src/packages.lisp

   1 ;;; -*- mode: lisp -*-
   2
   3 ;;; Time-stamp: <2010-01-03 16:21:25 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--2010, AJ Rossini.  MIT License.  See
   8 ;;;             LICENSE.mit in top level directory for details.
   9 ;;; Purpose:    packages for Common Lisp Statistics
  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 ;;; Current structure, dependencies:
  18 #|
  19  '((:ls-user       :depends-on   lisp-stat)
  20    (:lisp-stat     :depends-on '(cls-dataframe
  21                                 cls-data
  22                                 lisp-matrix
  23                                 ))
  24    (:cls-data      :depends-on  )
  25    (:cls-dataframe :depends-on   cls-data)
  26    (:cls-dataio    : )
  27    (:cls-datatrans : )
  28 |#
  29
  30
  31
  32 ;;; Basics
  33
  34 (defpackage :lisp-stat-object-system
  35   (:nicknames :ls-objects :lsos)
  36   (:use :common-lisp)
  37   (:shadow :call-method :call-next-method)
  38   (:export ls-object objectp *object* kind-of-p make-object
  39            *message-hook*
  40            *set-slot-hook* proto-slot-value self
  41            send call-next-method call-method
  42            defmeth defproto instance-slots proto-name))
  43
  44 ;;; -types and -float probably ought to be moved into a -numerics
  45 ;;; package.
  46
  47 (defpackage :lisp-stat-types
  48   (:documentation "Provides some typeing for LispStat, but is clearly
  49   a bit incomplete.")
  50   (:use :common-lisp)
  51   (:export fixnump
  52            check-nonneg-fixnum check-one-nonneg-fixnum
  53            check-one-fixnum check-one-real check-one-number))
  54
  55 (defpackage :lisp-stat-float
  56   (:use :common-lisp)
  57   (:export +stat-float-typing+ +stat-cfloat-typing+ +stat-float-template+
  58            machine-epsilon base-float makedouble
  59
  60            make-base-trans-fun-2 make-base-trans-fun
  61
  62            base-log base-exp base-expt base-sqrt base-sin base-cos
  63            base-tan base-asin base-acos base-atan base-sinh
  64            BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
  65            BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
  66            BASE-FROUND BASE-SIGNUM BASE-CIS))
  67
  68 ;;; Probably should move into cls-data package.
  69
  70 (defpackage :lisp-stat-compound-data
  71   (:use :common-lisp
  72         :lisp-stat-object-system
  73         :lisp-stat-types)
  74   (:shadowing-import-from :lisp-stat-object-system
  75                           call-next-method call-method)
  76   (:export compound-data-p *compound-data-proto*
  77            compound-object-p
  78            compound-data-seq compound-data-length
  79            element-list element-seq
  80            sort-data order rank
  81            recursive-map-elements map-elements repeat
  82            check-sequence
  83            get-next-element make-next-element set-next-element
  84            ;; sequencep
  85            iseq ordered-nneg-seq
  86            select split-list which
  87            difference rseq
  88            flatten-list))
  89
  90 (defpackage :lisp-stat-macros
  91   (:use :common-lisp
  92         :lisp-stat-compound-data)
  93   (:export make-rv-function make-rv-function-1))
  94
  95 (defpackage :lisp-stat-basics
  96     (:use :common-lisp
  97           :lisp-stat-object-system
  98           :lisp-stat-types
  99           :lisp-stat-float
 100           :lisp-stat-macros
 101           :lisp-stat-compound-data)
 102   (:shadowing-import-from :lisp-stat-object-system
 103                           call-method call-next-method)
 104   (:export permute-array sum prod count-elements mean
 105            if-else sample))
 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 (defpackage :lisp-stat-macros
 121   (:use :common-lisp
 122         :lisp-stat-compound-data)
 123   (:export make-rv-function make-rv-function-1))
 124
 125
 126 (defpackage :cls-matrix
 127   (:documentation "basic utilities for using lisp arrays as numerical
 128   matrices.  Not optimized, and must consider this slow.  Routines
 129   should be optimized, it is only that we need them first, optimize
 130   them later.")
 131   (:use :common-lisp)
 132   (:export matrixp num-rows num-cols matmult identity-matrix diagonal
 133            row-list column-list inner-product outer-product
 134            cross-product transpose bind-columns bind-rows
 135            array-data-vector vector-to-array))
 136
 137
 138 ;;; NEW CLOS STRUCTURE
 139
 140 ;; CLS-DATA contains the basic variable structure, classes, support/indexing, and mixins.
 141 ;; CLS-DATAFRAME leverages CLS-DATA, XARRAY, and LISP-MATRIX
 142 ;; CLS-DATAIO stores/saves structures
 143 ;; CLS-DATATRANS converts between structures, and from DATAFRAMES to MODEL-MATRIXES
 144
 145 (defpackage :cls-data
 146   (:use :common-lisp)
 147   (:shadowing-import-from :xarray slice)
 148   (:export
 149    ;; must work out what is needed for stat variable metadata, support
 150    ;; functions, etc
 151    ))
 152
 153 ;;; cls-data... in dataframe, though.
 154 (defpackage :cls-dataframe
 155   (:use :common-lisp
 156         :cls-data
 157         :xarray
 158         :lisp-matrix)
 159   (:shadowing-import-from :xarray slice)
 160   (:export
 161    ;; generic container class for data -- if small enough
 162    ;; could be value, otherwise might be reference.
 163    dataframe-like
 164    dataframe-array
 165    make-dataframe
 166
 167    dataset
 168    list-of-columns ;; list-of-variables
 169    list-of-rows ;; list-of-observations
 170
 171    ;; accessors
 172    varlabels caselabels  nrows ncols
 173    dataframe-dimension dataframe-dimensons
 174    xref xtype xdims xdim xrank slice take carray
 175
 176    ;; support
 177    make-labels
 178    ))
 179
 180 (defpackage :cls-dataio
 181   (:documentation "Data I/O and similar import technologies.")
 182   (:use :common-lisp
 183         :rsm.string
 184         :lisp-stat-object-system
 185         :cls-data
 186         :cls-dataframe)
 187   (:shadowing-import-from :lisp-stat-object-system
 188                           call-method call-next-method)
 189   (:export dsvstream->dataframe
 190            dsvstream->matrix
 191            dsvstream->listoflist
 192
 193            filename.dsv->dataframe
 194            ))
 195
 196 (defpackage :cls-datatrans
 197   (:documentation "Data I/O and similar import technologies.")
 198   (:use :common-lisp
 199         :listoflist
 200         :lisp-stat-object-system
 201         :cls-data
 202         :cls-dataframe)
 203   (:shadowing-import-from :lisp-stat-object-system
 204                           call-method call-next-method)
 205   (:export listoflist->dataframe   dataframe->listoflist
 206            listoflist->array       array->listoflist
 207            listoflist->matrix-like matrix-like->listoflist
 208
 209            ))
 210
 211 ;;;; MODELING
 212
 213 (defpackage :lisp-stat-model
 214   (:documentation "Model management for data analysis.")
 215   (:use :common-lisp
 216         :lisp-matrix)
 217   (:export
 218    ;; data structures for model and model/data combination
 219    model statistical-model analysis))
 220
 221 ;;; visualization
 222
 223 (defpackage :cls-visualize
 224   (:use :common-lisp
 225         :lisp-matrix
 226         :cls-dataframe)
 227   (:shadowing-import-from :xarray slice)
 228   )
 229
 230 #|
 231 (defpackage :cls-visualize-plplot
 232   (:use :common-lisp
 233         :lisp-matrix
 234         :cls-dataframe
 235         :cl-plplot-system)
 236   (:export
 237    ;; examples
 238    plot-ex contour-plot-ex fn-contour-plot-ex shade-plot-ex 3D-plot-ex))
 239 |#
 240
 241 ;;; USER PACKAGES
 242
 243 (defpackage :lisp-stat-ffi-int
 244   (:use :common-lisp
 245         :cffi)
 246   (:export ccl-store-integer ccl-store-double ccl-store-ptr
 247            get-buf ))
 248
 249 (defpackage :lisp-stat-probability
 250   (:use :common-lisp
 251         :cffi
 252         :lisp-stat-ffi-int
 253         :lisp-stat-macros)
 254   (:export log-gamma set-seed
 255            uniform-rand
 256            normal-cdf normal-quant normal-dens normal-rand
 257            bivnorm-cdf
 258            cauchy-cdf cauchy-quant cauchy-dens cauchy-rand
 259            gamma-cdf gamma-quant gamma-dens gamma-rand
 260            chisq-cdf chisq-quant chisq-dens chisq-rand
 261            beta-cdf beta-quant beta-dens beta-rand
 262            t-cdf t-quant t-dens t-rand
 263            f-cdf f-quant f-dens f-rand
 264            poisson-cdf poisson-quant poisson-pmf poisson-rand
 265            binomial-cdf binomial-quant binomial-pmf binomial-rand))
 266
 267
 268
 269 (defpackage :lisp-stat-math
 270    (:use :common-lisp
 271          :lisp-stat-object-system
 272          :lisp-stat-macros
 273          :lisp-stat-compound-data
 274          :lisp-stat-float)
 275    (:shadowing-import-from :lisp-stat-object-system
 276                            call-method call-next-method)
 277    (:shadow expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 278            asin acos atan sinh cosh tanh asinh acosh atanh float random
 279            truncate floor ceiling round minusp zerop plusp evenp oddp
 280            < <= = /= >= > ;; complex
 281            conjugate realpart imagpart phase
 282            min max logand logior logxor lognot ffloor fceiling
 283            ftruncate fround signum cis)
 284    (:export ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 285            tan 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 min max
 289            logand logior logxor lognot ffloor fceiling ftruncate fround
 290            signum cis)
 291    (:documentation "Vectorization of numerical functions"))
 292
 293
 294 #| ;; some of this goes back in, but not all of it?
 295 (defpackage :lisp-stat-linalg
 296   (:use :common-lisp
 297         :cffi
 298         :lisp-matrix
 299         :lisp-stat-math
 300         :lisp-stat-types
 301         :lisp-stat-float
 302         :lisp-stat-compound-data)
 303   (:shadowing-import-from :lisp-stat-math
 304           expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 305           asin acos atan sinh cosh tanh asinh acosh atanh float random
 306           truncate floor ceiling round minusp zerop plusp evenp oddp
 307           < <= = /= >= > complex conjugate realpart imagpart phase
 308           min max logand logior logxor lognot ffloor fceiling
 309           ftruncate fround signum cis)
 310   (:export chol-decomp lu-decomp lu-solve determinant inverse
 311            sv-decomp qr-decomp rcondest make-rotation spline
 312            kernel-dens kernel-smooth
 313            fft make-sweep-matrix sweep-operator ax+y eigen
 314
 315            check-real ;; for optimize
 316
 317            covariance-matrix matrix print-matrix solve
 318            backsolve eigenvalues eigenvectors accumulate cumsum combine
 319            lowess))
 320
 321 |#
 322
 323
 324
 325
 326 (defpackage :lisp-stat-data
 327   (:documentation "Data management, integration, I/O, and other data technologies.")
 328   (:nicknames :ls-data)
 329   (:use :common-lisp
 330         :lisp-stat-object-system
 331         :lisp-stat-config
 332         :lisp-stat-types
 333         :lisp-stat-compound-data)
 334   (:shadowing-import-from :lisp-stat-object-system
 335                           call-method call-next-method)
 336   (:export
 337    ;; generic structures
 338    ;; Variables
 339    empirical-statistical-variable
 340    modelbased-statistical-variable
 341    categorical-statistical-variable
 342    nominal-statistical-variable
 343    ordinal-statistical-variable
 344    continuous-statistical-variable
 345
 346    ordering factor-levels nobs support pdmf draw
 347    print-object
 348
 349    ;; Observations
 350    statistical-observation
 351    measurement-types record
 352    ;; XLS compat tools
 353    open-file-dialog read-data-file read-data-columns load-data
 354            load-example *variables* *ask-on-redefine*
 355            def variables savevar undef))
 356
 357 (defpackage :lisp-stat-descriptive-statistics
 358  (:use :common-lisp
 359        :lisp-matrix
 360        :lisp-stat-data
 361        :lisp-stat-math
 362        :lisp-stat-compound-data
 363        :lisp-stat-basics)
 364    (:shadowing-import-from :lisp-stat-math ;; life is a vector!
 365       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 366       asin acos atan sinh cosh tanh asinh acosh atanh float random
 367       truncate floor ceiling round minusp zerop plusp evenp oddp
 368       < <= = /= >= > ;; complex
 369       conjugate realpart imagpart phase
 370       min max logand logior logxor lognot ffloor fceiling
 371       ftruncate fround signum cis)
 372    (:export mean standard-deviation variance
 373             quantile median interquartile-range
 374             fivnum sample))
 375
 376 (defpackage :lisp-stat-regression-linear
 377   (:use :common-lisp
 378         :lisp-matrix
 379         :lisp-stat-basics
 380         :lisp-stat-compound-data
 381         :lisp-stat-descriptive-statistics )
 382   (:shadowing-import-from :lisp-stat-object-system
 383                           call-method call-next-method)
 384   (:export regression-model fit-model
 385
 386            estimates covariance-matrix
 387            ;; functions for helpers
 388            lm xtxinv
 389            print-object ;; for method dispatch
 390            ))
 391
 392 (defpackage :common-lisp-statistics
 393   (:documentation "Experimentation package for LispStat.  Serious work
 394     should be packaged up as a separate but similar package to help
 395     drive reproducibility.  By this I mean, creating a
 396     data/analytics/analysis package with the minimal set of
 397     objects/packages required.")
 398   (:nicknames :cls :common-lisp-statistics :lisp-stat)
 399   (:use :common-lisp
 400
 401         ;; extern packages
 402         :xarray ;; generic reference -- internally supporting array, lol structs
 403         :listoflist
 404         :lisp-matrix ;; conversion to a more robust linalg approach
 405
 406         ;; intern packages
 407         :lisp-stat-config
 408         :lisp-stat-object-system
 409         :lisp-stat-compound-data
 410         :lisp-stat-probability
 411         :lisp-stat-types
 412         :lisp-stat-float
 413         :lisp-stat-basics
 414         :lisp-stat-data
 415
 416         :cls-data
 417         :cls-dataframe
 418         :cls-dataio
 419         :cls-datatrans
 420
 421         :lisp-stat-math
 422         :lisp-stat-descriptive-statistics
 423         :lisp-stat-regression-linear
 424         :cls-visualize
 425         ;; :cls-visualize-plplot
 426         ;; :cls-visualize-cl2d
 427         )
 428   (:shadowing-import-from :xarray slice)
 429   (:shadowing-import-from :lisp-stat-object-system
 430                           call-method call-next-method)
 431   (:shadowing-import-from :lisp-stat-math
 432         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 433         asin acos atan sinh cosh tanh asinh acosh atanh float random
 434         truncate floor ceiling round minusp zerop plusp evenp oddp
 435         < <= = /= >= >
 436         ;;complex
 437         conjugate realpart imagpart phase
 438
 439         min max
 440         logand logior logxor lognot
 441         ffloor fceiling ftruncate fround
 442         signum cis)
 443   (:export
 444    ;; lisp-stat-config:
 445    *default-path* *lsos-files* *basic-files* *ls-files*
 446    *cls-home-dir* *cls-data-dir* *cls-examples-dir*
 447
 448    ;; lsobjects :
 449    defproto defproto2
 450    defmeth send proto-slot-value
 451
 452    ;; lstypes :
 453    fixnump check-nonneg-fixnum check-one-fixnum
 454    check-one-nonneg-fixnum
 455    check-one-real check-one-number
 456
 457    ;; lsmacros:
 458
 459    ;; lsfloat :
 460    machine-epsilon
 461
 462    ;; compound :
 463    compound-data-p *compound-data-proto* compound-object-p
 464    compound-data-seq compound-data-length
 465    element-list element-seq
 466    sort-data order rank
 467    recursive-map-elements map-elements
 468    repeat
 469    check-sequence
 470    get-next-element make-next-element set-next-element
 471    ;; sequencep
 472    iseq
 473    ordered-nneg-seq
 474    select which
 475    difference rseq
 476
 477    ;; lsmath.lsp
 478    ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 479    tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 480    truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 481    /= >= > ;; complex
 482    conjugate realpart imagpart phase min max
 483    logand logior logxor lognot ffloor fceiling ftruncate fround
 484    signum cis
 485
 486 #| ;; The following need to be re-found in lisp-matrix...
 487
 488    ;; matrices.lisp
 489    matrixp num-rows num-cols matmult identity-matrix diagonal row-list
 490    column-list inner-product outer-product cross-product transpose
 491    bind-columns bind-rows
 492
 493    ;; linalg.lisp
 494    chol-decomp lu-decomp lu-solve determinant inverse
 495    sv-decomp qr-decomp rcondest make-rotation spline
 496    kernel-dens kernel-smooth
 497    fft make-sweep-matrix sweep-operator ax+y eigen
 498    check-real
 499    covariance-matrix matrix print-matrix solve
 500    backsolve eigenvalues eigenvectors accumulate cumsum combine
 501    lowess
 502
 503    ;; in linalg.lisp, possibly not supported by matlisp
 504    spline kernel-dens kernel-smooth
 505
 506 |#
 507
 508    ;; optimize.lsp
 509    newtonmax nelmeadmax
 510
 511    ;; package LISPSTAT-MACROS
 512    make-rv-function make-rv-function-1
 513
 514    ;; package XARRAY
 515    xref xtype xdims xdim xdims*
 516
 517    ;; package LISTOFLIST
 518    sublists-of-same-size-p equal-listoflist transpose-listoflist
 519
 520    ;; package DATA
 521    ;; need to take this list and make it symbols...  specs could mean
 522    ;; that we process the strings in different ways?  Create such a
 523    ;; macro to enable export within this package?
 524 #|
 525    (let ((lst ()))
 526      (unlist
 527        (mapc #'symbol-for-symbol-to-string-or-symbol
 528          (do-external-symbols (s (find-package 'lisp-stat-data) lst) (push s lst))))
 529      lst)
 530 |#
 531    open-file-dialog read-data-file read-data-columns load-data
 532    load-example *variables* *ask-on-redefine*
 533    def variables savevar undef
 534    ;; dataframe
 535    dataframe-like dataframe-array make-dataframe
 536    varlabels caselabels nrows ncols
 537    dataframe-dimension dataframe-dimensons
 538    dfref dfref-case dfref-var
 539    consistent-dataframe-p
 540    dataset list-of-columns list-of-rows
 541    make-labels
 542
 543    ;; listoflist
 544    listoflist->dataframe listoflist->array listoflist->matrix-like
 545    sublists-of-same-size-p
 546
 547    ;; cls-dataio
 548    dsvstream->dataframe dsvstream->matrix dsvstream->listoflist
 549    filename.dsv->dataframe
 550
 551    ;; cls-datatrans
 552    listoflist->dataframe   dataframe->listoflist
 553    listoflist->array       array->listoflist
 554    listoflist->matrix-like matrix-like->listoflist
 555
 556
 557    ;; statistics.lsp  (descriptions, should probably be moved
 558    ;; later...?
 559    standard-deviation quantile median interquartile-range
 560    fivnum sample
 561
 562    ;; probability (dists.lisp)
 563    log-gamma set-seed
 564    uniform-rand normal-cdf normal-quant normal-dens
 565    normal-rand bivnorm-cdf cauchy-cdf cauchy-quant cauchy-dens
 566    cauchy-rand gamma-cdf gamma-quant gamma-dens gamma-rand
 567    chisq-cdf chisq-quant chisq-dens chisq-rand beta-cdf beta-quant
 568    beta-dens beta-rand t-cdf t-quant t-dens t-rand f-cdf f-quant
 569    f-dens f-rand poisson-cdf poisson-quant poisson-pmf poisson-rand
 570    binomial-cdf binomial-quant binomial-pmf binomial-rand
 571
 572    ;; Here is where we have a problem -- lispstat core should be core
 573    ;; data management and config problems, with packages providing
 574    ;; specialized extensions to LispStat, i.e. regression, nonlin
 575    ;; regression, bayesian regression via laplace approximation, etc.
 576
 577    ;; The following could be considered "recommended packages",
 578    ;; similar to the idea of the recommended packages in R.  Probably
 579    ;; we want them to do the exporting within that package, therefore
 580    ;; NOT being able to lock the "data-ish" package, but only the
 581    ;; subpackages prior to export.
 582
 583    ;; regression.lsp
 584    ;; -- linear regressin models.
 585    regression-model fit-model
 586    estimates covariance-matrix
 587
 588    regression-model-proto x y intercept sweep-matrix
 589    basis weights included total-sum-of-squares residual-sum-of-squares
 590    predictor-names response-name case-labels
 591    lm xtxinv
 592
 593    ;; nonlin.lsp
 594    ;; -- nonlinear regression models
 595    nreg-model nreg-model-proto mean-function theta-hat epsilon
 596    count-limit verbose
 597    ;; we might need something like xtxinv here?  But should be
 598    ;; encapsulated, so we use the one in regression.lisp
 599
 600    ;; bayes.lsp
 601    bayes-model bayes-model-proto bayes-internals
 602
 603    ;; plots.lisp
 604    plot-ex
 605    contour-plot-ex
 606    fn-contour-plot-ex
 607    shade-plot-ex
 608    3D-plot-ex
 609
 610    ))
 611
 612
 613 ;;;; PACKAGES FOR USEABILITY
 614
 615 (defpackage :lisp-stat-data-examples
 616   (:documentation "Example data for unittests, examples, illustrations,")
 617   (:use :common-lisp
 618         :common-lisp-statistics)
 619   (:shadowing-import-from :lisp-stat
 620                           call-method call-next-method
 621
 622       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 623       asin acos atan sinh cosh tanh asinh acosh atanh float random
 624       truncate floor ceiling round minusp zerop plusp evenp oddp
 625       < <= = /= >= > > ;; complex
 626       conjugate realpart imagpart phase
 627       min max logand logior logxor lognot ffloor fceiling
 628       ftruncate fround signum cis
 629
 630       <= float imagpart)
 631   (:export iron aluminum absorbtion
 632            diabetes dlabs))
 633
 634
 635 (defpackage :lisp-stat-user
 636   (:documentation "Experimentation package for LispStat.  Serious work
 637     should be placed in a similar package elsewhere for
 638     reproducibility.  But this should hint as to what needs to be done
 639     for a user- or analysis-package.")
 640   (:nicknames :ls-user :cls-user)
 641   (:use :common-lisp ; always needed for user playgrounds!
 642         :lisp-matrix
 643         :common-lisp-statistics
 644         :lisp-stat-data-examples) ;; this last is to have 'things to play with'
 645   (:shadowing-import-from :lisp-stat
 646                           call-method call-next-method
 647
 648       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 649       asin acos atan sinh cosh tanh asinh acosh atanh float random
 650       truncate floor ceiling round minusp zerop plusp evenp oddp
 651       < <= = /= >= > > ;; complex
 652       conjugate realpart imagpart phase
 653       min max logand logior logxor lognot ffloor fceiling
 654       ftruncate fround signum cis
 655
 656       <= float imagpart))
 657
 658 (defpackage :lisp-stat-unittests
 659   (:use :common-lisp
 660         :lift :lisp-matrix
 661         :lisp-stat :lisp-stat-data-examples)
 662   (:shadowing-import-from :lisp-stat
 663                           call-method call-next-method ;; objects
 664         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan ;; lsmath
 665         asin acos atan sinh cosh tanh asinh acosh atanh float random
 666         truncate floor ceiling round minusp zerop plusp evenp oddp
 667         < <= = /= >= > ;; complex
 668         conjugate realpart imagpart phase
 669         min max logand logior logxor lognot ffloor fceiling
 670         ftruncate fround signum cis)
 671   (:export run-lisp-stat-tests run-lisp-stat-test scoreboard ; exec
 672            almost= almost=lists numerical=)) ; compare
 673
 674 (defpackage :cls-dataframe-example
 675   (:use :common-lisp
 676         :lift  :lisp-stat-unittests
 677         :lisp-stat-data-examples
 678         :cls-dataframe)
 679   (:export absorbtion aluminum iron))
 680
 681
 682 (defpackage :lisp-stat-optimize
 683  (:use :common-lisp
 684        :cffi
 685        :lisp-matrix
 686        :lisp-stat-ffi-int
 687        :lisp-stat-object-system
 688        :lisp-stat-types
 689        :lisp-stat-compound-data
 690        :lisp-stat-math
 691        :lisp-stat-float
 692        :lisp-stat-basics
 693 #|
 694        :lisp-stat-matrix
 695        :lisp-stat-linalg-data
 696        :lisp-stat-linalg
 697 |#
 698        )
 699  (:shadowing-import-from :lisp-stat-object-system
 700                          call-method call-next-method)
 701  (:shadowing-import-from :lisp-stat-math
 702            expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 703            asin acos atan sinh cosh tanh asinh acosh atanh float random
 704            truncate floor ceiling round minusp zerop plusp evenp oddp
 705            < <= = /= >= > complex conjugate realpart imagpart phase
 706            min max logand logior logxor lognot ffloor fceiling
 707            ftruncate fround signum cis)
 708  (:export
 709      ;; derivatives
 710      numgrad numhess
 711
 712      ;; optimization
 713      newtonmax nelmeadmax))