src/packages.lisp

   1 ;;; -*- mode: lisp -*-
   2
   3 ;;; Time-stamp: <2010-11-10 14:03:10 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 (defpackage :cls-probability
 278   (:use common-lisp
 279         cl-variates
 280         )
 281   (:export probability-law distribution
 282            density-fcn quantile-fcn survivorship-fcn ))
 283
 284 (defpackage :lisp-stat-math
 285    (:use :common-lisp
 286          :lisp-stat-object-system
 287          :lisp-stat-macros
 288          :lisp-stat-compound-data
 289          :lisp-stat-float)
 290    (:shadowing-import-from :lisp-stat-object-system
 291                            call-method call-next-method)
 292    (:shadow expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 293            asin acos atan sinh cosh tanh asinh acosh atanh float random
 294            truncate floor ceiling round minusp zerop plusp evenp oddp
 295            < <= = /= >= > ;; complex
 296            conjugate realpart imagpart phase
 297            min max logand logior logxor lognot ffloor fceiling
 298            ftruncate fround signum cis)
 299    (:export ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 300            tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 301            truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 302            /= >= > ;; complex
 303            conjugate realpart imagpart phase min max
 304            logand logior logxor lognot ffloor fceiling ftruncate fround
 305            signum cis)
 306    (:documentation "Vectorization of numerical functions"))
 307
 308
 309 #| ;; some of this goes back in, but not all of it?
 310 (defpackage :lisp-stat-linalg
 311   (:use :common-lisp
 312         :cffi
 313         :lisp-matrix
 314         :lisp-stat-math
 315         :lisp-stat-types
 316         :lisp-stat-float
 317         :lisp-stat-compound-data)
 318   (:shadowing-import-from :lisp-stat-math
 319           expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 320           asin acos atan sinh cosh tanh asinh acosh atanh float random
 321           truncate floor ceiling round minusp zerop plusp evenp oddp
 322           < <= = /= >= > complex conjugate realpart imagpart phase
 323           min max logand logior logxor lognot ffloor fceiling
 324           ftruncate fround signum cis)
 325   (:export chol-decomp lu-decomp lu-solve determinant inverse
 326            sv-decomp qr-decomp rcondest make-rotation spline
 327            kernel-dens kernel-smooth
 328            fft make-sweep-matrix sweep-operator ax+y eigen
 329
 330            check-real ;; for optimize
 331
 332            covariance-matrix matrix print-matrix solve
 333            backsolve eigenvalues eigenvectors accumulate cumsum combine
 334            lowess))
 335
 336 |#
 337
 338
 339
 340
 341 (defpackage :lisp-stat-data
 342   (:documentation "Data management, integration, I/O, and other data technologies.")
 343   (:nicknames :ls-data)
 344   (:use :common-lisp
 345         :lisp-stat-object-system
 346         :lisp-stat-config
 347         :lisp-stat-types
 348         :lisp-stat-compound-data)
 349   (:shadowing-import-from :lisp-stat-object-system
 350                           call-method call-next-method)
 351   (:export
 352    ;; generic structures
 353    ;; Variables
 354    empirical-statistical-variable
 355    modelbased-statistical-variable
 356    categorical-statistical-variable
 357    nominal-statistical-variable
 358    ordinal-statistical-variable
 359    continuous-statistical-variable
 360
 361    ordering factor-levels nobs support pdmf draw
 362    print-object
 363
 364    ;; Observations
 365    statistical-observation
 366    measurement-types record
 367    ;; XLS compat tools
 368    open-file-dialog read-data-file read-data-columns load-data
 369            load-example *variables* *ask-on-redefine*
 370            def variables savevar undef))
 371
 372 (defpackage :lisp-stat-descriptive-statistics
 373  (:use :common-lisp
 374        :lisp-matrix
 375        :lisp-stat-data
 376        :lisp-stat-math
 377        :lisp-stat-compound-data
 378        :lisp-stat-basics)
 379    (:shadowing-import-from :lisp-stat-math ;; life is a vector!
 380       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 381       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
 385       min max logand logior logxor lognot ffloor fceiling
 386       ftruncate fround signum cis)
 387    (:export mean standard-deviation variance
 388             quantile median interquartile-range
 389             fivnum sample))
 390
 391 (defpackage :lisp-stat-regression-linear
 392   (:use :common-lisp
 393         :lisp-matrix
 394         :lisp-stat-basics
 395         :lisp-stat-compound-data
 396         :lisp-stat-descriptive-statistics )
 397   (:shadowing-import-from :lisp-stat-object-system
 398                           call-method call-next-method)
 399   (:export regression-model fit-model
 400
 401            estimates covariance-matrix
 402            ;; functions for helpers
 403            lm xtxinv
 404            print-object ;; for method dispatch
 405            ))
 406
 407 (defpackage :common-lisp-statistics
 408   (:documentation "Experimentation package for LispStat.  Serious work
 409     should be packaged up as a separate but similar package to help
 410     drive reproducibility.  By this I mean, creating a
 411     data/analytics/analysis package with the minimal set of
 412     objects/packages required.")
 413   (:nicknames :cls :common-lisp-statistics :lisp-stat)
 414   (:use :common-lisp
 415
 416         ;; extern packages
 417         :xarray ;; generic reference -- internally supporting array, lol structs
 418         :listoflist
 419         :lisp-matrix ;; conversion to a more robust linalg approach
 420
 421         ;; intern packages
 422         :lisp-stat-config
 423         :lisp-stat-object-system
 424         :lisp-stat-compound-data
 425         :lisp-stat-probability
 426         :lisp-stat-types
 427         :lisp-stat-float
 428         :lisp-stat-basics
 429         :lisp-stat-data
 430
 431         :cls-data
 432         :cls-dataframe
 433         :cls-dataio
 434         :cls-datatrans
 435
 436         :lisp-stat-math
 437         :lisp-stat-descriptive-statistics
 438         :lisp-stat-regression-linear
 439         :cls-visualize
 440         ;; :cls-visualize-plplot
 441         ;; :cls-visualize-cl2d
 442         )
 443   (:shadowing-import-from :xarray slice)
 444   (:shadowing-import-from :lisp-stat-object-system
 445                           call-method call-next-method)
 446   (:shadowing-import-from :lisp-stat-math
 447         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 448         asin acos atan sinh cosh tanh asinh acosh atanh float random
 449         truncate floor ceiling round minusp zerop plusp evenp oddp
 450         < <= = /= >= >
 451         ;;complex
 452         conjugate realpart imagpart phase
 453
 454         min max
 455         logand logior logxor lognot
 456         ffloor fceiling ftruncate fround
 457         signum cis)
 458   (:export
 459    ;; lisp-stat-config:
 460    *default-path* *lsos-files* *basic-files* *ls-files*
 461    *cls-installation-home-dir* *cls-data-dir* *cls-examples-dir*
 462
 463    ;; lsobjects :
 464    defproto defproto2
 465    defmeth send proto-slot-value
 466
 467    ;; lstypes :
 468    fixnump check-nonneg-fixnum check-one-fixnum
 469    check-one-nonneg-fixnum
 470    check-one-real check-one-number
 471
 472    ;; lsmacros:
 473
 474    ;; lsfloat :
 475    machine-epsilon
 476
 477    ;; compound :
 478    compound-data-p *compound-data-proto* compound-object-p
 479    compound-data-seq compound-data-length
 480    element-list element-seq
 481    sort-data order rank
 482    recursive-map-elements map-elements
 483    repeat
 484    check-sequence
 485    get-next-element make-next-element set-next-element
 486    ;; sequencep
 487    iseq
 488    ordered-nneg-seq
 489    select which
 490    difference rseq
 491
 492    ;; lsmath.lsp
 493    ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 494    tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 495    truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 496    /= >= > ;; complex
 497    conjugate realpart imagpart phase min max
 498    logand logior logxor lognot ffloor fceiling ftruncate fround
 499    signum cis
 500
 501 #| ;; The following need to be re-found in lisp-matrix...
 502
 503    ;; matrices.lisp
 504    matrixp num-rows num-cols matmult identity-matrix diagonal row-list
 505    column-list inner-product outer-product cross-product transpose
 506    bind-columns bind-rows
 507
 508    ;; linalg.lisp
 509    chol-decomp lu-decomp lu-solve determinant inverse
 510    sv-decomp qr-decomp rcondest make-rotation spline
 511    kernel-dens kernel-smooth
 512    fft make-sweep-matrix sweep-operator ax+y eigen
 513    check-real
 514    covariance-matrix matrix print-matrix solve
 515    backsolve eigenvalues eigenvectors accumulate cumsum combine
 516    lowess
 517
 518    ;; in linalg.lisp, possibly not supported by matlisp
 519    spline kernel-dens kernel-smooth
 520
 521 |#
 522
 523    ;; optimize.lsp
 524    newtonmax nelmeadmax
 525
 526    ;; package LISPSTAT-MACROS
 527    make-rv-function make-rv-function-1
 528
 529    ;; package XARRAY
 530    xref xtype xdims xdim xdims*
 531
 532    ;; package LISTOFLIST
 533    sublists-of-same-size-p equal-listoflist transpose-listoflist
 534
 535    ;; package DATA
 536    ;; need to take this list and make it symbols...  specs could mean
 537    ;; that we process the strings in different ways?  Create such a
 538    ;; macro to enable export within this package?
 539 #|
 540    (let ((lst ()))
 541      (unlist
 542        (mapc #'symbol-for-symbol-to-string-or-symbol
 543          (do-external-symbols (s (find-package 'lisp-stat-data) lst) (push s lst))))
 544      lst)
 545 |#
 546    open-file-dialog read-data-file read-data-columns load-data
 547    load-example *variables* *ask-on-redefine*
 548    def variables savevar undef
 549    ;; dataframe
 550    dataframe-like dataframe-array make-dataframe
 551    varlabels caselabels nrows ncols
 552    dataframe-dimension dataframe-dimensons
 553    dfref dfref-case dfref-var
 554    consistent-dataframe-p
 555    dataset list-of-columns list-of-rows
 556    make-labels
 557
 558    ;; listoflist
 559    listoflist->dataframe listoflist->array listoflist->matrix-like
 560    sublists-of-same-size-p
 561
 562    ;; cls-dataio
 563    dsvstream->dataframe dsvstream->matrix dsvstream->listoflist
 564    filename.dsv->dataframe
 565
 566    ;; cls-datatrans
 567    listoflist->dataframe   dataframe->listoflist
 568    listoflist->array       array->listoflist
 569    listoflist->matrix-like matrix-like->listoflist
 570
 571
 572    ;; statistics.lsp  (descriptions, should probably be moved
 573    ;; later...?
 574    standard-deviation quantile median interquartile-range
 575    fivnum sample
 576
 577    ;; probability (dists.lisp)
 578    log-gamma set-seed
 579    uniform-rand normal-cdf normal-quant normal-dens
 580    normal-rand bivnorm-cdf cauchy-cdf cauchy-quant cauchy-dens
 581    cauchy-rand gamma-cdf gamma-quant gamma-dens gamma-rand
 582    chisq-cdf chisq-quant chisq-dens chisq-rand beta-cdf beta-quant
 583    beta-dens beta-rand t-cdf t-quant t-dens t-rand f-cdf f-quant
 584    f-dens f-rand poisson-cdf poisson-quant poisson-pmf poisson-rand
 585    binomial-cdf binomial-quant binomial-pmf binomial-rand
 586
 587    ;; Here is where we have a problem -- lispstat core should be core
 588    ;; data management and config problems, with packages providing
 589    ;; specialized extensions to LispStat, i.e. regression, nonlin
 590    ;; regression, bayesian regression via laplace approximation, etc.
 591
 592    ;; The following could be considered "recommended packages",
 593    ;; similar to the idea of the recommended packages in R.  Probably
 594    ;; we want them to do the exporting within that package, therefore
 595    ;; NOT being able to lock the "data-ish" package, but only the
 596    ;; subpackages prior to export.
 597
 598    ;; regression.lsp
 599    ;; -- linear regressin models.
 600    regression-model fit-model
 601    estimates covariance-matrix
 602
 603    regression-model-proto x y intercept sweep-matrix
 604    basis weights included total-sum-of-squares residual-sum-of-squares
 605    predictor-names response-name case-labels
 606    lm xtxinv
 607
 608    ;; nonlin.lsp
 609    ;; -- nonlinear regression models
 610    nreg-model nreg-model-proto mean-function theta-hat epsilon
 611    count-limit verbose
 612    ;; we might need something like xtxinv here?  But should be
 613    ;; encapsulated, so we use the one in regression.lisp
 614
 615    ;; bayes.lsp
 616    bayes-model bayes-model-proto bayes-internals
 617
 618    ;; plots.lisp
 619    plot-ex
 620    contour-plot-ex
 621    fn-contour-plot-ex
 622    shade-plot-ex
 623    3D-plot-ex
 624
 625    ))
 626
 627
 628 ;;;; PACKAGES FOR USEABILITY
 629
 630 (defpackage :lisp-stat-data-examples
 631   (:documentation "Example data for unittests, examples, illustrations,")
 632   (:use :common-lisp
 633         :common-lisp-statistics)
 634   (:shadowing-import-from :lisp-stat
 635                           call-method call-next-method
 636
 637       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 638       asin acos atan sinh cosh tanh asinh acosh atanh float random
 639       truncate floor ceiling round minusp zerop plusp evenp oddp
 640       < <= = /= >= > > ;; complex
 641       conjugate realpart imagpart phase
 642       min max logand logior logxor lognot ffloor fceiling
 643       ftruncate fround signum cis
 644
 645       <= float imagpart)
 646   (:export iron aluminum absorbtion
 647            diabetes dlabs))
 648
 649
 650 (defpackage :lisp-stat-user
 651   (:documentation "Experimentation package for LispStat.  Serious work
 652     should be placed in a similar package elsewhere for
 653     reproducibility.  But this should hint as to what needs to be done
 654     for a user- or analysis-package.")
 655   (:nicknames :ls-user :cls-user)
 656   (:use :common-lisp ; always needed for user playgrounds!
 657         :lisp-matrix
 658         :common-lisp-statistics
 659         :lisp-stat-data-examples) ;; this last is to have 'things to play with'
 660   (:shadowing-import-from :lisp-stat
 661                           call-method call-next-method
 662
 663       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 664       asin acos atan sinh cosh tanh asinh acosh atanh float random
 665       truncate floor ceiling round minusp zerop plusp evenp oddp
 666       < <= = /= >= > > ;; complex
 667       conjugate realpart imagpart phase
 668       min max logand logior logxor lognot ffloor fceiling
 669       ftruncate fround signum cis
 670
 671       <= float imagpart))
 672
 673 (defpackage :lisp-stat-unittests
 674   (:use :common-lisp
 675         :lift :lisp-matrix
 676         :lisp-stat :lisp-stat-data-examples)
 677   (:shadowing-import-from :lisp-stat
 678                           call-method call-next-method ;; objects
 679         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan ;; lsmath
 680         asin acos atan sinh cosh tanh asinh acosh atanh float random
 681         truncate floor ceiling round minusp zerop plusp evenp oddp
 682         < <= = /= >= > ;; complex
 683         conjugate realpart imagpart phase
 684         min max logand logior logxor lognot ffloor fceiling
 685         ftruncate fround signum cis)
 686   (:export run-lisp-stat-tests run-lisp-stat-test scoreboard ; exec
 687            almost= almost=lists numerical=)) ; compare
 688
 689 (defpackage :cls-dataframe-example
 690   (:use :common-lisp
 691         :lift  :lisp-stat-unittests
 692         :lisp-stat-data-examples
 693         :cls-dataframe)
 694   (:export absorbtion aluminum iron))
 695
 696
 697 (defpackage :lisp-stat-optimize
 698  (:use :common-lisp
 699        :cffi
 700        :lisp-matrix
 701        :lisp-stat-ffi-int
 702        :lisp-stat-object-system
 703        :lisp-stat-types
 704        :lisp-stat-compound-data
 705        :lisp-stat-math
 706        :lisp-stat-float
 707        :lisp-stat-basics
 708 #|
 709        :lisp-stat-matrix
 710        :lisp-stat-linalg-data
 711        :lisp-stat-linalg
 712 |#
 713        )
 714  (:shadowing-import-from :lisp-stat-object-system
 715                          call-method call-next-method)
 716  (:shadowing-import-from :lisp-stat-math
 717            expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 718            asin acos atan sinh cosh tanh asinh acosh atanh float random
 719            truncate floor ceiling round minusp zerop plusp evenp oddp
 720            < <= = /= >= > complex conjugate realpart imagpart phase
 721            min max logand logior logxor lognot ffloor fceiling
 722            ftruncate fround signum cis)
 723  (:export
 724      ;; derivatives
 725      numgrad numhess
 726
 727      ;; optimization
 728      newtonmax nelmeadmax))