list-of-list packaging mods
[CommonLispStat.git] / src / packages.lisp
blob01ccb212047fd04e22c920e31aeff9d0d16688e6
1 ;;; -*- mode: lisp -*-
3 ;;; Time-stamp: <2009-08-27 08:40:10 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--2008, AJ Rossini. BSD, LLGPL, or GPLv2, depending
8 ;;; on how it arrives.
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.
15 (in-package :cl-user)
17 ;;; Basics
20 (defpackage :lisp-stat-object-system
21 (:nicknames :ls-objects :lsos)
22 (:use :common-lisp)
23 (:shadow :call-method :call-next-method)
24 (:export ls-object objectp *object* kind-of-p make-object
25 *message-hook*
26 *set-slot-hook* proto-slot-value self
27 send call-next-method call-method
28 defmeth defproto instance-slots proto-name))
30 ;;; -types and -float probably ought to be moved into a -numerics
31 ;;; package.
33 (defpackage :lisp-stat-types
34 (:documentation "Provides some typeing for LispStat, but is clearly
35 a bit incomplete.")
36 (:use :common-lisp)
37 (:export fixnump
38 check-nonneg-fixnum check-one-nonneg-fixnum
39 check-one-fixnum check-one-real check-one-number))
41 (defpackage :lisp-stat-float
42 (:use :common-lisp)
43 (:export +stat-float-typing+ +stat-cfloat-typing+ +stat-float-template+
44 machine-epsilon base-float makedouble
46 make-base-trans-fun-2 make-base-trans-fun
48 base-log base-exp base-expt base-sqrt base-sin base-cos
49 base-tan base-asin base-acos base-atan base-sinh
50 BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
51 BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
52 BASE-FROUND BASE-SIGNUM BASE-CIS))
54 ;;; Probably should move into cls-data package.
56 (defpackage :lisp-stat-compound-data
57 (:use :common-lisp
58 :lisp-stat-object-system
59 :lisp-stat-types)
60 (:shadowing-import-from :lisp-stat-object-system
61 call-next-method call-method)
62 (:export compound-data-p *compound-data-proto*
63 compound-object-p
64 compound-data-seq compound-data-length
65 element-list element-seq
66 sort-data order rank
67 recursive-map-elements map-elements repeat
68 check-sequence
69 get-next-element make-next-element set-next-element
70 ;; sequencep
71 iseq ordered-nneg-seq
72 select split-list which
73 difference rseq
74 flatten-list))
76 (defpackage :lisp-stat-macros
77 (:use :common-lisp
78 :lisp-stat-compound-data)
79 (:export make-rv-function make-rv-function-1))
81 (defpackage :lisp-stat-basics
82 (:use :common-lisp
83 :lisp-stat-object-system
84 :lisp-stat-types
85 :lisp-stat-float
86 :lisp-stat-macros
87 :lisp-stat-compound-data)
88 (:shadowing-import-from :lisp-stat-object-system
89 call-method call-next-method)
90 (:export permute-array sum prod count-elements mean
91 if-else sample))
93 (defpackage :lisp-stat-float
94 (:use :common-lisp)
95 (:export +stat-float-typing+ +stat-cfloat-typing+ +stat-float-template+
96 machine-epsilon base-float makedouble
98 make-base-trans-fun-2 make-base-trans-fun
100 BASE-LOG BASE-EXP BASE-EXPT BASE-SQRT BASE-SIN BASE-COS
101 BASE-TAN BASE-ASIN BASE-ACOS BASE-ATAN BASE-SINH
102 BASE-COSH BASE-TANH BASE-ASINH BASE-ACOSH BASE-ATANH
103 BASE-ABS BASE-PHASE BASE-FFLOOR BASE-FCEILING BASE-FTRUNCATE
104 BASE-FROUND BASE-SIGNUM BASE-CIS))
106 (defpackage :lisp-stat-macros
107 (:use :common-lisp
108 :lisp-stat-compound-data)
109 (:export make-rv-function make-rv-function-1))
112 (defpackage :cls-matrix
113 (:documentation "basic utilities for using lisp arrays as numerical
114 matrices. Not optimized, and must consider this slow. Routines
115 should be optimized, it is only that we need them first, optimize
116 them later.")
117 (:use :common-lisp)
118 (:export matrixp num-rows num-cols matmult identity-matrix diagonal
119 row-list column-list inner-product outer-product
120 cross-product transpose bind-columns bind-rows
121 array-data-vector vector-to-array))
124 ;;; NEW CLOS STRUCTURE
126 ;;; cls-data... in dataframe, though.
127 (defpackage :cls-dataframe
128 (:use :common-lisp
129 :xarray
130 :lisp-matrix)
131 (:shadowing-import-from :xarray slice)
132 (:export
133 ;; generic container class for data -- if small enough
134 ;; could be value, otherwise might be reference.
135 dataframe-like
136 dataframe-array
137 make-dataframe
139 ;; accessors
140 varlabels caselabels nrows ncols
141 dataframe-dimension dataframe-dimensons
142 xref xtype xdims xdim xrank slice take carray
144 dfref dfref-case dfref-var
145 consistent-dataframe-p
148 dataset
149 list-of-columns ;; list-of-variables
150 list-of-rows ;; list-of-observations
153 (defpackage :cls-data
154 (:use :common-lisp
155 :xarray
156 :lisp-matrix
157 :cls-dataframe) ; for dataframe
158 (:shadowing-import-from :xarray slice)
159 (:export lists-of-same-size
160 equal-listoflist
161 transpose-listoflist
162 listoflist->dataframe
163 listoflist->array
164 listoflist->matrix-like))
167 (defpackage :cls-dataimport
168 (:documentation "Data I/O and similar import technologies.")
169 (:use :common-lisp
170 :lisp-stat-object-system
171 :cls-dataframe
172 :cls-data
173 :rsm.string)
174 (:shadowing-import-from :lisp-stat-object-system
175 call-method call-next-method)
176 (:export dsvstream->dataframe dsvstream->matrix dsvstream->listoflist))
179 (defpackage :lisp-stat-model
180 (:documentation "Model management for data analysis.")
181 (:use :common-lisp
182 :lisp-matrix)
183 (:export
184 ;; data structures for model and model/data combination
185 model statistical-model analysis))
187 ;;; visualization
189 (defpackage :cls-visualize
190 (:use :common-lisp
191 :lisp-matrix
192 :cls-dataframe)
193 (:shadowing-import-from :xarray slice)
197 (defpackage :cls-visualize-plplot
198 (:use :common-lisp
199 :lisp-matrix
200 :cls-dataframe
201 :cl-plplot-system)
202 (:export
203 ;; examples
204 plot-ex contour-plot-ex fn-contour-plot-ex shade-plot-ex 3D-plot-ex))
207 ;;; USER PACKAGES
209 (defpackage :lisp-stat-ffi-int
210 (:use :common-lisp
211 :cffi)
212 (:export ccl-store-integer ccl-store-double ccl-store-ptr
213 get-buf ))
215 (defpackage :lisp-stat-probability
216 (:use :common-lisp
217 :cffi
218 :lisp-stat-ffi-int
219 :lisp-stat-macros)
220 (:export log-gamma set-seed
221 uniform-rand
222 normal-cdf normal-quant normal-dens normal-rand
223 bivnorm-cdf
224 cauchy-cdf cauchy-quant cauchy-dens cauchy-rand
225 gamma-cdf gamma-quant gamma-dens gamma-rand
226 chisq-cdf chisq-quant chisq-dens chisq-rand
227 beta-cdf beta-quant beta-dens beta-rand
228 t-cdf t-quant t-dens t-rand
229 f-cdf f-quant f-dens f-rand
230 poisson-cdf poisson-quant poisson-pmf poisson-rand
231 binomial-cdf binomial-quant binomial-pmf binomial-rand))
235 (defpackage :lisp-stat-math
236 (:use :common-lisp
237 :lisp-stat-object-system
238 :lisp-stat-macros
239 :lisp-stat-compound-data
240 :lisp-stat-float)
241 (:shadowing-import-from :lisp-stat-object-system
242 call-method call-next-method)
243 (:shadow expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
244 asin acos atan sinh cosh tanh asinh acosh atanh float random
245 truncate floor ceiling round minusp zerop plusp evenp oddp
246 < <= = /= >= > ;; complex
247 conjugate realpart imagpart phase
248 min max logand logior logxor lognot ffloor fceiling
249 ftruncate fround signum cis)
250 (:export ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
251 tan asin acos atan sinh cosh tanh asinh acosh atanh float random
252 truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
253 /= >= > ;; complex
254 conjugate realpart imagpart phase min max
255 logand logior logxor lognot ffloor fceiling ftruncate fround
256 signum cis)
257 (:documentation "Vectorization of numerical functions"))
260 #| ;; some of this goes back in, but not all of it?
261 (defpackage :lisp-stat-linalg
262 (:use :common-lisp
263 :cffi
264 :lisp-matrix
265 :lisp-stat-math
266 :lisp-stat-types
267 :lisp-stat-float
268 :lisp-stat-compound-data)
269 (:shadowing-import-from :lisp-stat-math
270 expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
271 asin acos atan sinh cosh tanh asinh acosh atanh float random
272 truncate floor ceiling round minusp zerop plusp evenp oddp
273 < <= = /= >= > complex conjugate realpart imagpart phase
274 min max logand logior logxor lognot ffloor fceiling
275 ftruncate fround signum cis)
276 (:export chol-decomp lu-decomp lu-solve determinant inverse
277 sv-decomp qr-decomp rcondest make-rotation spline
278 kernel-dens kernel-smooth
279 fft make-sweep-matrix sweep-operator ax+y eigen
281 check-real ;; for optimize
283 covariance-matrix matrix print-matrix solve
284 backsolve eigenvalues eigenvectors accumulate cumsum combine
285 lowess))
292 (defpackage :lisp-stat-data
293 (:documentation "Data management, integration, I/O, and other data technologies.")
294 (:nicknames :ls-data)
295 (:use :common-lisp
296 :lisp-stat-object-system
297 :lisp-stat-config
298 :lisp-stat-types
299 :lisp-stat-compound-data)
300 (:shadowing-import-from :lisp-stat-object-system
301 call-method call-next-method)
302 (:export open-file-dialog read-data-file read-data-columns load-data
303 load-example *variables* *ask-on-redefine*
304 def variables savevar undef))
306 (defpackage :lisp-stat-descriptive-statistics
307 (:use :common-lisp
308 :lisp-matrix
309 :lisp-stat-data
310 :lisp-stat-math
311 :lisp-stat-compound-data
312 :lisp-stat-basics)
313 (:shadowing-import-from :lisp-stat-math ;; life is a vector!
314 expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
315 asin acos atan sinh cosh tanh asinh acosh atanh float random
316 truncate floor ceiling round minusp zerop plusp evenp oddp
317 < <= = /= >= > ;; complex
318 conjugate realpart imagpart phase
319 min max logand logior logxor lognot ffloor fceiling
320 ftruncate fround signum cis)
321 (:export mean standard-deviation variance
322 quantile median interquartile-range
323 fivnum sample))
325 (defpackage :lisp-stat-regression-linear
326 (:use :common-lisp
327 :lisp-matrix
328 :lisp-stat-basics
329 :lisp-stat-compound-data
330 :lisp-stat-descriptive-statistics )
331 (:shadowing-import-from :lisp-stat-object-system
332 call-method call-next-method)
333 (:export regression-model fit-model
335 estimates covariance-matrix
336 ;; functions for helpers
337 lm xtxinv
338 print-object ;; for method dispatch
341 (defpackage :common-lisp-statistics
342 (:documentation "Experimentation package for LispStat. Serious work
343 should be packaged up as a separate but similar package to help
344 drive reproducibility. By this I mean, creating a
345 data/analytics/analysis package with the minimal set of
346 objects/packages required.")
347 (:nicknames :cls :common-lisp-statistics :lisp-stat)
348 (:use :common-lisp
349 :xarray
350 :lisp-matrix ;; conversion to a more robust linalg approach
351 :lisp-stat-config
352 :lisp-stat-object-system
353 :lisp-stat-compound-data
354 :lisp-stat-probability
355 :lisp-stat-types
356 :lisp-stat-float
357 :lisp-stat-basics
358 :lisp-stat-data
359 :cls-dataframe
360 :cls-data
361 :lisp-stat-math
362 :lisp-stat-descriptive-statistics
363 :lisp-stat-regression-linear
364 :cls-visualize
365 ;; :cybertiggyr-dsv
366 ;; :cls-visualize-plplot
368 (:shadowing-import-from :xarray slice)
369 (:shadowing-import-from :lisp-stat-object-system
370 call-method call-next-method)
371 (:shadowing-import-from :lisp-stat-math
372 expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
373 asin acos atan sinh cosh tanh asinh acosh atanh float random
374 truncate floor ceiling round minusp zerop plusp evenp oddp
375 < <= = /= >= >
376 ;;complex
377 conjugate realpart imagpart phase
379 min max
380 logand logior logxor lognot
381 ffloor fceiling ftruncate fround
382 signum cis)
383 (:export
384 ;; lisp-stat-config:
385 *default-path* *lsos-files* *basic-files* *ls-files*
386 *lispstat-home-dir* *lispstat-data-dir* *lispstat-examples-dir*
388 ;; lsobjects :
389 defproto defproto2
390 defmeth send proto-slot-value
392 ;; lstypes :
393 fixnump check-nonneg-fixnum check-one-fixnum
394 check-one-nonneg-fixnum
395 check-one-real check-one-number
397 ;; lsmacros:
399 ;; lsfloat :
400 machine-epsilon
402 ;; compound :
403 compound-data-p *compound-data-proto* compound-object-p
404 compound-data-seq compound-data-length
405 element-list element-seq
406 sort-data order rank
407 recursive-map-elements map-elements
408 repeat
409 check-sequence
410 get-next-element make-next-element set-next-element
411 ;; sequencep
412 iseq
413 ordered-nneg-seq
414 select which
415 difference rseq
417 ;; lsmath.lsp
418 ^ ** expt + - * / mod rem pmin pmax abs 1+ 1- log exp sqrt sin cos
419 tan asin acos atan sinh cosh tanh asinh acosh atanh float random
420 truncate floor ceiling round minusp zerop plusp evenp oddp < <= =
421 /= >= > ;; complex
422 conjugate realpart imagpart phase min max
423 logand logior logxor lognot ffloor fceiling ftruncate fround
424 signum cis
426 #| ;; The following need to be re-found in lisp-matrix...
428 ;; matrices.lisp
429 matrixp num-rows num-cols matmult identity-matrix diagonal row-list
430 column-list inner-product outer-product cross-product transpose
431 bind-columns bind-rows
433 ;; linalg.lisp
434 chol-decomp lu-decomp lu-solve determinant inverse
435 sv-decomp qr-decomp rcondest make-rotation spline
436 kernel-dens kernel-smooth
437 fft make-sweep-matrix sweep-operator ax+y eigen
438 check-real
439 covariance-matrix matrix print-matrix solve
440 backsolve eigenvalues eigenvectors accumulate cumsum combine
441 lowess
443 ;; in linalg.lisp, possibly not supported by matlisp
444 spline kernel-dens kernel-smooth
448 ;; optimize.lsp
449 newtonmax nelmeadmax
451 ;; lispstat-macros
452 make-rv-function make-rv-function-1
454 ;; xarray
455 xref xtype xdims xdim xdims*
457 ;; data
458 open-file-dialog read-data-file read-data-columns load-data
459 load-example *variables* *ask-on-redefine*
460 def variables savevar undef
462 ;; dataframe
463 dataframe-like dataframe-array make-dataframe
464 varlabels caselabels nrows ncols
465 dataframe-dimension dataframe-dimensons
466 dfref dfref-case dfref-var
467 consistent-dataframe-p
468 dataset list-of-columns list-of-rows
470 ;; listoflist
471 lists-of-same-size equal-listoflist
472 transpose-listoflist
473 listoflist->dataframe listoflist->array listoflist->matrix-like
475 ;; statistics.lsp (descriptions, should probably be moved
476 ;; later...?
477 standard-deviation quantile median interquartile-range
478 fivnum sample
480 ;; probability (dists.lisp)
481 log-gamma set-seed
482 uniform-rand normal-cdf normal-quant normal-dens
483 normal-rand bivnorm-cdf cauchy-cdf cauchy-quant cauchy-dens
484 cauchy-rand gamma-cdf gamma-quant gamma-dens gamma-rand
485 chisq-cdf chisq-quant chisq-dens chisq-rand beta-cdf beta-quant
486 beta-dens beta-rand t-cdf t-quant t-dens t-rand f-cdf f-quant
487 f-dens f-rand poisson-cdf poisson-quant poisson-pmf poisson-rand
488 binomial-cdf binomial-quant binomial-pmf binomial-rand
490 ;; Here is where we have a problem -- lispstat core should be core
491 ;; data management and config problems, with packages providing
492 ;; specialized extensions to LispStat, i.e. regression, nonlin
493 ;; regression, bayesian regression via laplace approximation, etc.
495 ;; The following could be considered "recommended packages",
496 ;; similar to the idea of the recommended packages in R. Probably
497 ;; we want them to do the exporting within that package, therefore
498 ;; NOT being able to lock the "data-ish" package, but only the
499 ;; subpackages prior to export.
501 ;; regression.lsp
502 ;; -- linear regressin models.
503 regression-model fit-model
504 estimates covariance-matrix
506 regression-model-proto x y intercept sweep-matrix
507 basis weights included total-sum-of-squares residual-sum-of-squares
508 predictor-names response-name case-labels
509 lm xtxinv
511 ;; nonlin.lsp
512 ;; -- nonlinear regression models
513 nreg-model nreg-model-proto mean-function theta-hat epsilon
514 count-limit verbose
515 ;; we might need something like xtxinv here? But should be
516 ;; encapsulated, so we use the one in regression.lisp
518 ;; bayes.lsp
519 bayes-model bayes-model-proto bayes-internals
521 ;; plots.lisp
522 plot-ex
523 contour-plot-ex
524 fn-contour-plot-ex
525 shade-plot-ex
526 3D-plot-ex
531 ;;;; PACKAGES FOR USEABILITY
533 (defpackage :lisp-stat-data-examples
534 (:documentation "Example data for unittests, examples, illustrations,")
535 (:use :common-lisp
536 :common-lisp-statistics)
537 (:shadowing-import-from :lisp-stat
538 call-method call-next-method
540 expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
541 asin acos atan sinh cosh tanh asinh acosh atanh float random
542 truncate floor ceiling round minusp zerop plusp evenp oddp
543 < <= = /= >= > > ;; complex
544 conjugate realpart imagpart phase
545 min max logand logior logxor lognot ffloor fceiling
546 ftruncate fround signum cis
548 <= float imagpart)
549 (:export iron aluminum absorbtion
550 diabetes dlabs))
553 (defpackage :lisp-stat-user
554 (:documentation "Experimentation package for LispStat. Serious work
555 should be placed in a similar package elsewhere for
556 reproducibility. But this should hint as to what needs to be done
557 for a user- or analysis-package.")
558 (:nicknames :ls-user)
559 (:use :common-lisp ; always needed for user playgrounds!
560 :lisp-matrix
561 :common-lisp-statistics
562 :lisp-stat-data-examples) ;; this last is to have 'things to play with'
563 (:shadowing-import-from :lisp-stat
564 call-method call-next-method
566 expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
567 asin acos atan sinh cosh tanh asinh acosh atanh float random
568 truncate floor ceiling round minusp zerop plusp evenp oddp
569 < <= = /= >= > > ;; complex
570 conjugate realpart imagpart phase
571 min max logand logior logxor lognot ffloor fceiling
572 ftruncate fround signum cis
574 <= float imagpart))
576 (defpackage :lisp-stat-unittests
577 (:use :common-lisp
578 :lift :lisp-matrix
579 :lisp-stat :lisp-stat-data-examples)
580 (:shadowing-import-from :lisp-stat
581 call-method call-next-method ;; objects
582 expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan ;; lsmath
583 asin acos atan sinh cosh tanh asinh acosh atanh float random
584 truncate floor ceiling round minusp zerop plusp evenp oddp
585 < <= = /= >= > ;; complex
586 conjugate realpart imagpart phase
587 min max logand logior logxor lognot ffloor fceiling
588 ftruncate fround signum cis)
589 (:export run-lisp-stat-tests run-lisp-stat-test scoreboard ; exec
590 almost= almost=lists numerical=)) ; compare
592 (defpackage :cls-dataframe-example
593 (:use :common-lisp
594 :lift :lisp-stat-unittests
595 :lisp-stat-data-examples
596 :cls-dataframe)
597 (:export absorbtion aluminum iron))
600 (defpackage :lisp-stat-optimize
601 (:use :common-lisp
602 :cffi
603 :lisp-matrix
604 :lisp-stat-ffi-int
605 :lisp-stat-object-system
606 :lisp-stat-types
607 :lisp-stat-compound-data
608 :lisp-stat-math
609 :lisp-stat-float
610 :lisp-stat-basics
612 :lisp-stat-matrix
613 :lisp-stat-linalg-data
614 :lisp-stat-linalg
617 (:shadowing-import-from :lisp-stat-object-system
618 call-method call-next-method)
619 (:shadowing-import-from :lisp-stat-math
620 expt + - * / ** mod rem abs 1+ 1- log exp sqrt sin cos tan
621 asin acos atan sinh cosh tanh asinh acosh atanh float random
622 truncate floor ceiling round minusp zerop plusp evenp oddp
623 < <= = /= >= > complex conjugate realpart imagpart phase
624 min max logand logior logxor lognot ffloor fceiling
625 ftruncate fround signum cis)
626 (:export
627 ;; derivatives
628 numgrad numhess
630 ;; optimization
631 newtonmax nelmeadmax))