src/packages.lisp

   1 ;;; -*- mode: lisp -*-
   2
   3 ;;; Time-stamp: <2008-10-03 02:38:51 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 ;;; This organization and structure is new to the 21st Century
  16 ;;; version.
  17
  18 (in-package :cl-user)
  19
  20 ;;; LispStat Basics
  21
  22 (defpackage :lisp-stat-basics
  23     (:use :common-lisp
  24           :lisp-stat-object-system
  25           :lisp-stat-types
  26           :lisp-stat-float
  27           :lisp-stat-macros
  28           :lisp-stat-compound-data)
  29   (:shadowing-import-from :lisp-stat-object-system
  30                           slot-value call-method call-next-method)
  31   (:export permute-array sum prod count-elements mean
  32            if-else sample))
  33
  34
  35 ;;;
  36
  37
  38
  39 (defpackage :lisp-stat-float
  40   (:use :common-lisp)
  41   (:export +stat-float-typing+ +stat-cfloat-typing+ +stat-float-template+
  42            machine-epsilon base-float makedouble
  43
  44            make-base-trans-fun-2 make-base-trans-fun
  45
  46            BASE-LOG BASE-EXP BASE-EXPT BASE-SQRT BASE-SIN BASE-COS
  47            BASE-TAN BASE-ASIN BASE-ACOS BASE-ATAN BASE-SINH
  48            BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
  49            BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
  50            BASE-FROUND BASE-SIGNUM BASE-CIS))
  51
  52 ;;;
  53
  54 (defpackage :lisp-stat-macros
  55   (:use :common-lisp
  56         :lisp-stat-compound-data)
  57   (:export make-rv-function make-rv-function-1))
  58
  59 ;;; NEW CLOS STRUCTURE
  60
  61 (defpackage :lisp-stat-data-clos
  62   (:use :common-lisp
  63         :lisp-matrix)
  64   (:export get-variable-matrix get-variable-vector
  65            ;; generic container class for data -- if small enough
  66            ;; could be value, otherwise might be reference.
  67            data-pointer))
  68
  69 (defpackage :lisp-stat-regression-linear-clos
  70   (:use :common-lisp
  71         :lisp-matrix
  72         :lisp-stat-data-clos)
  73   (:export regression-model))
  74
  75
  76
  77 ;;; USER PACKAGES
  78
  79 (defpackage :lisp-stat
  80     (:documentation "Experimentation package for LispStat.  Serious work
  81 should be packaged up elsewhere for reproducibility.")
  82   (:use :common-lisp
  83         :lisp-stat-object-system
  84         :lisp-stat-compound-data
  85         :lisp-stat-probability
  86         :lisp-stat-types
  87         :lisp-stat-float
  88         :lisp-stat-basics
  89         :lisp-stat-data
  90         :lisp-stat-math
  91         :lisp-stat-matrix
  92         :lisp-stat-linalg
  93         :lisp-stat-descriptive-statistics
  94         :lisp-stat-regression-linear)
  95   (:shadowing-import-from :lisp-stat-object-system
  96         slot-value call-method call-next-method)
  97   (:shadowing-import-from :lisp-stat-math
  98         expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
  99         asin acos atan sinh cosh tanh asinh acosh atanh float random
 100         truncate floor ceiling round minusp zerop plusp evenp oddp
 101         < <= = /= >= > ;;complex
 102         conjugate realpart imagpart phase
 103         min max logand logior logxor lognot ffloor fceiling
 104         ftruncate fround signum cis)
 105   (:export
 106    ;; lsobjects :
 107    defproto defproto2
 108    defmeth send
 109
 110    ;; lstypes :
 111    fixnump check-nonneg-fixnum check-one-fixnum
 112    check-one-real check-one-number
 113
 114    ;; lsmacros:
 115
 116    ;; lsfloat :
 117    machine-epsilon
 118
 119    ;; compound :
 120    compound-data-p *compound-data-proto* compound-object-p
 121    compound-data-seq compound-data-length
 122    element-list element-seq
 123    sort-data order rank
 124    recursive-map-elements map-elements
 125    repeat
 126    check-sequence
 127    get-next-element make-next-element set-next-element
 128    sequencep iseq
 129    ordered-nneg-seq
 130    select which
 131    difference rseq
 132
 133    ;; lsmath.lsp
 134    ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
 135    tan asin acos atan sinh cosh tanh asinh acosh atanh float random
 136    truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
 137    /= >= > ;; complex
 138    conjugate realpart imagpart phase min max
 139    logand logior logxor lognot ffloor fceiling ftruncate fround
 140    signum cis
 141
 142    ;; matrices.lisp
 143    matrixp num-rows num-cols matmult identity-matrix diagonal row-list
 144    column-list inner-product outer-product cross-product transpose
 145    bind-columns bind-rows
 146
 147    ;; linalg.lisp
 148    chol-decomp lu-decomp lu-solve determinant inverse
 149    sv-decomp qr-decomp rcondest make-rotation spline
 150    kernel-dens kernel-smooth
 151    fft make-sweep-matrix sweep-operator ax+y eigen
 152    check-real
 153    covariance-matrix matrix print-matrix solve
 154    backsolve eigenvalues eigenvectors accumulate cumsum combine
 155    lowess
 156
 157    ;; in linalg.lisp, possibly not supported by matlisp
 158    spline kernel-dens kernel-smooth
 159
 160    ;; optimize.lsp
 161    newtonmax nelmeadmax
 162
 163    ;; lispstat-macros
 164    make-rv-function make-rv-function-1
 165
 166    ;; data.lisp
 167    open-file-dialog read-data-file read-data-columns load-data
 168    load-example *variables* *ask-on-redefine*
 169    def variables savevar undef
 170
 171    ;; statistics.lsp
 172    standard-deviation quantile median interquartile-range
 173    fivnum sample
 174
 175    ;; dists
 176    log-gamma set-seed
 177    uniform-rand normal-cdf normal-quant normal-dens
 178    normal-rand bivnorm-cdf cauchy-cdf cauchy-quant cauchy-dens
 179    cauchy-rand gamma-cdf gamma-quant gamma-dens gamma-rand
 180    chisq-cdf chisq-quant chisq-dens chisq-rand beta-cdf beta-quant
 181    beta-dens beta-rand t-cdf t-quant t-dens t-rand f-cdf f-quant
 182    f-dens f-rand poisson-cdf poisson-quant poisson-pmf poisson-rand
 183    binomial-cdf binomial-quant binomial-pmf binomial-rand
 184
 185 ;;; Here is where we have a problem -- lispstat core should be core
 186 ;;; data management and config problems, with packages providing
 187 ;;; specialized extensions to LispStat, i.e. regression, nonlin
 188 ;;; regression, bayesian regression via laplace approximation, etc.
 189
 190 ;;; The following could be considered "recommended packages", similar
 191 ;;; to the idea of the recommended packages in R.
 192
 193    ;; regression.lsp
 194    regression-model regression-model-proto x y intercept sweep-matrix
 195    basis weights included total-sum-of-squares residual-sum-of-squares
 196    predictor-names response-name case-labels
 197
 198    ;; nonlin.lsp
 199    nreg-model nreg-model-proto mean-function theta-hat epsilon
 200    count-limit verbose
 201
 202    ;; bayes.lsp
 203    bayes-model bayes-model-proto bayes-internals))
 204
 205
 206
 207 (defpackage :lisp-stat-user
 208   (:documentation "Experimentation package for LispStat.
 209 Serious work should be placed in a similar package elsewhere for
 210 reproducibility.  But this should hint as to what needs to be
 211 done for a user- or analysis-package.")
 212   (:nicknames :ls-user)
 213   (:use :common-lisp
 214         :lisp-stat)
 215   (:shadowing-import-from :lisp-stat
 216       slot-value call-method call-next-method
 217
 218       expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
 219       asin acos atan sinh cosh tanh asinh acosh atanh float random
 220       truncate floor ceiling round minusp zerop plusp evenp oddp
 221       < <= = /= >= > > ;; complex
 222       conjugate realpart imagpart phase
 223       min max logand logior logxor lognot ffloor fceiling
 224       ftruncate fround signum cis
 225
 226       <= float imagpart))
 227
 228