 475   (:documentation "Experimentation package for LispStat.
 476 Serious work should be placed in a similar package elsewhere for
 477 reproducibility.  But this should hint as to what needs to be
 478 done for a user- or analysis-package.")
 479   (:nicknames :ls-user)
 480   (:use :common-lisp
 481         :lisp-stat
 482         :lisp-stat-data-examples) ;; this last is to have 'things to play with'
 483   (:shadowing-import-from :lisp-stat
 484       slot-value call-method call-next-method
 485
 486       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 487       asin acos atan sinh cosh tanh asinh acosh atanh float random
 488       truncate floor ceiling round minusp zerop plusp evenp oddp
 489       < <= = /= >= > > ;; complex
 490       conjugate realpart imagpart phase
 491       min max logand logior logxor lognot ffloor fceiling
 492       ftruncate fround signum cis
 493
 494       <= float imagpart))
 495
 496 (defpackage :lisp-stat-unittests
 497   (:use :common-lisp :lift :lisp-stat :lisp-stat-data-examples)
 498   (:shadowing-import-from :lisp-stat
 499         slot-value call-method call-next-method ;; objects
 500         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan ;; lsmath
 501         asin acos atan sinh cosh tanh asinh acosh atanh float random
 502         truncate floor ceiling round minusp zerop plusp evenp oddp
 503         < <= = /= >= > ;; complex
 504         conjugate realpart imagpart phase
 505         min max logand logior logxor lognot ffloor fceiling
 506         ftruncate fround signum cis)
 507   (:export run-lisp-stat-tests run-lisp-stat-test scoreboard ; exec
 508            almost= almost=lists numerical=)) ; compare
 509
 510 (defpackage :lisp-stat-data-clos-example
 511   (:use :common-lisp
 512         :lift  :lisp-stat-unittests
 513         :lisp-stat-data-examples
 514         :lisp-stat-data-clos)
 515   (:export absorbtion aluminum iron))