src/packages.lisp

   1 ;;; -*- mode: lisp -*-
   2
   3 ;;; Time-stamp: <2010-11-04 16:45:44 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
  35 (defpackage :lisp-stat-config
  36   (:documentation "holds Common Lisp Statistics configuration/loading variables and related functions.")
  37   (:nicknames :cls-config)
  38   (:use :common-lisp)
  39   (:export *common-lisp-stat-version*
  40            *default-path*
  41            *lsos-files* *basic-files* *ls-files*
  42            *cls-installation-home-dir* *cls-data-dir* *cls-examples-dir*))
  43
  44 (defpackage :lisp-stat-object-system
  45   (:nicknames :ls-objects :lsos)
  46   (:use :common-lisp)
  47   (:shadow :call-method :call-next-method)
  48   (:export ls-object objectp *object* kind-of-p make-object
  49            *message-hook*
  50            *set-slot-hook* proto-slot-value self
  51            send call-next-method call-method
  52            defmeth defproto instance-slots proto-name))
  53
  54 ;;; -types and -float probably ought to be moved into a -numerics
  55 ;;; package.
  56
  57 (defpackage :lisp-stat-types
  58   (:documentation "Provides some typeing for LispStat, but is clearly
  59   a bit incomplete.")
  60   (:use :common-lisp)
  61   (:export fixnump
  62            check-nonneg-fixnum check-one-nonneg-fixnum
  63            check-one-fixnum check-one-real check-one-number))
  64
  65 (defpackage :lisp-stat-float
  66   (:use :common-lisp)
  67   (:export +stat-float-typing+ +stat-cfloat-typing+ +stat-float-template+
  68            machine-epsilon base-float makedouble
  69
  70            make-base-trans-fun-2 make-base-trans-fun
  71
  72            base-log base-exp base-expt base-sqrt base-sin base-cos
  73            base-tan base-asin base-acos base-atan base-sinh
  74            BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
  75            BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
  76            BASE-FROUND BASE-SIGNUM BASE-CIS))
  77
  78 ;;; Probably should move into cls-data package.
  79
  80 (defpackage :lisp-stat-compound-data
  81   (:use :common-lisp
  82         :lisp-stat-object-system
  83         :lisp-stat-types)
  84   (:shadowing-import-from :lisp-stat-object-system
  85                           call-next-method call-method)
  86   (:export compound-data-p *compound-data-proto*
  87            compound-object-p
  88            compound-data-seq compound-data-length
  89            element-list element-seq
  90            sort-data order rank
  91            recursive-map-elements map-elements repeat
  92            check-sequence
  93            get-next-element make-next-element set-next-element
  94            ;; sequencep
  95            iseq ordered-nneg-seq
  96            select split-list which
  97            difference rseq
  98            flatten-list))
  99
 100 (defpackage :lisp-stat-macros
 101   (:use :common-lisp
 102         :lisp-stat-compound-data)
 103   (:export make-rv-function make-rv-function-1))
 104
 105 (defpackage :lisp-stat-basics
 106     (:use :common-lisp
 107           :lisp-stat-object-system
 108           :lisp-stat-types
 109           :lisp-stat-float
 110           :lisp-stat-macros
 111           :lisp-stat-compound-data)
 112   (:shadowing-import-from :lisp-stat-object-system
 113                           call-method call-next-method)
 114   (:export permute-array sum prod count-elements mean
 115            if-else sample))
 116
 117 (defpackage :lisp-stat-float
 118   (:use :common-lisp)
 119   (:export +stat-float-typing+ +stat-cfloat-typing+ +stat-float-template+
 120            machine-epsilon base-float makedouble
 121
 122            make-base-trans-fun-2 make-base-trans-fun
 123
 124            BASE-LOG BASE-EXP BASE-EXPT BASE-SQRT BASE-SIN BASE-COS
 125            BASE-TAN BASE-ASIN BASE-ACOS BASE-ATAN BASE-SINH
 126            BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
 127            BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
 128            BASE-FROUND BASE-SIGNUM BASE-CIS))
 129
 130 (defpackage :lisp-stat-macros
 131   (:use :common-lisp
 132         :lisp-stat-compound-data)
 133   (:export make-rv-function make-rv-function-1))
 134
 135
 136 (defpackage :cls-matrix
 137   (:documentation "basic utilities for using lisp arrays as numerical
 138   matrices.  Not optimized, and must consider this slow.  Routines
 139   should be optimized, it is only that we need them first, optimize
 140   them later.")
 141   (:use :common-lisp)
 142   (:export matrixp num-rows num-cols matmult identity-matrix diagonal
 143            row-list column-list inner-product outer-product
 144            cross-product transpose bind-columns bind-rows
 145            array-data-vector vector-to-array))
 146
 147
 148 ;;; NEW CLOS STRUCTURE
 149
 150 ;; CLS-DATA contains the basic variable structure, classes, support/indexing, and mixins.
 151 ;; CLS-DATAFRAME leverages CLS-DATA, XARRAY, and LISP-MATRIX
 152 ;; CLS-DATAIO stores/saves structures
 153 ;; CLS-DATATRANS converts between structures, and from DATAFRAMES to MODEL-MATRIXES
 154
 155 (defpackage :cls-data
 156   (:use :common-lisp)
 157   (:shadowing-import-from :xarray slice)
 158   (:export
 159    ;; must work out what is needed for stat variable metadata, support
 160    ;; functions, etc
 161    ))
 162
 163 ;;; cls-data... in dataframe, though.
 164 (defpackage :cls-dataframe
 165   (:use :common-lisp
 166         :cls-data
 167         :xarray
 168         :lisp-matrix)
 169   (:shadowing-import-from :xarray slice)
 170   (:export
 171    ;; generic container class for data -- if small enough
 172    ;; could be value, otherwise might be reference.
 173    dataframe-like
 174    dataframe-array
 175    make-dataframe
 176
 177    dataset
 178    list-of-columns ;; list-of-variables
 179    list-of-rows ;; list-of-observations
 180
 181    ;; accessors
 182    varlabels caselabels  nrows ncols
 183    dataframe-dimension dataframe-dimensons
 184    xref xtype xdims xdim xrank slice take carray
 185
 186    ;; support
 187    make-labels
 188    ))
 189
 190 (defpackage :cls-dataio
 191   (:documentation "Data I/O and similar import technologies.")
 192   (:use :common-lisp
 193         :rsm.string
 194         :lisp-stat-object-system
 195         :cls-data
 196         :cls-dataframe)
 197   (:shadowing-import-from :lisp-stat-object-system
 198                           call-method call-next-method)
 199   (:export dsvstream->dataframe
 200            dsvstream->matrix
 201            dsvstream->listoflist
 202
 203            filename.dsv->dataframe
 204            ))
 205
 206 (defpackage :cls-datatrans
 207   (:documentation "Data I/O and similar import technologies.")
 208   (:use :common-lisp
 209         :listoflist
 210         :lisp-stat-object-system
 211         :cls-data
 212         :cls-dataframe)
 213   (:shadowing-import-from :lisp-stat-object-system
 214                           call-method call-next-method)
 215   (:export listoflist->dataframe   dataframe->listoflist
 216            listoflist->array       array->listoflist
 217            listoflist->matrix-like matrix-like->listoflist
 218
 219            ))
 220
 221 ;;;; MODELING
 222
 223 (defpackage :lisp-stat-model
 224   (:documentation "Model management for data analysis.")
 225   (:use :common-lisp
 226         :lisp-matrix)
 227   (:export
 228    ;; data structures for model and model/data combination
 229    model statistical-model analysis))
 230
 231 ;;; visualization
 232
 233 (defpackage :cls-visualize
 234   (:use :common-lisp
 235         :lisp-matrix
 236         :cls-dataframe)
 237   (:shadowing-import-from :xarray slice)
 238   )
 239
 240 #|
 241 (defpackage :cls-visualize-plplot
 242   (:use :common-lisp
 243         :lisp-matrix
 244         :cls-dataframe
 245         :cl-plplot-system)
 246   (:export
 247    ;; examples
 248    plot-ex contour-plot-ex fn-contour-plot-ex shade-plot-ex 3D-plot-ex))
 249 |#
 250
 251 ;;; USER PACKAGES
 252
 253 (defpackage :lisp-stat-ffi-int
 254   (:use :common-lisp
 255         :cffi)
 256   (:export ccl-store-integer ccl-store-double ccl-store-ptr
 257            get-buf ))
 258
 259 (defpackage :lisp-stat-probability
 260   (:use :common-lisp
 261         :cffi
 262         :lisp-stat-ffi-int
 263         :lisp-stat-macros)
 264   (:export log-gamma set-seed
 265            uniform-rand
 266            normal-cdf normal-quant normal-dens normal-rand
 267            bivnorm-cdf
 268            cauchy-cdf cauchy-quant cauchy-dens cauchy-rand
 269            gamma-cdf gamma-quant gamma-dens gamma-rand
 270            chisq-cdf chisq-quant chisq-dens chisq-rand
 271            beta-cdf beta-quant beta-dens beta-rand
 272            t-cdf t-quant t-dens t-rand
 273            f-cdf f-quant f-dens f-rand
 274            poisson-cdf poisson-quant poisson-pmf poisson-rand
 275            binomial-cdf binomial-quant binomial-pmf binomial-rand))
 276
 277
 278
 279 (defpackage :lisp-stat-math
 280    (:use :common-lisp
 281          :lisp-stat-object-system
 282          :lisp-stat-macros
 283          :lisp-stat-compound-data
 284          :lisp-stat-float)
 285    (:shadowing-import-from :lisp-stat-object-system
 286                            call-method call-next-method)
 287    (:shadow expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 288            asin acos atan sinh cosh tanh asinh acosh atanh float random
 289            truncate floor ceiling round minusp zerop plusp evenp oddp
 290            < <= = /= >= > ;; complex
 291            conjugate realpart imagpart phase
 292            min max logand logior logxor lognot ffloor fceiling
 293            ftruncate fround signum cis)
 294    (:export ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 295            tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 296            truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 297            /= >= > ;; complex
 298            conjugate realpart imagpart phase min max
 299            logand logior logxor lognot ffloor fceiling ftruncate fround
 300            signum cis)
 301    (:documentation "Vectorization of numerical functions"))
 302
 303
 304 #| ;; some of this goes back in, but not all of it?
 305 (defpackage :lisp-stat-linalg
 306   (:use :common-lisp
 307         :cffi
 308         :lisp-matrix
 309         :lisp-stat-math
 310         :lisp-stat-types
 311         :lisp-stat-float
 312         :lisp-stat-compound-data)
 313   (:shadowing-import-from :lisp-stat-math
 314           expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 315           asin acos atan sinh cosh tanh asinh acosh atanh float random
 316           truncate floor ceiling round minusp zerop plusp evenp oddp
 317           < <= = /= >= > complex conjugate realpart imagpart phase
 318           min max logand logior logxor lognot ffloor fceiling
 319           ftruncate fround signum cis)
 320   (:export chol-decomp lu-decomp lu-solve determinant inverse
 321            sv-decomp qr-decomp rcondest make-rotation spline
 322            kernel-dens kernel-smooth
 323            fft make-sweep-matrix sweep-operator ax+y eigen
 324
 325            check-real ;; for optimize
 326
 327            covariance-matrix matrix print-matrix solve
 328            backsolve eigenvalues eigenvectors accumulate cumsum combine
 329            lowess))
 330
 331 |#
 332
 333
 334
 335
 336 (defpackage :lisp-stat-data
 337   (:documentation "Data management, integration, I/O, and other data technologies.")
 338   (:nicknames :ls-data)
 339   (:use :common-lisp
 340         :lisp-stat-object-system
 341         :lisp-stat-config
 342         :lisp-stat-types
 343         :lisp-stat-compound-data)
 344   (:shadowing-import-from :lisp-stat-object-system
 345                           call-method call-next-method)
 346   (:export
 347    ;; generic structures
 348    ;; Variables
 349    empirical-statistical-variable
 350    modelbased-statistical-variable
 351    categorical-statistical-variable
 352    nominal-statistical-variable
 353    ordinal-statistical-variable
 354    continuous-statistical-variable
 355
 356    ordering factor-levels nobs support pdmf draw
 357    print-object
 358
 359    ;; Observations
 360    statistical-observation
 361    measurement-types record
 362    ;; XLS compat tools
 363    open-file-dialog read-data-file read-data-columns load-data
 364            load-example *variables* *ask-on-redefine*
 365            def variables savevar undef))
 366
 367 (defpackage :lisp-stat-descriptive-statistics
 368  (:use :common-lisp
 369        :lisp-matrix
 370        :lisp-stat-data
 371        :lisp-stat-math
 372        :lisp-stat-compound-data
 373        :lisp-stat-basics)
 374    (:shadowing-import-from :lisp-stat-math ;; life is a vector!
 375       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 376       asin acos atan sinh cosh tanh asinh acosh atanh float random
 377       truncate floor ceiling round minusp zerop plusp evenp oddp
 378       < <= = /= >= > ;; complex
 379       conjugate realpart imagpart phase
 380       min max logand logior logxor lognot ffloor fceiling
 381       ftruncate fround signum cis)
 382    (:export mean standard-deviation variance
 383             quantile median interquartile-range
 384             fivnum sample))
 385
 386 (defpackage :lisp-stat-regression-linear
 387   (:use :common-lisp
 388         :lisp-matrix
 389         :lisp-stat-basics
 390         :lisp-stat-compound-data
 391         :lisp-stat-descriptive-statistics )
 392   (:shadowing-import-from :lisp-stat-object-system
 393                           call-method call-next-method)
 394   (:export regression-model fit-model
 395
 396            estimates covariance-matrix
 397            ;; functions for helpers
 398            lm xtxinv
 399            print-object ;; for method dispatch
 400            ))
 401
 402 (defpackage :common-lisp-statistics
 403   (:documentation "Experimentation package for LispStat.  Serious work
 404     should be packaged up as a separate but similar package to help
 405     drive reproducibility.  By this I mean, creating a
 406     data/analytics/analysis package with the minimal set of
 407     objects/packages required.")
 408   (:nicknames :cls :common-lisp-statistics :lisp-stat)
 409   (:use :common-lisp
 410
 411         ;; extern packages
 412         :xarray ;; generic reference -- internally supporting array, lol structs
 413         :listoflist
 414         :lisp-matrix ;; conversion to a more robust linalg approach
 415
 416         ;; intern packages
 417         :lisp-stat-config
 418         :lisp-stat-object-system
 419         :lisp-stat-compound-data
 420         :lisp-stat-probability
 421         :lisp-stat-types
 422         :lisp-stat-float
 423         :lisp-stat-basics
 424         :lisp-stat-data
 425
 426         :cls-data
 427         :cls-dataframe
 428         :cls-dataio
 429         :cls-datatrans
 430
 431         :lisp-stat-math
 432         :lisp-stat-descriptive-statistics
 433         :lisp-stat-regression-linear
 434         :cls-visualize
 435         ;; :cls-visualize-plplot
 436         ;; :cls-visualize-cl2d
 437         )
 438   (:shadowing-import-from :xarray slice)
 439   (:shadowing-import-from :lisp-stat-object-system
 440                           call-method call-next-method)
 441   (:shadowing-import-from :lisp-stat-math
 442         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 443         asin acos atan sinh cosh tanh asinh acosh atanh float random
 444         truncate floor ceiling round minusp zerop plusp evenp oddp
 445         < <= = /= >= >
 446         ;;complex
 447         conjugate realpart imagpart phase
 448
 449         min max
 450         logand logior logxor lognot
 451         ffloor fceiling ftruncate fround
 452         signum cis)
 453   (:export
 454    ;; lisp-stat-config:
 455    *default-path* *lsos-files* *basic-files* *ls-files*
 456    *cls-installation-home-dir* *cls-data-dir* *cls-examples-dir*
 457
 458    ;; lsobjects :
 459    defproto defproto2
 460    defmeth send proto-slot-value
 461
 462    ;; lstypes :
 463    fixnump check-nonneg-fixnum check-one-fixnum
 464    check-one-nonneg-fixnum
 465    check-one-real check-one-number
 466
 467    ;; lsmacros:
 468
 469    ;; lsfloat :
 470    machine-epsilon
 471
 472    ;; compound :
 473    compound-data-p *compound-data-proto* compound-object-p
 474    compound-data-seq compound-data-length
 475    element-list element-seq
 476    sort-data order rank
 477    recursive-map-elements map-elements
 478    repeat
 479    check-sequence
 480    get-next-element make-next-element set-next-element
 481    ;; sequencep
 482    iseq
 483    ordered-nneg-seq
 484    select which
 485    difference rseq
 486
 487    ;; lsmath.lsp
 488    ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 489    tan 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 min max
 493    logand logior logxor lognot ffloor fceiling ftruncate fround
 494    signum cis
 495
 496 #| ;; The following need to be re-found in lisp-matrix...
 497
 498    ;; matrices.lisp
 499    matrixp num-rows num-cols matmult identity-matrix diagonal row-list
 500    column-list inner-product outer-product cross-product transpose
 501    bind-columns bind-rows
 502
 503    ;; linalg.lisp
 504    chol-decomp lu-decomp lu-solve determinant inverse
 505    sv-decomp qr-decomp rcondest make-rotation spline
 506    kernel-dens kernel-smooth
 507    fft make-sweep-matrix sweep-operator ax+y eigen
 508    check-real
 509    covariance-matrix matrix print-matrix solve
 510    backsolve eigenvalues eigenvectors accumulate cumsum combine
 511    lowess
 512
 513    ;; in linalg.lisp, possibly not supported by matlisp
 514    spline kernel-dens kernel-smooth
 515
 516 |#
 517
 518    ;; optimize.lsp
 519    newtonmax nelmeadmax
 520
 521    ;; package LISPSTAT-MACROS
 522    make-rv-function make-rv-function-1
 523
 524    ;; package XARRAY
 525    xref xtype xdims xdim xdims*
 526
 527    ;; package LISTOFLIST
 528    sublists-of-same-size-p equal-listoflist transpose-listoflist
 529
 530    ;; package DATA
 531    ;; need to take this list and make it symbols...  specs could mean
 532    ;; that we process the strings in different ways?  Create such a
 533    ;; macro to enable export within this package?
 534 #|
 535    (let ((lst ()))
 536      (unlist
 537        (mapc #'symbol-for-symbol-to-string-or-symbol
 538          (do-external-symbols (s (find-package 'lisp-stat-data) lst) (push s lst))))
 539      lst)
 540 |#
 541    open-file-dialog read-data-file read-data-columns load-data
 542    load-example *variables* *ask-on-redefine*
 543    def variables savevar undef
 544    ;; dataframe
 545    dataframe-like dataframe-array make-dataframe
 546    varlabels caselabels nrows ncols
 547    dataframe-dimension dataframe-dimensons
 548    dfref dfref-case dfref-var
 549    consistent-dataframe-p
 550    dataset list-of-columns list-of-rows
 551    make-labels
 552
 553    ;; listoflist
 554    listoflist->dataframe listoflist->array listoflist->matrix-like
 555    sublists-of-same-size-p
 556
 557    ;; cls-dataio
 558    dsvstream->dataframe dsvstream->matrix dsvstream->listoflist
 559    filename.dsv->dataframe
 560
 561    ;; cls-datatrans
 562    listoflist->dataframe   dataframe->listoflist
 563    listoflist->array       array->listoflist
 564    listoflist->matrix-like matrix-like->listoflist
 565
 566
 567    ;; statistics.lsp  (descriptions, should probably be moved
 568    ;; later...?
 569    standard-deviation quantile median interquartile-range
 570    fivnum sample
 571
 572    ;; probability (dists.lisp)
 573    log-gamma set-seed
 574    uniform-rand normal-cdf normal-quant normal-dens
 575    normal-rand bivnorm-cdf cauchy-cdf cauchy-quant cauchy-dens
 576    cauchy-rand gamma-cdf gamma-quant gamma-dens gamma-rand
 577    chisq-cdf chisq-quant chisq-dens chisq-rand beta-cdf beta-quant
 578    beta-dens beta-rand t-cdf t-quant t-dens t-rand f-cdf f-quant
 579    f-dens f-rand poisson-cdf poisson-quant poisson-pmf poisson-rand
 580    binomial-cdf binomial-quant binomial-pmf binomial-rand
 581
 582    ;; Here is where we have a problem -- lispstat core should be core
 583    ;; data management and config problems, with packages providing
 584    ;; specialized extensions to LispStat, i.e. regression, nonlin
 585    ;; regression, bayesian regression via laplace approximation, etc.
 586
 587    ;; The following could be considered "recommended packages",
 588    ;; similar to the idea of the recommended packages in R.  Probably
 589    ;; we want them to do the exporting within that package, therefore
 590    ;; NOT being able to lock the "data-ish" package, but only the
 591    ;; subpackages prior to export.
 592
 593    ;; regression.lsp
 594    ;; -- linear regressin models.
 595    regression-model fit-model
 596    estimates covariance-matrix
 597
 598    regression-model-proto x y intercept sweep-matrix
 599    basis weights included total-sum-of-squares residual-sum-of-squares
 600    predictor-names response-name case-labels
 601    lm xtxinv
 602
 603    ;; nonlin.lsp
 604    ;; -- nonlinear regression models
 605    nreg-model nreg-model-proto mean-function theta-hat epsilon
 606    count-limit verbose
 607    ;; we might need something like xtxinv here?  But should be
 608    ;; encapsulated, so we use the one in regression.lisp
 609
 610    ;; bayes.lsp
 611    bayes-model bayes-model-proto bayes-internals
 612
 613    ;; plots.lisp
 614    plot-ex
 615    contour-plot-ex
 616    fn-contour-plot-ex
 617    shade-plot-ex
 618    3D-plot-ex
 619
 620    ))
 621
 622
 623 ;;;; PACKAGES FOR USEABILITY
 624
 625 (defpackage :lisp-stat-data-examples
 626   (:documentation "Example data for unittests, examples, illustrations,")
 627   (:use :common-lisp
 628         :common-lisp-statistics)
 629   (:shadowing-import-from :lisp-stat
 630                           call-method call-next-method
 631
 632       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 633       asin acos atan sinh cosh tanh asinh acosh atanh float random
 634       truncate floor ceiling round minusp zerop plusp evenp oddp
 635       < <= = /= >= > > ;; complex
 636       conjugate realpart imagpart phase
 637       min max logand logior logxor lognot ffloor fceiling
 638       ftruncate fround signum cis
 639
 640       <= float imagpart)
 641   (:export iron aluminum absorbtion
 642            diabetes dlabs))
 643
 644
 645 (defpackage :lisp-stat-user
 646   (:documentation "Experimentation package for LispStat.  Serious work
 647     should be placed in a similar package elsewhere for
 648     reproducibility.  But this should hint as to what needs to be done
 649     for a user- or analysis-package.")
 650   (:nicknames :ls-user :cls-user)
 651   (:use :common-lisp ; always needed for user playgrounds!
 652         :lisp-matrix
 653         :common-lisp-statistics
 654         :lisp-stat-data-examples) ;; this last is to have 'things to play with'
 655   (:shadowing-import-from :lisp-stat
 656                           call-method call-next-method
 657
 658       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 659       asin acos atan sinh cosh tanh asinh acosh atanh float random
 660       truncate floor ceiling round minusp zerop plusp evenp oddp
 661       < <= = /= >= > > ;; complex
 662       conjugate realpart imagpart phase
 663       min max logand logior logxor lognot ffloor fceiling
 664       ftruncate fround signum cis
 665
 666       <= float imagpart))
 667
 668 (defpackage :lisp-stat-unittests
 669   (:use :common-lisp
 670         :lift :lisp-matrix
 671         :lisp-stat :lisp-stat-data-examples)
 672   (:shadowing-import-from :lisp-stat
 673                           call-method call-next-method ;; objects
 674         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan ;; lsmath
 675         asin acos atan sinh cosh tanh asinh acosh atanh float random
 676         truncate floor ceiling round minusp zerop plusp evenp oddp
 677         < <= = /= >= > ;; complex
 678         conjugate realpart imagpart phase
 679         min max logand logior logxor lognot ffloor fceiling
 680         ftruncate fround signum cis)
 681   (:export run-lisp-stat-tests run-lisp-stat-test scoreboard ; exec
 682            almost= almost=lists numerical=)) ; compare
 683
 684 (defpackage :cls-dataframe-example
 685   (:use :common-lisp
 686         :lift  :lisp-stat-unittests
 687         :lisp-stat-data-examples
 688         :cls-dataframe)
 689   (:export absorbtion aluminum iron))
 690
 691
 692 (defpackage :lisp-stat-optimize
 693  (:use :common-lisp
 694        :cffi
 695        :lisp-matrix
 696        :lisp-stat-ffi-int
 697        :lisp-stat-object-system
 698        :lisp-stat-types
 699        :lisp-stat-compound-data
 700        :lisp-stat-math
 701        :lisp-stat-float
 702        :lisp-stat-basics
 703 #|
 704        :lisp-stat-matrix
 705        :lisp-stat-linalg-data
 706        :lisp-stat-linalg
 707 |#
 708        )
 709  (:shadowing-import-from :lisp-stat-object-system
 710                          call-method call-next-method)
 711  (:shadowing-import-from :lisp-stat-math
 712            expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 713            asin acos atan sinh cosh tanh asinh acosh atanh float random
 714            truncate floor ceiling round minusp zerop plusp evenp oddp
 715            < <= = /= >= > complex conjugate realpart imagpart phase
 716            min max logand logior logxor lognot ffloor fceiling
 717            ftruncate fround signum cis)
 718  (:export
 719      ;; derivatives
 720      numgrad numhess
 721
 722      ;; optimization
 723      newtonmax nelmeadmax))