src/packages.lisp

   1 ;;; -*- mode: lisp -*-
   2
   3 ;;; Time-stamp: <2009-12-23 08:33:58 tony>
   4 ;;; Creation:   <2008-03-11 19:18:34 user>
   5 ;;; File:       packages.lisp
   6 ;;; Author:     AJ Rossini <blindglobe@gmail.com>
   7 ;;; Copyright:  (c)2007--2008, AJ Rossini.  BSD, LLGPL, or GPLv2, depending
   8 ;;;             on how it arrives.
   9 ;;; Purpose:    package structure description for lispstat
  10
  11 ;;; What is this talk of 'release'? Klingons do not make software
  12 ;;; 'releases'.  Our software 'escapes', leaving a bloody trail of
  13 ;;; designers and quality assurance people in its wake.
  14
  15 (in-package :cl-user)
  16
  17 ;;; Current structure, dependencies:
  18 #|
  19  (progn
  20    (ls-user :depends-on lisp-stat)
  21    (lisp-stat :depends-on '(cls-dataframe
  22                             cls-data
  23                             lisp-matrix
  24                             ))
  25    (cls-dataframe :depends-on cls-data)
  26 |#
  27
  28
  29
  30 ;;; Basics
  31
  32 #|
  33
  34   This is setup in cls.asd upon ASDF-style loading.  For any other
  35   system loader, we will need to ensure the same.
  36
  37 (defpackage :lisp-stat-config
  38   (:documentation "global settings and variables. Probably need a
  39                    localization tool as well.")
  40   (:use :common-lisp)
  41   (:export *common-lisp-stat-version*
  42            *default-path* *lsos-files* *basic-files* *ls-files*
  43
  44            *cls-data-dir* *cls-home-dir* *cls-examples-dir*))
  45
  46 |#
  47
  48 (defpackage :lisp-stat-object-system
  49   (:nicknames :ls-objects :lsos)
  50   (:use :common-lisp)
  51   (:shadow :call-method :call-next-method)
  52   (:export ls-object objectp *object* kind-of-p make-object
  53            *message-hook*
  54            *set-slot-hook* proto-slot-value self
  55            send call-next-method call-method
  56            defmeth defproto instance-slots proto-name))
  57
  58 ;;; -types and -float probably ought to be moved into a -numerics
  59 ;;; package.
  60
  61 (defpackage :lisp-stat-types
  62   (:documentation "Provides some typeing for LispStat, but is clearly
  63   a bit incomplete.")
  64   (:use :common-lisp)
  65   (:export fixnump
  66            check-nonneg-fixnum check-one-nonneg-fixnum
  67            check-one-fixnum check-one-real check-one-number))
  68
  69 (defpackage :lisp-stat-float
  70   (:use :common-lisp)
  71   (:export +stat-float-typing+ +stat-cfloat-typing+ +stat-float-template+
  72            machine-epsilon base-float makedouble
  73
  74            make-base-trans-fun-2 make-base-trans-fun
  75
  76            base-log base-exp base-expt base-sqrt base-sin base-cos
  77            base-tan base-asin base-acos base-atan base-sinh
  78            BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
  79            BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
  80            BASE-FROUND BASE-SIGNUM BASE-CIS))
  81
  82 ;;; Probably should move into cls-data package.
  83
  84 (defpackage :lisp-stat-compound-data
  85   (:use :common-lisp
  86         :lisp-stat-object-system
  87         :lisp-stat-types)
  88   (:shadowing-import-from :lisp-stat-object-system
  89                           call-next-method call-method)
  90   (:export compound-data-p *compound-data-proto*
  91            compound-object-p
  92            compound-data-seq compound-data-length
  93            element-list element-seq
  94            sort-data order rank
  95            recursive-map-elements map-elements repeat
  96            check-sequence
  97            get-next-element make-next-element set-next-element
  98            ;; sequencep
  99            iseq ordered-nneg-seq
 100            select split-list which
 101            difference rseq
 102            flatten-list))
 103
 104 (defpackage :lisp-stat-macros
 105   (:use :common-lisp
 106         :lisp-stat-compound-data)
 107   (:export make-rv-function make-rv-function-1))
 108
 109 (defpackage :lisp-stat-basics
 110     (:use :common-lisp
 111           :lisp-stat-object-system
 112           :lisp-stat-types
 113           :lisp-stat-float
 114           :lisp-stat-macros
 115           :lisp-stat-compound-data)
 116   (:shadowing-import-from :lisp-stat-object-system
 117                           call-method call-next-method)
 118   (:export permute-array sum prod count-elements mean
 119            if-else sample))
 120
 121 (defpackage :lisp-stat-float
 122   (:use :common-lisp)
 123   (:export +stat-float-typing+ +stat-cfloat-typing+ +stat-float-template+
 124            machine-epsilon base-float makedouble
 125
 126            make-base-trans-fun-2 make-base-trans-fun
 127
 128            BASE-LOG BASE-EXP BASE-EXPT BASE-SQRT BASE-SIN BASE-COS
 129            BASE-TAN BASE-ASIN BASE-ACOS BASE-ATAN BASE-SINH
 130            BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
 131            BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
 132            BASE-FROUND BASE-SIGNUM BASE-CIS))
 133
 134 (defpackage :lisp-stat-macros
 135   (:use :common-lisp
 136         :lisp-stat-compound-data)
 137   (:export make-rv-function make-rv-function-1))
 138
 139
 140 (defpackage :cls-matrix
 141   (:documentation "basic utilities for using lisp arrays as numerical
 142   matrices.  Not optimized, and must consider this slow.  Routines
 143   should be optimized, it is only that we need them first, optimize
 144   them later.")
 145   (:use :common-lisp)
 146   (:export matrixp num-rows num-cols matmult identity-matrix diagonal
 147            row-list column-list inner-product outer-product
 148            cross-product transpose bind-columns bind-rows
 149            array-data-vector vector-to-array))
 150
 151
 152 ;;; NEW CLOS STRUCTURE
 153
 154 ;; CLS-DATA contains the basic variable structure, classes, support/indexing, and mixins.
 155 ;; CLS-DATAFRAME leverages CLS-DATA, XARRAY, and LISP-MATRIX
 156 ;; CLS-DATAIO stores/saves structures
 157 ;; CLS-DATATRANS converts between structures, and from DATAFRAMES to MODEL-MATRIXES
 158
 159 (defpackage :cls-data
 160   (:use :common-lisp)
 161   (:shadowing-import-from :xarray slice)
 162   (:export
 163
 164    ))
 165
 166 ;;; cls-data... in dataframe, though.
 167 (defpackage :cls-dataframe
 168   (:use :common-lisp
 169         :cls-data
 170         :xarray
 171         :lisp-matrix)
 172   (:shadowing-import-from :xarray slice)
 173   (:export
 174    ;; generic container class for data -- if small enough
 175    ;; could be value, otherwise might be reference.
 176    dataframe-like
 177    dataframe-array
 178    make-dataframe
 179
 180    dataset
 181    list-of-columns ;; list-of-variables
 182    list-of-rows ;; list-of-observations
 183
 184    ;; accessors
 185    varlabels caselabels  nrows ncols
 186    dataframe-dimension dataframe-dimensons
 187    xref xtype xdims xdim xrank slice take carray
 188
 189
 190  ))
 191
 192 (defpackage :cls-dataio
 193   (:documentation "Data I/O and similar import technologies.")
 194   (:use :common-lisp
 195         :lisp-stat-object-system
 196         :cls-data
 197         :cls-dataframe
 198         :rsm.string)
 199   (:shadowing-import-from :lisp-stat-object-system
 200                           call-method call-next-method)
 201   (:export dsvstream->dataframe dsvstream->matrix dsvstream->listoflist))
 202
 203 (defpackage :cls-datatrans
 204   (:documentation "Data I/O and similar import technologies.")
 205   (:use :common-lisp
 206         :lisp-stat-object-system
 207         :cls-data
 208         :cls-dataframe
 209         :rsm.string)
 210   (:shadowing-import-from :lisp-stat-object-system
 211                           call-method call-next-method)
 212   (:export dsvstream->dataframe dsvstream->matrix dsvstream->listoflist
 213
 214            listoflist->dataframe
 215            listoflist->array
 216            listoflist->matrix-like
 217            filename.dsv->dataframe   ))
 218
 219 ;;;; MODELING
 220
 221 (defpackage :lisp-stat-model
 222   (:documentation "Model management for data analysis.")
 223   (:use :common-lisp
 224         :lisp-matrix)
 225   (:export
 226    ;; data structures for model and model/data combination
 227    model statistical-model analysis))
 228
 229 ;;; visualization
 230
 231 (defpackage :cls-visualize
 232   (:use :common-lisp
 233         :lisp-matrix
 234         :cls-dataframe)
 235   (:shadowing-import-from :xarray slice)
 236   )
 237
 238 #|
 239 (defpackage :cls-visualize-plplot
 240   (:use :common-lisp
 241         :lisp-matrix
 242         :cls-dataframe
 243         :cl-plplot-system)
 244   (:export
 245    ;; examples
 246    plot-ex contour-plot-ex fn-contour-plot-ex shade-plot-ex 3D-plot-ex))
 247 |#
 248
 249 ;;; USER PACKAGES
 250
 251 (defpackage :lisp-stat-ffi-int
 252   (:use :common-lisp
 253         :cffi)
 254   (:export ccl-store-integer ccl-store-double ccl-store-ptr
 255            get-buf ))
 256
 257 (defpackage :lisp-stat-probability
 258   (:use :common-lisp
 259         :cffi
 260         :lisp-stat-ffi-int
 261         :lisp-stat-macros)
 262   (:export log-gamma set-seed
 263            uniform-rand
 264            normal-cdf normal-quant normal-dens normal-rand
 265            bivnorm-cdf
 266            cauchy-cdf cauchy-quant cauchy-dens cauchy-rand
 267            gamma-cdf gamma-quant gamma-dens gamma-rand
 268            chisq-cdf chisq-quant chisq-dens chisq-rand
 269            beta-cdf beta-quant beta-dens beta-rand
 270            t-cdf t-quant t-dens t-rand
 271            f-cdf f-quant f-dens f-rand
 272            poisson-cdf poisson-quant poisson-pmf poisson-rand
 273            binomial-cdf binomial-quant binomial-pmf binomial-rand))
 274
 275
 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         :xarray ;; generic reference -- internally supporting array, lol structs
 409         :listoflist
 410         :lisp-matrix ;; conversion to a more robust linalg approach
 411         :lisp-stat-config
 412         :lisp-stat-object-system
 413         :lisp-stat-compound-data
 414         :lisp-stat-probability
 415         :lisp-stat-types
 416         :lisp-stat-float
 417         :lisp-stat-basics
 418         :lisp-stat-data
 419         :cls-dataframe
 420         :cls-data
 421         :lisp-stat-math
 422         :lisp-stat-descriptive-statistics
 423         :lisp-stat-regression-linear
 424         :cls-visualize
 425         ;; :cybertiggyr-dsv
 426         ;; :cls-visualize-plplot
 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 l   *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
 542    ;; listoflist
 543    listoflist->dataframe listoflist->array listoflist->matrix-like
 544
 545    ;; statistics.lsp  (descriptions, should probably be moved
 546    ;; later...?
 547    standard-deviation quantile median interquartile-range
 548    fivnum sample
 549
 550    ;; probability (dists.lisp)
 551    log-gamma set-seed
 552    uniform-rand normal-cdf normal-quant normal-dens
 553    normal-rand bivnorm-cdf cauchy-cdf cauchy-quant cauchy-dens
 554    cauchy-rand gamma-cdf gamma-quant gamma-dens gamma-rand
 555    chisq-cdf chisq-quant chisq-dens chisq-rand beta-cdf beta-quant
 556    beta-dens beta-rand t-cdf t-quant t-dens t-rand f-cdf f-quant
 557    f-dens f-rand poisson-cdf poisson-quant poisson-pmf poisson-rand
 558    binomial-cdf binomial-quant binomial-pmf binomial-rand
 559
 560    ;; Here is where we have a problem -- lispstat core should be core
 561    ;; data management and config problems, with packages providing
 562    ;; specialized extensions to LispStat, i.e. regression, nonlin
 563    ;; regression, bayesian regression via laplace approximation, etc.
 564
 565    ;; The following could be considered "recommended packages",
 566    ;; similar to the idea of the recommended packages in R.  Probably
 567    ;; we want them to do the exporting within that package, therefore
 568    ;; NOT being able to lock the "data-ish" package, but only the
 569    ;; subpackages prior to export.
 570
 571    ;; regression.lsp
 572    ;; -- linear regressin models.
 573    regression-model fit-model
 574    estimates covariance-matrix
 575
 576    regression-model-proto x y intercept sweep-matrix
 577    basis weights included total-sum-of-squares residual-sum-of-squares
 578    predictor-names response-name case-labels
 579    lm xtxinv
 580
 581    ;; nonlin.lsp
 582    ;; -- nonlinear regression models
 583    nreg-model nreg-model-proto mean-function theta-hat epsilon
 584    count-limit verbose
 585    ;; we might need something like xtxinv here?  But should be
 586    ;; encapsulated, so we use the one in regression.lisp
 587
 588    ;; bayes.lsp
 589    bayes-model bayes-model-proto bayes-internals
 590
 591    ;; plots.lisp
 592    plot-ex
 593    contour-plot-ex
 594    fn-contour-plot-ex
 595    shade-plot-ex
 596    3D-plot-ex
 597
 598    ))
 599
 600
 601 ;;;; PACKAGES FOR USEABILITY
 602
 603 (defpackage :lisp-stat-data-examples
 604   (:documentation "Example data for unittests, examples, illustrations,")
 605   (:use :common-lisp
 606         :common-lisp-statistics)
 607   (:shadowing-import-from :lisp-stat
 608                           call-method call-next-method
 609
 610       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 611       asin acos atan sinh cosh tanh asinh acosh atanh float random
 612       truncate floor ceiling round minusp zerop plusp evenp oddp
 613       < <= = /= >= > > ;; complex
 614       conjugate realpart imagpart phase
 615       min max logand logior logxor lognot ffloor fceiling
 616       ftruncate fround signum cis
 617
 618       <= float imagpart)
 619   (:export iron aluminum absorbtion
 620            diabetes dlabs))
 621
 622
 623 (defpackage :lisp-stat-user
 624   (:documentation "Experimentation package for LispStat.  Serious work
 625     should be placed in a similar package elsewhere for
 626     reproducibility.  But this should hint as to what needs to be done
 627     for a user- or analysis-package.")
 628   (:nicknames :ls-user :cls-user)
 629   (:use :common-lisp ; always needed for user playgrounds!
 630         :lisp-matrix
 631         :common-lisp-statistics
 632         :lisp-stat-data-examples) ;; this last is to have 'things to play with'
 633   (:shadowing-import-from :lisp-stat
 634                           call-method call-next-method
 635
 636       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 637       asin acos atan sinh cosh tanh asinh acosh atanh float random
 638       truncate floor ceiling round minusp zerop plusp evenp oddp
 639       < <= = /= >= > > ;; complex
 640       conjugate realpart imagpart phase
 641       min max logand logior logxor lognot ffloor fceiling
 642       ftruncate fround signum cis
 643
 644       <= float imagpart))
 645
 646 (defpackage :lisp-stat-unittests
 647   (:use :common-lisp
 648         :lift :lisp-matrix
 649         :lisp-stat :lisp-stat-data-examples)
 650   (:shadowing-import-from :lisp-stat
 651                           call-method call-next-method ;; objects
 652         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan ;; lsmath
 653         asin acos atan sinh cosh tanh asinh acosh atanh float random
 654         truncate floor ceiling round minusp zerop plusp evenp oddp
 655         < <= = /= >= > ;; complex
 656         conjugate realpart imagpart phase
 657         min max logand logior logxor lognot ffloor fceiling
 658         ftruncate fround signum cis)
 659   (:export run-lisp-stat-tests run-lisp-stat-test scoreboard ; exec
 660            almost= almost=lists numerical=)) ; compare
 661
 662 (defpackage :cls-dataframe-example
 663   (:use :common-lisp
 664         :lift  :lisp-stat-unittests
 665         :lisp-stat-data-examples
 666         :cls-dataframe)
 667   (:export absorbtion aluminum iron))
 668
 669
 670 (defpackage :lisp-stat-optimize
 671  (:use :common-lisp
 672        :cffi
 673        :lisp-matrix
 674        :lisp-stat-ffi-int
 675        :lisp-stat-object-system
 676        :lisp-stat-types
 677        :lisp-stat-compound-data
 678        :lisp-stat-math
 679        :lisp-stat-float
 680        :lisp-stat-basics
 681 #|
 682        :lisp-stat-matrix
 683        :lisp-stat-linalg-data
 684        :lisp-stat-linalg
 685 |#
 686        )
 687  (:shadowing-import-from :lisp-stat-object-system
 688                          call-method call-next-method)
 689  (:shadowing-import-from :lisp-stat-math
 690            expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 691            asin acos atan sinh cosh tanh asinh acosh atanh float random
 692            truncate floor ceiling round minusp zerop plusp evenp oddp
 693            < <= = /= >= > complex conjugate realpart imagpart phase
 694            min max logand logior logxor lognot ffloor fceiling
 695            ftruncate fround signum cis)
 696  (:export
 697      ;; derivatives
 698      numgrad numhess
 699
 700      ;; optimization
 701      newtonmax nelmeadmax))