3 ;;; Time-stamp: <2009-06-23 07:52:13 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 :lisp-stat
318 (:documentation
"Experimentation package for LispStat. Serious
319 work should be packaged up elsewhere for reproducibility. By this
320 I mean, creating a data/analytics/analysis package with the
321 minimal set of objects required.")
323 :lisp-stat-object-system
324 :lisp-stat-compound-data
325 :lisp-stat-probability
333 :lisp-matrix
;; conversion to a more robust linalg approach
334 :lisp-stat-descriptive-statistics
335 :lisp-stat-regression-linear
338 ;; :cls-visualize-plplot
340 (:shadowing-import-from
:lisp-stat-object-system
341 call-method call-next-method
)
342 (:shadowing-import-from
:lisp-stat-math
343 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
344 asin acos atan sinh cosh tanh asinh acosh atanh float random
345 truncate floor ceiling round minusp zerop plusp evenp oddp
348 conjugate realpart imagpart phase
351 logand logior logxor lognot
352 ffloor fceiling ftruncate fround
361 fixnump check-nonneg-fixnum check-one-fixnum
362 check-one-nonneg-fixnum
363 check-one-real check-one-number
371 compound-data-p
*compound-data-proto
* compound-object-p
372 compound-data-seq compound-data-length
373 element-list element-seq
375 recursive-map-elements map-elements
378 get-next-element make-next-element set-next-element
386 ^
** expt
+ -
* / mod rem pmin pmax abs
1+ 1- log exp sqrt sin cos
387 tan asin acos atan sinh cosh tanh asinh acosh atanh float random
388 truncate floor ceiling round minusp zerop plusp evenp oddp
< <= =
390 conjugate realpart imagpart phase min max
391 logand logior logxor lognot ffloor fceiling ftruncate fround
394 #|
;; The following need to be re-found in lisp-matrix...
397 matrixp num-rows num-cols matmult identity-matrix diagonal row-list
398 column-list inner-product outer-product cross-product transpose
399 bind-columns bind-rows
402 chol-decomp lu-decomp lu-solve determinant inverse
403 sv-decomp qr-decomp rcondest make-rotation spline
404 kernel-dens kernel-smooth
405 fft make-sweep-matrix sweep-operator ax
+y eigen
407 covariance-matrix matrix print-matrix solve
408 backsolve eigenvalues eigenvectors accumulate cumsum combine
411 ;; in linalg.lisp, possibly not supported by matlisp
412 spline kernel-dens kernel-smooth
420 make-rv-function make-rv-function-1
423 xref xtype xdims xdim xdims
*
426 open-file-dialog read-data-file read-data-columns load-data
427 load-example
*variables
* *ask-on-redefine
*
428 def variables savevar undef
431 dataframe-like dataframe-array make-dataframe
432 varlabels caselabels nrows ncols
433 dataframe-dimension dataframe-dimensons
434 dfref dfref-case dfref-var
435 consistent-dataframe-p
437 list-of-columns list-of-rows
442 lists-of-same-size equal-listoflist
444 listoflist-
>dataframe listoflist-
>array listoflist-
>matrix-like
446 ;; statistics.lsp (descriptions, should probably be moved
448 standard-deviation quantile median interquartile-range
451 ;; probability (dists.lisp)
453 uniform-rand normal-cdf normal-quant normal-dens
454 normal-rand bivnorm-cdf cauchy-cdf cauchy-quant cauchy-dens
455 cauchy-rand gamma-cdf gamma-quant gamma-dens gamma-rand
456 chisq-cdf chisq-quant chisq-dens chisq-rand beta-cdf beta-quant
457 beta-dens beta-rand t-cdf t-quant t-dens t-rand f-cdf f-quant
458 f-dens f-rand poisson-cdf poisson-quant poisson-pmf poisson-rand
459 binomial-cdf binomial-quant binomial-pmf binomial-rand
461 ;; Here is where we have a problem -- lispstat core should be core
462 ;; data management and config problems, with packages providing
463 ;; specialized extensions to LispStat, i.e. regression, nonlin
464 ;; regression, bayesian regression via laplace approximation, etc.
466 ;; The following could be considered "recommended packages",
467 ;; similar to the idea of the recommended packages in R. Probably
468 ;; we want them to do the exporting within that package, therefore
469 ;; NOT being able to lock the "data-ish" package, but only the
470 ;; subpackages prior to export.
473 ;; -- linear regressin models.
474 regression-model fit-model
475 estimates covariance-matrix
477 regression-model-proto x y intercept sweep-matrix
478 basis weights included total-sum-of-squares residual-sum-of-squares
479 predictor-names response-name case-labels
483 ;; -- nonlinear regression models
484 nreg-model nreg-model-proto mean-function theta-hat epsilon
486 ;; we might need something like xtxinv here? But should be
487 ;; encapsulated, so we use the one in regression.lisp
490 bayes-model bayes-model-proto bayes-internals
502 ;;;; PACKAGES FOR USEABILITY
504 (defpackage :lisp-stat-data-examples
505 (:documentation
"Example data for unittests, examples, illustrations,")
508 (:shadowing-import-from
:lisp-stat
509 call-method call-next-method
511 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
512 asin acos atan sinh cosh tanh asinh acosh atanh float random
513 truncate floor ceiling round minusp zerop plusp evenp oddp
514 < <= = /= >= > > ;; complex
515 conjugate realpart imagpart phase
516 min max logand logior logxor lognot ffloor fceiling
517 ftruncate fround signum cis
520 (:export iron aluminum absorbtion
524 (defpackage :lisp-stat-user
525 (:documentation
"Experimentation package for LispStat.
526 Serious work should be placed in a similar package elsewhere for
527 reproducibility. But this should hint as to what needs to be
528 done for a user- or analysis-package.")
529 (:nicknames
:ls-user
)
533 :lisp-stat-data-examples
) ;; this last is to have 'things to play with'
534 (:shadowing-import-from
:lisp-stat
535 call-method call-next-method
537 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
538 asin acos atan sinh cosh tanh asinh acosh atanh float random
539 truncate floor ceiling round minusp zerop plusp evenp oddp
540 < <= = /= >= > > ;; complex
541 conjugate realpart imagpart phase
542 min max logand logior logxor lognot ffloor fceiling
543 ftruncate fround signum cis
547 (defpackage :lisp-stat-unittests
550 :lisp-stat
:lisp-stat-data-examples
)
551 (:shadowing-import-from
:lisp-stat
552 call-method call-next-method
;; objects
553 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
;; lsmath
554 asin acos atan sinh cosh tanh asinh acosh atanh float random
555 truncate floor ceiling round minusp zerop plusp evenp oddp
556 < <= = /= >= > ;; complex
557 conjugate realpart imagpart phase
558 min max logand logior logxor lognot ffloor fceiling
559 ftruncate fround signum cis
)
560 (:export run-lisp-stat-tests run-lisp-stat-test scoreboard
; exec
561 almost
= almost
=lists numerical
=)) ; compare
563 (defpackage :cls-dataframe-example
565 :lift
:lisp-stat-unittests
566 :lisp-stat-data-examples
568 (:export absorbtion aluminum iron
))
571 (defpackage :lisp-stat-optimize
576 :lisp-stat-object-system
578 :lisp-stat-compound-data
584 :lisp-stat-linalg-data
588 (:shadowing-import-from
:lisp-stat-object-system
589 call-method call-next-method
)
590 (:shadowing-import-from
:lisp-stat-math
591 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
592 asin acos atan sinh cosh tanh asinh acosh atanh float random
593 truncate floor ceiling round minusp zerop plusp evenp oddp
594 < <= = /= >= > complex conjugate realpart imagpart phase
595 min max logand logior logxor lognot ffloor fceiling
596 ftruncate fround signum cis
)
602 newtonmax nelmeadmax
))