src/packages.lisp

   1 ;;; -*- mode: lisp -*-
   2
   3 ;;; Time-stamp: <2008-11-16 20:38:56 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 (defpackage :lisp-stat-regression-linear-clos
 136   (:use :common-lisp
 137         :lisp-matrix
 138         :lisp-stat-data-clos)
 139   (:export regression-model))
 140
 141
 142
 143 ;;; USER PACKAGES
 144
 145 (defpackage :lisp-stat-ffi-int
 146   (:use :common-lisp
 147         :cffi)
 148   (:export ccl-store-integer ccl-store-double ccl-store-ptr
 149            get-buf ))
 150
 151 (defpackage :lisp-stat-probability
 152   (:use :common-lisp
 153         :cffi
 154         :lisp-stat-ffi-int
 155         :lisp-stat-macros)
 156   (:export log-gamma set-seed
 157            uniform-rand
 158            normal-cdf normal-quant normal-dens normal-rand
 159            bivnorm-cdf
 160            cauchy-cdf cauchy-quant cauchy-dens cauchy-rand
 161            gamma-cdf gamma-quant gamma-dens gamma-rand
 162            chisq-cdf chisq-quant chisq-dens chisq-rand
 163            beta-cdf beta-quant beta-dens beta-rand
 164            t-cdf t-quant t-dens t-rand
 165            f-cdf f-quant f-dens f-rand
 166            poisson-cdf poisson-quant poisson-pmf poisson-rand
 167            binomial-cdf binomial-quant binomial-pmf binomial-rand))
 168
 169
 170
 171 (defpackage :lisp-stat-matrix
 172   (:use :common-lisp
 173         :cffi
 174         :lisp-stat-compound-data)
 175   (:export matrixp ;;  matrix -- conflicts!
 176            num-rows num-cols matmult identity-matrix diagonal
 177            row-list column-list inner-product outer-product
 178            cross-product transpose bind-columns bind-rows
 179            array-data-vector vector-to-array
 180
 181            check-matrix check-square-matrix
 182
 183            copy-array copy-vector
 184            ))
 185
 186 (defpackage :lisp-stat-linalg-data
 187   (:use :common-lisp
 188         :cffi
 189         :lisp-stat-ffi-int
 190         :lisp-stat-types
 191         :lisp-stat-compound-data
 192         :lisp-stat-matrix)
 193   (:export ;; more to add
 194       +mode-in+ +mode-re+ +mode-cx+ mode-of
 195
 196       la-data-mode la-allocate la-free
 197
 198       la-get-double la-put-double
 199       la-put-integer
 200
 201       la-matrix la-free-matrix la-matrix-to-data la-data-to-matrix
 202       la-vector la-free-vector la-vector-to-data la-data-to-vector ))
 203
 204
 205 (defpackage :lisp-stat-math
 206    (:use :common-lisp
 207          :lisp-stat-object-system
 208          :lisp-stat-macros
 209          :lisp-stat-compound-data
 210          :lisp-stat-float)
 211    (:shadowing-import-from :lisp-stat-object-system
 212                            slot-value call-method call-next-method)
 213    (:shadow expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 214            asin acos atan sinh cosh tanh asinh acosh atanh float random
 215            truncate floor ceiling round minusp zerop plusp evenp oddp
 216            < <= = /= >= > ;; complex
 217            conjugate realpart imagpart phase
 218            min max logand logior logxor lognot ffloor fceiling
 219            ftruncate fround signum cis)
 220    (:export ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 221            tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 222            truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 223            /= >= > ;; complex
 224            conjugate realpart imagpart phase min max
 225            logand logior logxor lognot ffloor fceiling ftruncate fround
 226            signum cis)
 227    (:documentation "Vectorization of numerical functions"))
 228
 229
 230 (defpackage :lisp-stat-linalg
 231   (:use :common-lisp
 232         :cffi
 233         :lisp-stat-ffi-int
 234         :lisp-stat-math
 235         :lisp-stat-types
 236         :lisp-stat-float
 237         :lisp-stat-compound-data
 238         :lisp-stat-linalg-data
 239         :lisp-stat-matrix)
 240   (:shadowing-import-from :lisp-stat-math
 241           expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 242           asin acos atan sinh cosh tanh asinh acosh atanh float random
 243           truncate floor ceiling round minusp zerop plusp evenp oddp
 244           < <= = /= >= > complex conjugate realpart imagpart phase
 245           min max logand logior logxor lognot ffloor fceiling
 246           ftruncate fround signum cis)
 247   (:export chol-decomp lu-decomp lu-solve determinant inverse
 248            sv-decomp qr-decomp rcondest make-rotation spline
 249            kernel-dens kernel-smooth
 250            fft make-sweep-matrix sweep-operator ax+y eigen
 251
 252            check-real ;; for optimize
 253
 254            covariance-matrix matrix print-matrix solve
 255            backsolve eigenvalues eigenvectors accumulate cumsum combine
 256            lowess))
 257
 258
 259
 260
 261 (defpackage :lisp-stat-data
 262   (:documentation "Data management, integration, I/O, and other data technologies.")
 263   (:nicknames :ls-data)
 264   (:use :common-lisp
 265         :lisp-stat-object-system
 266         :lisp-stat-config
 267         :lisp-stat-types
 268         :lisp-stat-compound-data)
 269   (:shadowing-import-from :lisp-stat-object-system
 270                           slot-value call-method call-next-method)
 271   (:export open-file-dialog read-data-file read-data-columns load-data
 272            load-example *variables* *ask-on-redefine*
 273            def variables savevar undef))
 274
 275 (defpackage :lisp-stat-descriptive-statistics
 276  (:use :common-lisp
 277        :lisp-stat-data
 278        :lisp-stat-math
 279        :lisp-stat-compound-data
 280        :lisp-stat-matrix
 281        :lisp-stat-linalg-data
 282        :lisp-stat-linalg
 283        :lisp-stat-basics)
 284    (:shadowing-import-from :lisp-stat-math ;; life is a vector!
 285       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 286       asin acos atan sinh cosh tanh asinh acosh atanh float random
 287       truncate floor ceiling round minusp zerop plusp evenp oddp
 288       < <= = /= >= > ;; complex
 289       conjugate realpart imagpart phase
 290       min max logand logior logxor lognot ffloor fceiling
 291       ftruncate fround signum cis)
 292    (:export standard-deviation quantile median interquartile-range
 293             fivnum sample))
 294
 295
 296 (defpackage :lisp-stat-regression-linear
 297   (:use :common-lisp
 298         :lisp-stat-object-system
 299         :lisp-stat-basics
 300         :lisp-stat-compound-data
 301         :lisp-stat-math
 302         :lisp-stat-matrix
 303         :lisp-stat-linalg
 304         :lisp-stat-descriptive-statistics)
 305   (:shadowing-import-from :lisp-stat-object-system
 306                           slot-value call-method call-next-method)
 307   (:shadowing-import-from :lisp-stat-math
 308       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 309       asin acos atan sinh cosh tanh asinh acosh atanh float random
 310       truncate floor ceiling round minusp zerop plusp evenp oddp
 311       < <= = /= >= > ;; complex
 312       conjugate realpart imagpart phase
 313       min max logand logior logxor lognot ffloor fceiling
 314       ftruncate fround signum cis)
 315   (:export regression-model regression-model-proto x y intercept sweep-matrix
 316            basis weights included total-sum-of-squares residual-sum-of-squares
 317            predictor-names response-name case-labels))
 318
 319 (defpackage :lisp-stat
 320     (:documentation "Experimentation package for LispStat.  Serious
 321     work should be packaged up elsewhere for reproducibility.  By this
 322     I mean, creating a data/analytics/analysis package with the
 323     minimal set of objects required.")
 324   (:use :common-lisp
 325         :lisp-stat-object-system
 326         :lisp-stat-compound-data
 327         :lisp-stat-probability
 328         :lisp-stat-types
 329         :lisp-stat-float
 330         :lisp-stat-basics
 331         :lisp-stat-data
 332         :lisp-stat-math
 333         :lisp-stat-matrix
 334         :lisp-stat-linalg
 335         :lisp-stat-descriptive-statistics
 336         :lisp-stat-regression-linear)
 337   (:shadowing-import-from :lisp-stat-object-system
 338         slot-value call-method call-next-method)
 339   (:shadowing-import-from :lisp-stat-math
 340         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 341         asin acos atan sinh cosh tanh asinh acosh atanh float random
 342         truncate floor ceiling round minusp zerop plusp evenp oddp
 343         < <= = /= >= > ;;complex
 344         conjugate realpart imagpart phase
 345         min max logand logior logxor lognot ffloor fceiling
 346         ftruncate fround signum cis)
 347   (:export
 348    ;; lsobjects :
 349    defproto defproto2
 350    defmeth send
 351
 352    ;; lstypes :
 353    fixnump check-nonneg-fixnum check-one-fixnum
 354    check-one-real check-one-number
 355
 356    ;; lsmacros:
 357
 358    ;; lsfloat :
 359    machine-epsilon
 360
 361    ;; compound :
 362    compound-data-p *compound-data-proto* compound-object-p
 363    compound-data-seq compound-data-length
 364    element-list element-seq
 365    sort-data order rank
 366    recursive-map-elements map-elements
 367    repeat
 368    check-sequence
 369    get-next-element make-next-element set-next-element
 370    ;; sequencep
 371    iseq
 372    ordered-nneg-seq
 373    select which
 374    difference rseq
 375
 376    ;; lsmath.lsp
 377    ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 378    tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 379    truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 380    /= >= > ;; complex
 381    conjugate realpart imagpart phase min max
 382    logand logior logxor lognot ffloor fceiling ftruncate fround
 383    signum cis
 384
 385    ;; matrices.lisp
 386    matrixp num-rows num-cols matmult identity-matrix diagonal row-list
 387    column-list inner-product outer-product cross-product transpose
 388    bind-columns bind-rows
 389
 390    ;; linalg.lisp
 391    chol-decomp lu-decomp lu-solve determinant inverse
 392    sv-decomp qr-decomp rcondest make-rotation spline
 393    kernel-dens kernel-smooth
 394    fft make-sweep-matrix sweep-operator ax+y eigen
 395    check-real
 396    covariance-matrix matrix print-matrix solve
 397    backsolve eigenvalues eigenvectors accumulate cumsum combine
 398    lowess
 399
 400    ;; in linalg.lisp, possibly not supported by matlisp
 401    spline kernel-dens kernel-smooth
 402
 403    ;; optimize.lsp
 404    newtonmax nelmeadmax
 405
 406    ;; lispstat-macros
 407    make-rv-function make-rv-function-1
 408
 409    ;; data.lisp
 410    open-file-dialog read-data-file read-data-columns load-data
 411    load-example *variables* *ask-on-redefine*
 412    def variables savevar undef
 413
 414    ;; statistics.lsp
 415    standard-deviation quantile median interquartile-range
 416    fivnum sample
 417
 418    ;; dists
 419    log-gamma set-seed
 420    uniform-rand normal-cdf normal-quant normal-dens
 421    normal-rand bivnorm-cdf cauchy-cdf cauchy-quant cauchy-dens
 422    cauchy-rand gamma-cdf gamma-quant gamma-dens gamma-rand
 423    chisq-cdf chisq-quant chisq-dens chisq-rand beta-cdf beta-quant
 424    beta-dens beta-rand t-cdf t-quant t-dens t-rand f-cdf f-quant
 425    f-dens f-rand poisson-cdf poisson-quant poisson-pmf poisson-rand
 426    binomial-cdf binomial-quant binomial-pmf binomial-rand
 427
 428 ;;; Here is where we have a problem -- lispstat core should be core
 429 ;;; data management and config problems, with packages providing
 430 ;;; specialized extensions to LispStat, i.e. regression, nonlin
 431 ;;; regression, bayesian regression via laplace approximation, etc.
 432
 433 ;;; The following could be considered "recommended packages", similar
 434 ;;; to the idea of the recommended packages in R.
 435
 436    ;; regression.lsp
 437    regression-model regression-model-proto x y intercept sweep-matrix
 438    basis weights included total-sum-of-squares residual-sum-of-squares
 439    predictor-names response-name case-labels
 440
 441    ;; nonlin.lsp
 442    nreg-model nreg-model-proto mean-function theta-hat epsilon
 443    count-limit verbose
 444
 445    ;; bayes.lsp
 446    bayes-model bayes-model-proto bayes-internals))
 447
 448
 449 ;;;; PACKAGES FOR USEABILITY
 450
 451 (defpackage :lisp-stat-data-examples
 452   (:documentation "Example data for unittests, examples, illustrations,")
 453   (:use :common-lisp
 454         :lisp-stat)
 455   (:shadowing-import-from :lisp-stat
 456       slot-value call-method call-next-method
 457
 458       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 459       asin acos atan sinh cosh tanh asinh acosh atanh float random
 460       truncate floor ceiling round minusp zerop plusp evenp oddp
 461       < <= = /= >= > > ;; complex
 462       conjugate realpart imagpart phase
 463       min max logand logior logxor lognot ffloor fceiling
 464       ftruncate fround signum cis
 465
 466       <= float imagpart)
 467   (:export iron aluminum absorbtion
 468            diabetes dlabs))
 469
 470
 471 (defpackage :lisp-stat-user
 472   (:documentation "Experimentation package for LispStat.
 473 Serious work should be placed in a similar package elsewhere for
 474 reproducibility.  But this should hint as to what needs to be
 475 done for a user- or analysis-package.")
 476   (:nicknames :ls-user)
 477   (:use :common-lisp
 478         :lisp-stat
 479         :lisp-stat-data-examples) ;; this last is to have 'things to play with'
 480   (:shadowing-import-from :lisp-stat
 481       slot-value call-method call-next-method
 482
 483       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 484       asin acos atan sinh cosh tanh asinh acosh atanh float random
 485       truncate floor ceiling round minusp zerop plusp evenp oddp
 486       < <= = /= >= > > ;; complex
 487       conjugate realpart imagpart phase
 488       min max logand logior logxor lognot ffloor fceiling
 489       ftruncate fround signum cis
 490
 491       <= float imagpart))
 492
 493 (defpackage :lisp-stat-unittests
 494   (:use :common-lisp :lift :lisp-stat :lisp-stat-data-examples)
 495   (:shadowing-import-from :lisp-stat
 496         slot-value call-method call-next-method ;; objects
 497         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan ;; lsmath
 498         asin acos atan sinh cosh tanh asinh acosh atanh float random
 499         truncate floor ceiling round minusp zerop plusp evenp oddp
 500         < <= = /= >= > ;; complex
 501         conjugate realpart imagpart phase
 502         min max logand logior logxor lognot ffloor fceiling
 503         ftruncate fround signum cis)
 504   (:export run-lisp-stat-tests run-lisp-stat-test scoreboard ; exec
 505            almost= almost=lists numerical=)) ; compare
 506
 507 (defpackage :lisp-stat-data-clos-example
 508   (:use :common-lisp
 509         :lift  :lisp-stat-unittests
 510         :lisp-stat-data-examples
 511         :lisp-stat-data-clos)
 512   (:export absorbtion aluminum iron))