3 ;;; Time-stamp: <2009-07-12 07:56:44 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--2008, AJ Rossini. BSD, LLGPL, or GPLv2, depending
9 ;;; Purpose: package structure description for lispstat
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.
20 (defpackage :lisp-stat-object-system
21 (:nicknames
:ls-objects
:lsos
)
23 (:shadow
:call-method
:call-next-method
)
24 (:export ls-object objectp
*object
* kind-of-p make-object
26 *set-slot-hook
* proto-slot-value self
27 send call-next-method call-method
28 defmeth defproto instance-slots proto-name
))
30 (defpackage :lisp-stat-types
31 (:documentation
"Provides some typeing for LispStat, but is clearly
35 check-nonneg-fixnum check-one-nonneg-fixnum
36 check-one-fixnum check-one-real check-one-number
))
38 (defpackage :lisp-stat-float
40 (:export
+stat-float-typing
+ +stat-cfloat-typing
+ +stat-float-template
+
41 machine-epsilon base-float makedouble
43 make-base-trans-fun-2 make-base-trans-fun
45 base-log base-exp base-expt base-sqrt base-sin base-cos
46 base-tan base-asin base-acos base-atan base-sinh
47 BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
48 BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
49 BASE-FROUND BASE-SIGNUM BASE-CIS
))
51 (defpackage :lisp-stat-compound-data
53 :lisp-stat-object-system
55 (:shadowing-import-from
:lisp-stat-object-system
56 call-next-method call-method
)
57 (:export compound-data-p
*compound-data-proto
*
59 compound-data-seq compound-data-length
60 element-list element-seq
62 recursive-map-elements map-elements repeat
64 get-next-element make-next-element set-next-element
67 select split-list which
71 (defpackage :lisp-stat-macros
73 :lisp-stat-compound-data
)
74 (:export make-rv-function make-rv-function-1
))
76 (defpackage :lisp-stat-basics
78 :lisp-stat-object-system
82 :lisp-stat-compound-data
)
83 (:shadowing-import-from
:lisp-stat-object-system
84 call-method call-next-method
)
85 (:export permute-array sum prod count-elements mean
88 (defpackage :lisp-stat-float
90 (:export
+stat-float-typing
+ +stat-cfloat-typing
+ +stat-float-template
+
91 machine-epsilon base-float makedouble
93 make-base-trans-fun-2 make-base-trans-fun
95 BASE-LOG BASE-EXP BASE-EXPT BASE-SQRT BASE-SIN BASE-COS
96 BASE-TAN BASE-ASIN BASE-ACOS BASE-ATAN BASE-SINH
97 BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
98 BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
99 BASE-FROUND BASE-SIGNUM BASE-CIS
))
101 (defpackage :lisp-stat-macros
103 :lisp-stat-compound-data
)
104 (:export make-rv-function make-rv-function-1
))
106 ;;; NEW CLOS STRUCTURE
110 (defpackage :cls-dataframe
114 ;; generic container class for data -- if small enough
115 ;; could be value, otherwise might be reference.
121 varlabels caselabels nrows ncols
122 dataframe-dimension dataframe-dimensons
123 dfref dfref-case dfref-var
124 consistent-dataframe-p
127 list-of-columns
;; list-of-variables
128 list-of-rows
;; list-of-observations
132 (defpackage :cls-data-listoflist
135 :cls-dataframe
) ; for dataframe
136 (:export lists-of-same-size
139 listoflist-
>dataframe
141 listoflist-
>matrix-like
))
144 (defpackage :cls-dataimport
145 (:documentation
"Data I/O and similar import technologies.")
147 :lisp-stat-object-system
151 (:shadowing-import-from
:lisp-stat-object-system
152 call-method call-next-method
)
153 (:export dsvstream-
>dataframe dsvstream-
>matrix dsvstream-
>listoflist
))
156 (defpackage :lisp-stat-model
157 (:documentation
"Model management for data analysis.")
161 ;; data structures for model and model/data combination
162 model statistical-model analysis
))
166 (defpackage :cls-visualize
172 (defpackage :cls-visualize-plplot
179 plot-ex contour-plot-ex fn-contour-plot-ex shade-plot-ex
3D-plot-ex
))
184 (defpackage :lisp-stat-ffi-int
187 (:export ccl-store-integer ccl-store-double ccl-store-ptr
190 (defpackage :lisp-stat-probability
195 (:export log-gamma set-seed
197 normal-cdf normal-quant normal-dens normal-rand
199 cauchy-cdf cauchy-quant cauchy-dens cauchy-rand
200 gamma-cdf gamma-quant gamma-dens gamma-rand
201 chisq-cdf chisq-quant chisq-dens chisq-rand
202 beta-cdf beta-quant beta-dens beta-rand
203 t-cdf t-quant t-dens t-rand
204 f-cdf f-quant f-dens f-rand
205 poisson-cdf poisson-quant poisson-pmf poisson-rand
206 binomial-cdf binomial-quant binomial-pmf binomial-rand
))
210 (defpackage :lisp-stat-math
212 :lisp-stat-object-system
214 :lisp-stat-compound-data
216 (:shadowing-import-from
:lisp-stat-object-system
217 call-method call-next-method
)
218 (:shadow 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 (:export ^
** expt
+ -
* / mod rem pmin pmax abs
1+ 1- log exp sqrt sin cos
226 tan asin acos atan sinh cosh tanh asinh acosh atanh float random
227 truncate floor ceiling round minusp zerop plusp evenp oddp
< <= =
229 conjugate realpart imagpart phase min max
230 logand logior logxor lognot ffloor fceiling ftruncate fround
232 (:documentation
"Vectorization of numerical functions"))
235 #|
;; some of this goes back in, but not all of it?
236 (defpackage :lisp-stat-linalg
243 :lisp-stat-compound-data
)
244 (:shadowing-import-from
:lisp-stat-math
245 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
246 asin acos atan sinh cosh tanh asinh acosh atanh float random
247 truncate floor ceiling round minusp zerop plusp evenp oddp
248 < <= = /= >= > complex conjugate realpart imagpart phase
249 min max logand logior logxor lognot ffloor fceiling
250 ftruncate fround signum cis
)
251 (:export chol-decomp lu-decomp lu-solve determinant inverse
252 sv-decomp qr-decomp rcondest make-rotation spline
253 kernel-dens kernel-smooth
254 fft make-sweep-matrix sweep-operator ax
+y eigen
256 check-real
;; for optimize
258 covariance-matrix matrix print-matrix solve
259 backsolve eigenvalues eigenvectors accumulate cumsum combine
267 (defpackage :lisp-stat-data
268 (:documentation
"Data management, integration, I/O, and other data technologies.")
269 (:nicknames
:ls-data
)
271 :lisp-stat-object-system
274 :lisp-stat-compound-data
)
275 (:shadowing-import-from
:lisp-stat-object-system
276 call-method call-next-method
)
277 (:export open-file-dialog read-data-file read-data-columns load-data
278 load-example
*variables
* *ask-on-redefine
*
279 def variables savevar undef
))
281 (defpackage :lisp-stat-descriptive-statistics
285 :lisp-stat-compound-data
288 (:shadowing-import-from
:lisp-stat-math
;; life is a vector!
289 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
290 asin acos atan sinh cosh tanh asinh acosh atanh float random
291 truncate floor ceiling round minusp zerop plusp evenp oddp
292 < <= = /= >= > ;; complex
293 conjugate realpart imagpart phase
294 min max logand logior logxor lognot ffloor fceiling
295 ftruncate fround signum cis
)
296 (:export standard-deviation
297 quantile median interquartile-range
301 (defpackage :lisp-stat-regression-linear
305 :lisp-stat-compound-data
306 :lisp-stat-descriptive-statistics
)
307 (:shadowing-import-from
:lisp-stat-object-system
308 call-method call-next-method
)
309 (:export regression-model fit-model
311 estimates covariance-matrix
312 ;; functions for helpers
314 print-object
;; for method dispatch
317 (defpackage :common-lisp-statistics
318 (:documentation
"Experimentation package for LispStat. Serious work
319 should be packaged up elsewhere for reproducibility. By this I
320 mean, creating a data/analytics/analysis package with the minimal
321 set of objects required.")
322 (:nicknames
:cls
:common-lisp-statistics
:lisp-stat
)
325 :lisp-stat-object-system
326 :lisp-stat-compound-data
327 :lisp-stat-probability
335 :lisp-matrix
;; conversion to a more robust linalg approach
336 :lisp-stat-descriptive-statistics
337 :lisp-stat-regression-linear
340 ;; :cls-visualize-plplot
342 (:shadowing-import-from
:lisp-stat-object-system
343 call-method call-next-method
)
344 (:shadowing-import-from
:lisp-stat-math
345 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
346 asin acos atan sinh cosh tanh asinh acosh atanh float random
347 truncate floor ceiling round minusp zerop plusp evenp oddp
350 conjugate realpart imagpart phase
353 logand logior logxor lognot
354 ffloor fceiling ftruncate fround
358 *default-path
* *lsos-files
* *basic-files
* *ls-files
*
359 *lispstat-home-dir
* *lispstat-data-dir
* *lispstat-examples-dir
*
367 fixnump check-nonneg-fixnum check-one-fixnum
368 check-one-nonneg-fixnum
369 check-one-real check-one-number
377 compound-data-p
*compound-data-proto
* compound-object-p
378 compound-data-seq compound-data-length
379 element-list element-seq
381 recursive-map-elements map-elements
384 get-next-element make-next-element set-next-element
392 ^
** expt
+ -
* / mod rem pmin pmax abs
1+ 1- log exp sqrt sin cos
393 tan asin acos atan sinh cosh tanh asinh acosh atanh float random
394 truncate floor ceiling round minusp zerop plusp evenp oddp
< <= =
396 conjugate realpart imagpart phase min max
397 logand logior logxor lognot ffloor fceiling ftruncate fround
400 #|
;; The following need to be re-found in lisp-matrix...
403 matrixp num-rows num-cols matmult identity-matrix diagonal row-list
404 column-list inner-product outer-product cross-product transpose
405 bind-columns bind-rows
408 chol-decomp lu-decomp lu-solve determinant inverse
409 sv-decomp qr-decomp rcondest make-rotation spline
410 kernel-dens kernel-smooth
411 fft make-sweep-matrix sweep-operator ax
+y eigen
413 covariance-matrix matrix print-matrix solve
414 backsolve eigenvalues eigenvectors accumulate cumsum combine
417 ;; in linalg.lisp, possibly not supported by matlisp
418 spline kernel-dens kernel-smooth
426 make-rv-function make-rv-function-1
429 xref xtype xdims xdim xdims
*
432 open-file-dialog read-data-file read-data-columns load-data
433 load-example
*variables
* *ask-on-redefine
*
434 def variables savevar undef
437 dataframe-like dataframe-array make-dataframe
438 varlabels caselabels nrows ncols
439 dataframe-dimension dataframe-dimensons
440 dfref dfref-case dfref-var
441 consistent-dataframe-p
443 list-of-columns list-of-rows
448 lists-of-same-size equal-listoflist
450 listoflist-
>dataframe listoflist-
>array listoflist-
>matrix-like
452 ;; statistics.lsp (descriptions, should probably be moved
454 standard-deviation quantile median interquartile-range
457 ;; probability (dists.lisp)
459 uniform-rand normal-cdf normal-quant normal-dens
460 normal-rand bivnorm-cdf cauchy-cdf cauchy-quant cauchy-dens
461 cauchy-rand gamma-cdf gamma-quant gamma-dens gamma-rand
462 chisq-cdf chisq-quant chisq-dens chisq-rand beta-cdf beta-quant
463 beta-dens beta-rand t-cdf t-quant t-dens t-rand f-cdf f-quant
464 f-dens f-rand poisson-cdf poisson-quant poisson-pmf poisson-rand
465 binomial-cdf binomial-quant binomial-pmf binomial-rand
467 ;; Here is where we have a problem -- lispstat core should be core
468 ;; data management and config problems, with packages providing
469 ;; specialized extensions to LispStat, i.e. regression, nonlin
470 ;; regression, bayesian regression via laplace approximation, etc.
472 ;; The following could be considered "recommended packages",
473 ;; similar to the idea of the recommended packages in R. Probably
474 ;; we want them to do the exporting within that package, therefore
475 ;; NOT being able to lock the "data-ish" package, but only the
476 ;; subpackages prior to export.
479 ;; -- linear regressin models.
480 regression-model fit-model
481 estimates covariance-matrix
483 regression-model-proto x y intercept sweep-matrix
484 basis weights included total-sum-of-squares residual-sum-of-squares
485 predictor-names response-name case-labels
489 ;; -- nonlinear regression models
490 nreg-model nreg-model-proto mean-function theta-hat epsilon
492 ;; we might need something like xtxinv here? But should be
493 ;; encapsulated, so we use the one in regression.lisp
496 bayes-model bayes-model-proto bayes-internals
508 ;;;; PACKAGES FOR USEABILITY
510 (defpackage :lisp-stat-data-examples
511 (:documentation
"Example data for unittests, examples, illustrations,")
513 :common-lisp-statistics
)
514 (:shadowing-import-from
:lisp-stat
515 call-method call-next-method
517 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
518 asin acos atan sinh cosh tanh asinh acosh atanh float random
519 truncate floor ceiling round minusp zerop plusp evenp oddp
520 < <= = /= >= > > ;; complex
521 conjugate realpart imagpart phase
522 min max logand logior logxor lognot ffloor fceiling
523 ftruncate fround signum cis
526 (:export iron aluminum absorbtion
530 (defpackage :lisp-stat-user
531 (:documentation
"Experimentation package for LispStat. Serious work
532 should be placed in a similar package elsewhere for
533 reproducibility. But this should hint as to what needs to be done
534 for a user- or analysis-package.")
535 (:nicknames
:ls-user
)
536 (:use
:common-lisp
; always needed for user playgrounds!
538 :common-lisp-statistics
539 :lisp-stat-data-examples
) ;; this last is to have 'things to play with'
540 (:shadowing-import-from
:lisp-stat
541 call-method call-next-method
543 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
544 asin acos atan sinh cosh tanh asinh acosh atanh float random
545 truncate floor ceiling round minusp zerop plusp evenp oddp
546 < <= = /= >= > > ;; complex
547 conjugate realpart imagpart phase
548 min max logand logior logxor lognot ffloor fceiling
549 ftruncate fround signum cis
553 (defpackage :lisp-stat-unittests
556 :lisp-stat
:lisp-stat-data-examples
)
557 (:shadowing-import-from
:lisp-stat
558 call-method call-next-method
;; objects
559 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
;; lsmath
560 asin acos atan sinh cosh tanh asinh acosh atanh float random
561 truncate floor ceiling round minusp zerop plusp evenp oddp
562 < <= = /= >= > ;; complex
563 conjugate realpart imagpart phase
564 min max logand logior logxor lognot ffloor fceiling
565 ftruncate fround signum cis
)
566 (:export run-lisp-stat-tests run-lisp-stat-test scoreboard
; exec
567 almost
= almost
=lists numerical
=)) ; compare
569 (defpackage :cls-dataframe-example
571 :lift
:lisp-stat-unittests
572 :lisp-stat-data-examples
574 (:export absorbtion aluminum iron
))
577 (defpackage :lisp-stat-optimize
582 :lisp-stat-object-system
584 :lisp-stat-compound-data
590 :lisp-stat-linalg-data
594 (:shadowing-import-from
:lisp-stat-object-system
595 call-method call-next-method
)
596 (:shadowing-import-from
:lisp-stat-math
597 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
598 asin acos atan sinh cosh tanh asinh acosh atanh float random
599 truncate floor ceiling round minusp zerop plusp evenp oddp
600 < <= = /= >= > complex conjugate realpart imagpart phase
601 min max logand logior logxor lognot ffloor fceiling
602 ftruncate fround signum cis
)
608 newtonmax nelmeadmax
))