3 ;;; Time-stamp: <2009-07-22 19:17:55 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 ;;; -types and -float probably ought to be moved into a -numerics
33 (defpackage :lisp-stat-types
34 (:documentation
"Provides some typeing for LispStat, but is clearly
38 check-nonneg-fixnum check-one-nonneg-fixnum
39 check-one-fixnum check-one-real check-one-number
))
41 (defpackage :lisp-stat-float
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
58 :lisp-stat-object-system
60 (:shadowing-import-from
:lisp-stat-object-system
61 call-next-method call-method
)
62 (:export compound-data-p
*compound-data-proto
*
64 compound-data-seq compound-data-length
65 element-list element-seq
67 recursive-map-elements map-elements repeat
69 get-next-element make-next-element set-next-element
72 select split-list which
76 (defpackage :lisp-stat-macros
78 :lisp-stat-compound-data
)
79 (:export make-rv-function make-rv-function-1
))
81 (defpackage :lisp-stat-basics
83 :lisp-stat-object-system
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
93 (defpackage :lisp-stat-float
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
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
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
131 (:shadowing-import-from
:xarray slice
)
133 ;; generic container class for data -- if small enough
134 ;; could be value, otherwise might be reference.
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
149 list-of-columns
;; list-of-variables
150 list-of-rows
;; list-of-observations
153 ;; move to cls-data -- but in listoflist.lisp
154 (defpackage :cls-data-listoflist
157 :cls-dataframe
) ; for dataframe
158 (:shadowing-import-from
:xarray slice
)
159 (:export lists-of-same-size
162 listoflist-
>dataframe
164 listoflist-
>matrix-like
))
167 (defpackage :cls-dataimport
168 (:documentation
"Data I/O and similar import technologies.")
170 :lisp-stat-object-system
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.")
184 ;; data structures for model and model/data combination
185 model statistical-model analysis
))
189 (defpackage :cls-visualize
193 (:shadowing-import-from
:xarray slice
)
197 (defpackage :cls-visualize-plplot
204 plot-ex contour-plot-ex fn-contour-plot-ex shade-plot-ex
3D-plot-ex
))
209 (defpackage :lisp-stat-ffi-int
212 (:export ccl-store-integer ccl-store-double ccl-store-ptr
215 (defpackage :lisp-stat-probability
220 (:export log-gamma set-seed
222 normal-cdf normal-quant normal-dens normal-rand
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
237 :lisp-stat-object-system
239 :lisp-stat-compound-data
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
< <= =
254 conjugate realpart imagpart phase min max
255 logand logior logxor lognot ffloor fceiling ftruncate fround
257 (:documentation
"Vectorization of numerical functions"))
260 #|
;; some of this goes back in, but not all of it?
261 (defpackage :lisp-stat-linalg
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
292 (defpackage :lisp-stat-data
293 (:documentation
"Data management, integration, I/O, and other data technologies.")
294 (:nicknames
:ls-data
)
296 :lisp-stat-object-system
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
311 :lisp-stat-compound-data
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
325 (defpackage :lisp-stat-regression-linear
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
338 print-object
;; for method dispatch
341 (defpackage :common-lisp-statistics
342 (:documentation
"Experimentation package for LispStat. Serious work
343 should be packaged up elsewhere for reproducibility. By this I
344 mean, creating a data/analytics/analysis package with the minimal
345 set of objects required.")
346 (:nicknames
:cls
:common-lisp-statistics
:lisp-stat
)
349 :lisp-stat-object-system
350 :lisp-stat-compound-data
351 :lisp-stat-probability
360 :lisp-matrix
;; conversion to a more robust linalg approach
361 :lisp-stat-descriptive-statistics
362 :lisp-stat-regression-linear
365 ;; :cls-visualize-plplot
367 (:shadowing-import-from
:xarray slice
)
368 (:shadowing-import-from
:lisp-stat-object-system
369 call-method call-next-method
)
370 (:shadowing-import-from
:lisp-stat-math
371 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
372 asin acos atan sinh cosh tanh asinh acosh atanh float random
373 truncate floor ceiling round minusp zerop plusp evenp oddp
376 conjugate realpart imagpart phase
379 logand logior logxor lognot
380 ffloor fceiling ftruncate fround
384 *default-path
* *lsos-files
* *basic-files
* *ls-files
*
385 *lispstat-home-dir
* *lispstat-data-dir
* *lispstat-examples-dir
*
389 defmeth send proto-slot-value
392 fixnump check-nonneg-fixnum check-one-fixnum
393 check-one-nonneg-fixnum
394 check-one-real check-one-number
402 compound-data-p
*compound-data-proto
* compound-object-p
403 compound-data-seq compound-data-length
404 element-list element-seq
406 recursive-map-elements map-elements
409 get-next-element make-next-element set-next-element
417 ^
** expt
+ -
* / mod rem pmin pmax abs
1+ 1- log exp sqrt sin cos
418 tan asin acos atan sinh cosh tanh asinh acosh atanh float random
419 truncate floor ceiling round minusp zerop plusp evenp oddp
< <= =
421 conjugate realpart imagpart phase min max
422 logand logior logxor lognot ffloor fceiling ftruncate fround
425 #|
;; The following need to be re-found in lisp-matrix...
428 matrixp num-rows num-cols matmult identity-matrix diagonal row-list
429 column-list inner-product outer-product cross-product transpose
430 bind-columns bind-rows
433 chol-decomp lu-decomp lu-solve determinant inverse
434 sv-decomp qr-decomp rcondest make-rotation spline
435 kernel-dens kernel-smooth
436 fft make-sweep-matrix sweep-operator ax
+y eigen
438 covariance-matrix matrix print-matrix solve
439 backsolve eigenvalues eigenvectors accumulate cumsum combine
442 ;; in linalg.lisp, possibly not supported by matlisp
443 spline kernel-dens kernel-smooth
451 make-rv-function make-rv-function-1
454 xref xtype xdims xdim xdims
*
457 open-file-dialog read-data-file read-data-columns load-data
458 load-example
*variables
* *ask-on-redefine
*
459 def variables savevar undef
462 dataframe-like dataframe-array make-dataframe
463 varlabels caselabels nrows ncols
464 dataframe-dimension dataframe-dimensons
465 dfref dfref-case dfref-var
466 consistent-dataframe-p
467 dataset list-of-columns list-of-rows
470 lists-of-same-size equal-listoflist
472 listoflist-
>dataframe listoflist-
>array listoflist-
>matrix-like
474 ;; statistics.lsp (descriptions, should probably be moved
476 standard-deviation quantile median interquartile-range
479 ;; probability (dists.lisp)
481 uniform-rand normal-cdf normal-quant normal-dens
482 normal-rand bivnorm-cdf cauchy-cdf cauchy-quant cauchy-dens
483 cauchy-rand gamma-cdf gamma-quant gamma-dens gamma-rand
484 chisq-cdf chisq-quant chisq-dens chisq-rand beta-cdf beta-quant
485 beta-dens beta-rand t-cdf t-quant t-dens t-rand f-cdf f-quant
486 f-dens f-rand poisson-cdf poisson-quant poisson-pmf poisson-rand
487 binomial-cdf binomial-quant binomial-pmf binomial-rand
489 ;; Here is where we have a problem -- lispstat core should be core
490 ;; data management and config problems, with packages providing
491 ;; specialized extensions to LispStat, i.e. regression, nonlin
492 ;; regression, bayesian regression via laplace approximation, etc.
494 ;; The following could be considered "recommended packages",
495 ;; similar to the idea of the recommended packages in R. Probably
496 ;; we want them to do the exporting within that package, therefore
497 ;; NOT being able to lock the "data-ish" package, but only the
498 ;; subpackages prior to export.
501 ;; -- linear regressin models.
502 regression-model fit-model
503 estimates covariance-matrix
505 regression-model-proto x y intercept sweep-matrix
506 basis weights included total-sum-of-squares residual-sum-of-squares
507 predictor-names response-name case-labels
511 ;; -- nonlinear regression models
512 nreg-model nreg-model-proto mean-function theta-hat epsilon
514 ;; we might need something like xtxinv here? But should be
515 ;; encapsulated, so we use the one in regression.lisp
518 bayes-model bayes-model-proto bayes-internals
530 ;;;; PACKAGES FOR USEABILITY
532 (defpackage :lisp-stat-data-examples
533 (:documentation
"Example data for unittests, examples, illustrations,")
535 :common-lisp-statistics
)
536 (:shadowing-import-from
:lisp-stat
537 call-method call-next-method
539 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
540 asin acos atan sinh cosh tanh asinh acosh atanh float random
541 truncate floor ceiling round minusp zerop plusp evenp oddp
542 < <= = /= >= > > ;; complex
543 conjugate realpart imagpart phase
544 min max logand logior logxor lognot ffloor fceiling
545 ftruncate fround signum cis
548 (:export iron aluminum absorbtion
552 (defpackage :lisp-stat-user
553 (:documentation
"Experimentation package for LispStat. Serious work
554 should be placed in a similar package elsewhere for
555 reproducibility. But this should hint as to what needs to be done
556 for a user- or analysis-package.")
557 (:nicknames
:ls-user
)
558 (:use
:common-lisp
; always needed for user playgrounds!
560 :common-lisp-statistics
561 :lisp-stat-data-examples
) ;; this last is to have 'things to play with'
562 (:shadowing-import-from
:lisp-stat
563 call-method call-next-method
565 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
566 asin acos atan sinh cosh tanh asinh acosh atanh float random
567 truncate floor ceiling round minusp zerop plusp evenp oddp
568 < <= = /= >= > > ;; complex
569 conjugate realpart imagpart phase
570 min max logand logior logxor lognot ffloor fceiling
571 ftruncate fround signum cis
575 (defpackage :lisp-stat-unittests
578 :lisp-stat
:lisp-stat-data-examples
)
579 (:shadowing-import-from
:lisp-stat
580 call-method call-next-method
;; objects
581 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
;; lsmath
582 asin acos atan sinh cosh tanh asinh acosh atanh float random
583 truncate floor ceiling round minusp zerop plusp evenp oddp
584 < <= = /= >= > ;; complex
585 conjugate realpart imagpart phase
586 min max logand logior logxor lognot ffloor fceiling
587 ftruncate fround signum cis
)
588 (:export run-lisp-stat-tests run-lisp-stat-test scoreboard
; exec
589 almost
= almost
=lists numerical
=)) ; compare
591 (defpackage :cls-dataframe-example
593 :lift
:lisp-stat-unittests
594 :lisp-stat-data-examples
596 (:export absorbtion aluminum iron
))
599 (defpackage :lisp-stat-optimize
604 :lisp-stat-object-system
606 :lisp-stat-compound-data
612 :lisp-stat-linalg-data
616 (:shadowing-import-from
:lisp-stat-object-system
617 call-method call-next-method
)
618 (:shadowing-import-from
:lisp-stat-math
619 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
620 asin acos atan sinh cosh tanh asinh acosh atanh float random
621 truncate floor ceiling round minusp zerop plusp evenp oddp
622 < <= = /= >= > complex conjugate realpart imagpart phase
623 min max logand logior logxor lognot ffloor fceiling
624 ftruncate fround signum cis
)
630 newtonmax nelmeadmax
))