src/packages.lisp

   1 ;;; -*- mode: lisp -*-
   2
   3 ;;; Time-stamp: <2012-10-05 04:08:40 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 ;;; Basics
  31
  32 (defpackage :lisp-stat-config
  33   (:documentation "holds Common Lisp Statistics configuration/loading variables and related functions.")
  34   (:nicknames :cls-config)
  35   (:use :common-lisp)
  36   (:export *common-lisp-stat-version*
  37            *default-path*
  38            *lsos-files* *basic-files* *ls-files*
  39            *cls-installation-home-dir* *cls-data-dir* *cls-examples-dir*))
  40
  41 (defpackage :lisp-stat-object-system
  42   (:nicknames :ls-objects :lsos)
  43   (:use :common-lisp)
  44   (:shadow :call-method :call-next-method)
  45   (:export ls-object objectp *object* kind-of-p make-object
  46            *message-hook*
  47            *set-slot-hook* proto-slot-value self
  48            send call-next-method call-method
  49            defmeth defproto instance-slots proto-name))
  50
  51 ;;; -types and -float probably ought to be moved into a -numerics
  52 ;;; package.
  53
  54 (defpackage :lisp-stat-types
  55   (:documentation "Provides some typeing for LispStat, but is clearly
  56   a bit incomplete.")
  57   (:use :common-lisp)
  58   (:export fixnump
  59            check-nonneg-fixnum check-one-nonneg-fixnum
  60            check-one-fixnum check-one-real check-one-number))
  61
  62 (defpackage :lisp-stat-float
  63   (:use :common-lisp)
  64   (:export +stat-float-typing+ +stat-cfloat-typing+ +stat-float-template+
  65            machine-epsilon base-float makedouble
  66
  67            make-base-trans-fun-2 make-base-trans-fun
  68
  69            base-log base-exp base-expt base-sqrt base-sin base-cos
  70            base-tan base-asin base-acos base-atan base-sinh
  71            BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
  72            BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
  73            BASE-FROUND BASE-SIGNUM BASE-CIS))
  74
  75 ;;; Probably should move into cls-data package.
  76
  77 (defpackage :lisp-stat-compound-data
  78   (:use :common-lisp
  79         :lisp-stat-object-system
  80         :lisp-stat-types)
  81   (:shadowing-import-from :lisp-stat-object-system
  82                           call-next-method call-method)
  83   (:export compound-data-p *compound-data-proto*
  84            compound-object-p
  85            compound-data-seq compound-data-length
  86            element-list element-seq
  87            sort-data order rank
  88            recursive-map-elements map-elements repeat
  89            check-sequence
  90            get-next-element make-next-element set-next-element
  91            ;; sequencep
  92            iseq ordered-nneg-seq
  93            select split-list which
  94            difference rseq
  95            flatten-list))
  96
  97 (defpackage :lisp-stat-macros
  98   (:use :common-lisp
  99         :lisp-stat-compound-data)
 100   (:export make-rv-function make-rv-function-1))
 101
 102 (defpackage :lisp-stat-basics
 103     (:use :common-lisp
 104           :lisp-stat-object-system
 105           :lisp-stat-types
 106           :lisp-stat-float
 107           :lisp-stat-macros
 108           :lisp-stat-compound-data)
 109   (:shadowing-import-from :lisp-stat-object-system
 110                           call-method call-next-method)
 111   (:export permute-array sum prod count-elements mean
 112            if-else sample))
 113
 114 (defpackage :lisp-stat-float
 115   (:use :common-lisp)
 116   (:export +stat-float-typing+ +stat-cfloat-typing+ +stat-float-template+
 117            machine-epsilon base-float makedouble
 118
 119            make-base-trans-fun-2 make-base-trans-fun
 120
 121            BASE-LOG BASE-EXP BASE-EXPT BASE-SQRT BASE-SIN BASE-COS
 122            BASE-TAN BASE-ASIN BASE-ACOS BASE-ATAN BASE-SINH
 123            BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
 124            BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
 125            BASE-FROUND BASE-SIGNUM BASE-CIS))
 126
 127 (defpackage :lisp-stat-macros
 128   (:use :common-lisp
 129         :lisp-stat-compound-data)
 130   (:export make-rv-function make-rv-function-1))
 131
 132 ;;;;;;;; NEw CLS structure
 133
 134 (defpackage :cls-matrix
 135   (:documentation "basic utilities for using lisp arrays as numerical
 136   matrices.  Not optimized, and must consider this slow.  Routines
 137   should be optimized, it is only that we need them first, optimize
 138   them later.")
 139   (:use :common-lisp)
 140   (:export matrixp num-rows num-cols matmult identity-matrix diagonal
 141            row-list column-list inner-product outer-product
 142            cross-product transpose bind-columns bind-rows
 143            array-data-vector vector-to-array))
 144
 145 ;;; NEW CLOS STRUCTURE
 146
 147 ;; CLS-DATA contains the basic variable structure, classes, support/indexing, and mixins.
 148 ;; CLS-DATAFRAME leverages CLS-DATA, XARRAY, and LISP-MATRIX
 149 ;; CLS-DATAIO stores/saves structures
 150 ;; CLS-DATATRANS converts between structures, and from DATAFRAMES to MODEL-MATRIXES
 151
 152 (defpackage :cls-data
 153   (:use :common-lisp)
 154   (:shadowing-import-from :xarray slice)
 155   (:export
 156    ;; must work out what is needed for stat variable metadata, support
 157    ;; functions, etc
 158    ))
 159
 160 ;;; cls-data... in dataframe, though.
 161 (defpackage :cls-dataframe
 162   (:use :common-lisp
 163         :cls-data
 164         :xarray
 165         :lisp-matrix)
 166   (:shadowing-import-from :xarray slice)
 167   (:export
 168    ;; generic container class for data -- if small enough
 169    ;; could be value, otherwise might be reference.
 170    dataframe-like
 171    dataframe-array
 172    make-dataframe
 173
 174    dataset
 175    list-of-columns ;; list-of-variables
 176    list-of-rows ;; list-of-observations
 177
 178    ;; accessors
 179    varlabels caselabels  nrows ncols
 180    dataframe-dimension dataframe-dimensons
 181    xref xtype xdims xdim xrank slice take carray
 182
 183    ;; support
 184    make-labels))
 185
 186 (defpackage :cls-dataio
 187   (:documentation "Data I/O and similar import technologies.")
 188   (:use :common-lisp
 189         :rsm.string
 190         :lisp-stat-object-system
 191         :cls-data
 192         :cls-dataframe)
 193   (:shadowing-import-from :lisp-stat-object-system
 194                           call-method call-next-method)
 195   (:export dsvstream->dataframe
 196            dsvstream->matrix
 197            dsvstream->listoflist
 198
 199            filename.dsv->dataframe))
 200
 201 (defpackage :cls-datatrans
 202   (:documentation "Data I/O and similar import technologies.")
 203   (:use :common-lisp
 204         :listoflist
 205         :lisp-stat-object-system
 206         :cls-data
 207         :cls-dataframe)
 208   (:shadowing-import-from :lisp-stat-object-system
 209                           call-method call-next-method)
 210   (:export listoflist->dataframe   dataframe->listoflist
 211            listoflist->array       array->listoflist
 212            listoflist->matrix-like matrix-like->listoflist))
 213
 214 ;;;; MODELING
 215
 216 (defpackage :lisp-stat-model
 217   (:documentation "Model management for data analysis.")
 218   (:use :common-lisp
 219         :lisp-matrix)
 220   (:export
 221    ;; data structures for model and model/data combination
 222    model statistical-model analysis))
 223
 224 ;;; visualization
 225
 226 (defpackage :cls-visualize
 227   (:use :common-lisp
 228         :lisp-matrix
 229         :cls-dataframe)
 230   (:shadowing-import-from :xarray slice)
 231   )
 232
 233 #|
 234 (defpackage :cls-visualize-plplot
 235   (:use :common-lisp
 236         :lisp-matrix
 237         :cls-dataframe
 238         :cl-plplot-system)
 239   (:export
 240    ;; examples
 241    plot-ex contour-plot-ex fn-contour-plot-ex shade-plot-ex 3D-plot-ex))
 242 |#
 243
 244 ;;; USER PACKAGES
 245
 246 ;; (defpackage :lisp-stat-ffi-int
 247 ;;   (:use :common-lisp
 248 ;;      :cffi)
 249 ;;   (:export ccl-store-integer ccl-store-double ccl-store-ptr
 250 ;;         get-buf ))
 251
 252 ;; (defpackage :lisp-stat-probability
 253 ;;   (:use :common-lisp
 254 ;;      :cffi
 255 ;;      :lisp-stat-ffi-int
 256 ;;      :lisp-stat-macros)
 257 ;;   (:export log-gamma set-seed
 258 ;;         uniform-rand
 259 ;;         normal-cdf normal-quant normal-dens normal-rand
 260 ;;         bivnorm-cdf
 261 ;;         cauchy-cdf cauchy-quant cauchy-dens cauchy-rand
 262 ;;         gamma-cdf gamma-quant gamma-dens gamma-rand
 263 ;;         chisq-cdf chisq-quant chisq-dens chisq-rand
 264 ;;         beta-cdf beta-quant beta-dens beta-rand
 265 ;;         t-cdf t-quant t-dens t-rand
 266 ;;         f-cdf f-quant f-dens f-rand
 267 ;;         poisson-cdf poisson-quant poisson-pmf poisson-rand
 268 ;;         binomial-cdf binomial-quant binomial-pmf binomial-rand))
 269
 270 (defpackage :cls-probability
 271   (:use common-lisp
 272         cl-variates
 273         )
 274   (:export probability-law distribution
 275            density-fcn quantile-fcn survivorship-fcn ))
 276
 277 (defpackage :lisp-stat-math
 278    (:use :common-lisp
 279          :lisp-stat-object-system
 280          :lisp-stat-macros
 281          :lisp-stat-compound-data
 282          :lisp-stat-float)
 283    (:shadowing-import-from :lisp-stat-object-system
 284                            call-method call-next-method)
 285    (:shadow 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 ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 293            tan 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 min max
 297            logand logior logxor lognot ffloor fceiling ftruncate fround
 298            signum cis)
 299    (:documentation "Vectorization of numerical functions"))
 300
 301
 302 #| ;; some of this goes back in, but not all of it?
 303 (defpackage :lisp-stat-linalg
 304   (:use :common-lisp
 305         :cffi
 306         :lisp-matrix
 307         :lisp-stat-math
 308         :lisp-stat-types
 309         :lisp-stat-float
 310         :lisp-stat-compound-data)
 311   (:shadowing-import-from :lisp-stat-math
 312           expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 313           asin acos atan sinh cosh tanh asinh acosh atanh float random
 314           truncate floor ceiling round minusp zerop plusp evenp oddp
 315           < <= = /= >= > complex conjugate realpart imagpart phase
 316           min max logand logior logxor lognot ffloor fceiling
 317           ftruncate fround signum cis)
 318   (:export chol-decomp lu-decomp lu-solve determinant inverse
 319            sv-decomp qr-decomp rcondest make-rotation spline
 320            kernel-dens kernel-smooth
 321            fft make-sweep-matrix sweep-operator ax+y eigen
 322
 323            check-real ;; for optimize
 324
 325            covariance-matrix matrix print-matrix solve
 326            backsolve eigenvalues eigenvectors accumulate cumsum combine
 327            lowess))
 328
 329 |#
 330
 331
 332
 333
 334 (defpackage :lisp-stat-data
 335   (:documentation "Data management, integration, I/O, and other data technologies.")
 336   (:nicknames :ls-data)
 337   (:use :common-lisp
 338         :lisp-stat-object-system
 339         :lisp-stat-config
 340         :lisp-stat-types
 341         :lisp-stat-compound-data)
 342   (:shadowing-import-from :lisp-stat-object-system
 343                           call-method call-next-method)
 344   (:export
 345    ;; generic structures
 346    ;; Variables
 347    empirical-statistical-variable
 348    modelbased-statistical-variable
 349    categorical-statistical-variable
 350    nominal-statistical-variable
 351    ordinal-statistical-variable
 352    continuous-statistical-variable
 353
 354    ordering factor-levels nobs support pdmf draw
 355    print-object
 356
 357    ;; Observations
 358    statistical-observation
 359    measurement-types record
 360    ;; XLS compat tools
 361    open-file-dialog read-data-file read-data-columns load-data
 362            load-example *variables* *ask-on-redefine*
 363            def variables savevar undef))
 364
 365 (defpackage :lisp-stat-descriptive-statistics
 366  (:use :common-lisp
 367        :lisp-matrix
 368        :lisp-stat-data
 369        :lisp-stat-math
 370        :lisp-stat-compound-data
 371        :lisp-stat-basics)
 372    (:shadowing-import-from :lisp-stat-math ;; life is a vector!
 373       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 374       asin acos atan sinh cosh tanh asinh acosh atanh float random
 375       truncate floor ceiling round minusp zerop plusp evenp oddp
 376       < <= = /= >= > ;; complex
 377       conjugate realpart imagpart phase
 378       min max logand logior logxor lognot ffloor fceiling
 379       ftruncate fround signum cis)
 380    (:export mean standard-deviation variance
 381             quantile median interquartile-range
 382             fivnum sample))
 383
 384 (defpackage :lisp-stat-regression-linear
 385   (:use :common-lisp
 386         :lisp-matrix
 387         :lisp-stat-basics
 388         :lisp-stat-compound-data
 389         :lisp-stat-descriptive-statistics )
 390   (:shadowing-import-from :lisp-stat-object-system
 391                           call-method call-next-method)
 392   (:export regression-model fit-model
 393
 394            estimates covariance-matrix
 395            ;; functions for helpers
 396            lm xtxinv
 397            print-object ;; for method dispatch
 398            ))
 399
 400 (defpackage :common-lisp-statistics
 401   (:documentation "Experimentation package for LispStat.  Serious work
 402     should be packaged up as a separate but similar package to help
 403     drive reproducibility.  By this I mean, creating a
 404     data/analytics/analysis package with the minimal set of
 405     objects/packages required.")
 406   (:nicknames :cls :common-lisp-statistics :lisp-stat)
 407   (:use :common-lisp
 408
 409         ;; extern packages
 410         :xarray ;; generic reference -- internally supporting array, lol structs
 411         :listoflist
 412         :lisp-matrix ;; conversion to a more robust linalg approach
 413
 414         ;; intern packages
 415         :lisp-stat-config
 416         :lisp-stat-object-system
 417         :lisp-stat-compound-data
 418         ;;      :lisp-stat-probability
 419         :lisp-stat-types
 420         :lisp-stat-float
 421         :lisp-stat-basics
 422         :lisp-stat-data
 423
 424         :cls-data
 425         :cls-dataframe
 426         :cls-dataio
 427         :cls-datatrans
 428
 429         :lisp-stat-math
 430         :lisp-stat-descriptive-statistics
 431         :lisp-stat-regression-linear
 432         :cls-visualize
 433         ;; :cls-visualize-plplot
 434         ;; :cls-visualize-cl2d
 435         )
 436   (:shadowing-import-from :xarray slice)
 437   (:shadowing-import-from :lisp-stat-object-system
 438                           call-method call-next-method)
 439   (:shadowing-import-from :lisp-stat-math
 440         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 441         asin acos atan sinh cosh tanh asinh acosh atanh float random
 442         truncate floor ceiling round minusp zerop plusp evenp oddp
 443         < <= = /= >= >
 444         ;;complex
 445         conjugate realpart imagpart phase
 446
 447         min max
 448         logand logior logxor lognot
 449         ffloor fceiling ftruncate fround
 450         signum cis)
 451   (:export
 452    ;; lisp-stat-config:
 453    *default-path* *lsos-files* *basic-files* *ls-files*
 454    *cls-installation-home-dir* *cls-data-dir* *cls-examples-dir*
 455
 456    ;; lsobjects :
 457    defproto defproto2
 458    defmeth send proto-slot-value
 459
 460    ;; lstypes :
 461    fixnump check-nonneg-fixnum check-one-fixnum
 462    check-one-nonneg-fixnum
 463    check-one-real check-one-number
 464
 465    ;; lsmacros:
 466
 467    ;; lsfloat :
 468    machine-epsilon
 469
 470    ;; compound :
 471    compound-data-p *compound-data-proto* compound-object-p
 472    compound-data-seq compound-data-length
 473    element-list element-seq
 474    sort-data order rank
 475    recursive-map-elements map-elements
 476    repeat
 477    check-sequence
 478    get-next-element make-next-element set-next-element
 479    ;; sequencep
 480    iseq
 481    ordered-nneg-seq
 482    select which
 483    difference rseq
 484
 485    ;; lsmath.lsp
 486    ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 487    tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 488    truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 489    /= >= > ;; complex
 490    conjugate realpart imagpart phase min max
 491    logand logior logxor lognot ffloor fceiling ftruncate fround
 492    signum cis
 493
 494 #| ;; The following need to be re-found in lisp-matrix...
 495
 496    ;; matrices.lisp
 497    matrixp num-rows num-cols matmult identity-matrix diagonal row-list
 498    column-list inner-product outer-product cross-product transpose
 499    bind-columns bind-rows
 500
 501    ;; linalg.lisp
 502    chol-decomp lu-decomp lu-solve determinant inverse
 503    sv-decomp qr-decomp rcondest make-rotation spline
 504    kernel-dens kernel-smooth
 505    fft make-sweep-matrix sweep-operator ax+y eigen
 506    check-real
 507    covariance-matrix matrix print-matrix solve
 508    backsolve eigenvalues eigenvectors accumulate cumsum combine
 509    lowess
 510
 511    ;; in linalg.lisp, possibly not supported by matlisp
 512    spline kernel-dens kernel-smooth
 513
 514 |#
 515
 516    ;; optimize.lsp
 517 ;;   newtonmax nelmeadmax
 518
 519    ;; package LISPSTAT-MACROS
 520    make-rv-function make-rv-function-1
 521
 522    ;; package XARRAY
 523    xref xtype xdims xdim xdims*
 524
 525    ;; package LISTOFLIST
 526    sublists-of-same-size-p equal-listoflist transpose-listoflist
 527
 528    ;; package DATA
 529    ;; need to take this list and make it symbols...  specs could mean
 530    ;; that we process the strings in different ways?  Create such a
 531    ;; macro to enable export within this package?
 532 #|
 533    (let ((lst ()))
 534      (unlist
 535        (mapc #'symbol-for-symbol-to-string-or-symbol
 536          (do-external-symbols (s (find-package 'lisp-stat-data) lst) (push s lst))))
 537      lst)
 538 |#
 539    open-file-dialog read-data-file read-data-columns load-data
 540    load-example *variables* *ask-on-redefine*
 541    def variables savevar undef
 542    ;; dataframe
 543    dataframe-like dataframe-array make-dataframe
 544    varlabels caselabels nrows ncols
 545    dataframe-dimension dataframe-dimensons
 546    dfref dfref-case dfref-var
 547    consistent-dataframe-p
 548    dataset list-of-columns list-of-rows
 549    make-labels
 550
 551    ;; listoflist
 552    listoflist->dataframe listoflist->array listoflist->matrix-like
 553    sublists-of-same-size-p
 554
 555    ;; cls-dataio
 556    dsvstream->dataframe dsvstream->matrix dsvstream->listoflist
 557    filename.dsv->dataframe
 558
 559    ;; cls-datatrans
 560    listoflist->dataframe   dataframe->listoflist
 561    listoflist->array       array->listoflist
 562    listoflist->matrix-like matrix-like->listoflist
 563
 564
 565    ;; statistics.lsp  (descriptions, should probably be moved
 566    ;; later...?
 567    standard-deviation quantile median interquartile-range
 568    fivnum sample
 569
 570    ;; probability (dists.lisp)
 571    ;; log-gamma set-seed
 572    ;; uniform-rand normal-cdf normal-quant normal-dens
 573    ;; normal-rand bivnorm-cdf cauchy-cdf cauchy-quant cauchy-dens
 574    ;; cauchy-rand gamma-cdf gamma-quant gamma-dens gamma-rand
 575    ;; chisq-cdf chisq-quant chisq-dens chisq-rand beta-cdf beta-quant
 576    ;; beta-dens beta-rand t-cdf t-quant t-dens t-rand f-cdf f-quant
 577    ;; f-dens f-rand poisson-cdf poisson-quant poisson-pmf poisson-rand
 578    ;; binomial-cdf binomial-quant binomial-pmf binomial-rand
 579
 580    ;; Here is where we have a problem -- lispstat core should be core
 581    ;; data management and config problems, with packages providing
 582    ;; specialized extensions to LispStat, i.e. regression, nonlin
 583    ;; regression, bayesian regression via laplace approximation, etc.
 584
 585    ;; The following could be considered "recommended packages",
 586    ;; similar to the idea of the recommended packages in R.  Probably
 587    ;; we want them to do the exporting within that package, therefore
 588    ;; NOT being able to lock the "data-ish" package, but only the
 589    ;; subpackages prior to export.
 590
 591    ;; regression.lsp
 592    ;; -- linear regressin models.
 593    regression-model fit-model
 594    estimates covariance-matrix
 595
 596    regression-model-proto x y intercept sweep-matrix
 597    basis weights included total-sum-of-squares residual-sum-of-squares
 598    predictor-names response-name case-labels
 599    lm xtxinv
 600
 601    ;; nonlin.lsp
 602    ;; -- nonlinear regression models
 603    nreg-model nreg-model-proto mean-function theta-hat epsilon
 604    count-limit verbose
 605    ;; we might need something like xtxinv here?  But should be
 606    ;; encapsulated, so we use the one in regression.lisp
 607
 608    ;; bayes.lsp
 609    bayes-model bayes-model-proto bayes-internals
 610
 611    ;; plots.lisp
 612    plot-ex
 613    contour-plot-ex
 614    fn-contour-plot-ex
 615    shade-plot-ex
 616    3D-plot-ex
 617
 618    ))
 619
 620
 621 ;;;; PACKAGES FOR USEABILITY
 622
 623 (defpackage :lisp-stat-data-examples
 624   (:documentation "Example data for unittests, examples, illustrations,")
 625   (:use :common-lisp
 626         :common-lisp-statistics)
 627   (:shadowing-import-from :lisp-stat
 628                           call-method call-next-method
 629
 630       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 631       asin acos atan sinh cosh tanh asinh acosh atanh float random
 632       truncate floor ceiling round minusp zerop plusp evenp oddp
 633       < <= = /= >= > > ;; complex
 634       conjugate realpart imagpart phase
 635       min max logand logior logxor lognot ffloor fceiling
 636       ftruncate fround signum cis
 637
 638       <= float imagpart)
 639   (:export iron aluminum absorbtion
 640            diabetes dlabs))
 641
 642
 643 (defpackage :lisp-stat-user
 644   (:documentation "Experimentation package for LispStat.  Serious work
 645     should be placed in a similar package elsewhere for
 646     reproducibility.  But this should hint as to what needs to be done
 647     for a user- or analysis-package.")
 648   (:nicknames :ls-user :cls-user)
 649   (:use :common-lisp ; always needed for user playgrounds!
 650         :lisp-matrix
 651         :common-lisp-statistics
 652         :lisp-stat-data-examples) ;; this last is to have 'things to play with'
 653   (:shadowing-import-from :lisp-stat
 654                           call-method call-next-method
 655
 656       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 657       asin acos atan sinh cosh tanh asinh acosh atanh float random
 658       truncate floor ceiling round minusp zerop plusp evenp oddp
 659       < <= = /= >= > > ;; complex
 660       conjugate realpart imagpart phase
 661       min max logand logior logxor lognot ffloor fceiling
 662       ftruncate fround signum cis
 663
 664       <= float imagpart))
 665
 666 (defpackage :lisp-stat-unittests
 667   (:use :common-lisp
 668         :lift :lisp-matrix
 669         :lisp-stat :lisp-stat-data-examples)
 670   (:shadowing-import-from :lisp-stat
 671                           call-method call-next-method ;; objects
 672         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan ;; lsmath
 673         asin acos atan sinh cosh tanh asinh acosh atanh float random
 674         truncate floor ceiling round minusp zerop plusp evenp oddp
 675         < <= = /= >= > ;; complex
 676         conjugate realpart imagpart phase
 677         min max logand logior logxor lognot ffloor fceiling
 678         ftruncate fround signum cis)
 679   (:export run-lisp-stat-tests run-lisp-stat-test scoreboard ; exec
 680            almost= almost=lists numerical=)) ; compare
 681
 682 (defpackage :cls-dataframe-example
 683   (:use :common-lisp
 684         :lift  :lisp-stat-unittests
 685         :lisp-stat-data-examples
 686         :cls-dataframe)
 687   (:export absorbtion aluminum iron))
 688
 689
 690 ;; (defpackage :lisp-stat-optimize
 691 ;;  (:use :common-lisp
 692 ;;        :cffi
 693 ;;        :lisp-matrix
 694 ;;        :lisp-stat-ffi-int
 695 ;;        :lisp-stat-object-system
 696 ;;        :lisp-stat-types
 697 ;;        :lisp-stat-compound-data
 698 ;;        :lisp-stat-math
 699 ;;        :lisp-stat-float
 700 ;;        :lisp-stat-basics
 701 ;; #|
 702 ;;        :lisp-stat-matrix
 703 ;;        :lisp-stat-linalg-data
 704 ;;        :lisp-stat-linalg
 705 ;; |#
 706 ;;        )
 707 ;;  (:shadowing-import-from :lisp-stat-object-system
 708 ;;                       call-method call-next-method)
 709 ;;  (:shadowing-import-from :lisp-stat-math
 710 ;;         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 711 ;;         asin acos atan sinh cosh tanh asinh acosh atanh float random
 712 ;;         truncate floor ceiling round minusp zerop plusp evenp oddp
 713 ;;         < <= = /= >= > complex conjugate realpart imagpart phase
 714 ;;         min max logand logior logxor lognot ffloor fceiling
 715 ;;         ftruncate fround signum cis)
 716 ;;  (:export
 717 ;;      ;; derivatives
 718 ;;      numgrad numhess
 719
 720 ;;      ;; optimization
 721 ;;      newtonmax nelmeadmax))