3 ;;; Time-stamp: <2009-07-11 14:17:46 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
)
324 :lisp-stat-object-system
325 :lisp-stat-compound-data
326 :lisp-stat-probability
334 :lisp-matrix
;; conversion to a more robust linalg approach
335 :lisp-stat-descriptive-statistics
336 :lisp-stat-regression-linear
339 ;; :cls-visualize-plplot
341 (:shadowing-import-from
:lisp-stat-object-system
342 call-method call-next-method
)
343 (:shadowing-import-from
:lisp-stat-math
344 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
345 asin acos atan sinh cosh tanh asinh acosh atanh float random
346 truncate floor ceiling round minusp zerop plusp evenp oddp
349 conjugate realpart imagpart phase
352 logand logior logxor lognot
353 ffloor fceiling ftruncate fround
362 fixnump check-nonneg-fixnum check-one-fixnum
363 check-one-nonneg-fixnum
364 check-one-real check-one-number
372 compound-data-p
*compound-data-proto
* compound-object-p
373 compound-data-seq compound-data-length
374 element-list element-seq
376 recursive-map-elements map-elements
379 get-next-element make-next-element set-next-element
387 ^
** expt
+ -
* / mod rem pmin pmax abs
1+ 1- log exp sqrt sin cos
388 tan asin acos atan sinh cosh tanh asinh acosh atanh float random
389 truncate floor ceiling round minusp zerop plusp evenp oddp
< <= =
391 conjugate realpart imagpart phase min max
392 logand logior logxor lognot ffloor fceiling ftruncate fround
395 #|
;; The following need to be re-found in lisp-matrix...
398 matrixp num-rows num-cols matmult identity-matrix diagonal row-list
399 column-list inner-product outer-product cross-product transpose
400 bind-columns bind-rows
403 chol-decomp lu-decomp lu-solve determinant inverse
404 sv-decomp qr-decomp rcondest make-rotation spline
405 kernel-dens kernel-smooth
406 fft make-sweep-matrix sweep-operator ax
+y eigen
408 covariance-matrix matrix print-matrix solve
409 backsolve eigenvalues eigenvectors accumulate cumsum combine
412 ;; in linalg.lisp, possibly not supported by matlisp
413 spline kernel-dens kernel-smooth
421 make-rv-function make-rv-function-1
424 xref xtype xdims xdim xdims
*
427 open-file-dialog read-data-file read-data-columns load-data
428 load-example
*variables
* *ask-on-redefine
*
429 def variables savevar undef
432 dataframe-like dataframe-array make-dataframe
433 varlabels caselabels nrows ncols
434 dataframe-dimension dataframe-dimensons
435 dfref dfref-case dfref-var
436 consistent-dataframe-p
438 list-of-columns list-of-rows
443 lists-of-same-size equal-listoflist
445 listoflist-
>dataframe listoflist-
>array listoflist-
>matrix-like
447 ;; statistics.lsp (descriptions, should probably be moved
449 standard-deviation quantile median interquartile-range
452 ;; probability (dists.lisp)
454 uniform-rand normal-cdf normal-quant normal-dens
455 normal-rand bivnorm-cdf cauchy-cdf cauchy-quant cauchy-dens
456 cauchy-rand gamma-cdf gamma-quant gamma-dens gamma-rand
457 chisq-cdf chisq-quant chisq-dens chisq-rand beta-cdf beta-quant
458 beta-dens beta-rand t-cdf t-quant t-dens t-rand f-cdf f-quant
459 f-dens f-rand poisson-cdf poisson-quant poisson-pmf poisson-rand
460 binomial-cdf binomial-quant binomial-pmf binomial-rand
462 ;; Here is where we have a problem -- lispstat core should be core
463 ;; data management and config problems, with packages providing
464 ;; specialized extensions to LispStat, i.e. regression, nonlin
465 ;; regression, bayesian regression via laplace approximation, etc.
467 ;; The following could be considered "recommended packages",
468 ;; similar to the idea of the recommended packages in R. Probably
469 ;; we want them to do the exporting within that package, therefore
470 ;; NOT being able to lock the "data-ish" package, but only the
471 ;; subpackages prior to export.
474 ;; -- linear regressin models.
475 regression-model fit-model
476 estimates covariance-matrix
478 regression-model-proto x y intercept sweep-matrix
479 basis weights included total-sum-of-squares residual-sum-of-squares
480 predictor-names response-name case-labels
484 ;; -- nonlinear regression models
485 nreg-model nreg-model-proto mean-function theta-hat epsilon
487 ;; we might need something like xtxinv here? But should be
488 ;; encapsulated, so we use the one in regression.lisp
491 bayes-model bayes-model-proto bayes-internals
503 ;;;; PACKAGES FOR USEABILITY
505 (defpackage :lisp-stat-data-examples
506 (:documentation
"Example data for unittests, examples, illustrations,")
508 :common-lisp-statistics
)
509 (:shadowing-import-from
:lisp-stat
510 call-method call-next-method
512 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
513 asin acos atan sinh cosh tanh asinh acosh atanh float random
514 truncate floor ceiling round minusp zerop plusp evenp oddp
515 < <= = /= >= > > ;; complex
516 conjugate realpart imagpart phase
517 min max logand logior logxor lognot ffloor fceiling
518 ftruncate fround signum cis
521 (:export iron aluminum absorbtion
525 (defpackage :lisp-stat-user
526 (:documentation
"Experimentation package for LispStat. Serious work
527 should be placed in a similar package elsewhere for
528 reproducibility. But this should hint as to what needs to be done
529 for a user- or analysis-package.")
530 (:nicknames
:ls-user
)
531 (:use
:common-lisp
; always needed for user playgrounds!
533 :common-lisp-statistics
534 :lisp-stat-data-examples
) ;; this last is to have 'things to play with'
535 (:shadowing-import-from
:lisp-stat
536 call-method call-next-method
538 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
539 asin acos atan sinh cosh tanh asinh acosh atanh float random
540 truncate floor ceiling round minusp zerop plusp evenp oddp
541 < <= = /= >= > > ;; complex
542 conjugate realpart imagpart phase
543 min max logand logior logxor lognot ffloor fceiling
544 ftruncate fround signum cis
548 (defpackage :lisp-stat-unittests
551 :lisp-stat
:lisp-stat-data-examples
)
552 (:shadowing-import-from
:lisp-stat
553 call-method call-next-method
;; objects
554 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
;; lsmath
555 asin acos atan sinh cosh tanh asinh acosh atanh float random
556 truncate floor ceiling round minusp zerop plusp evenp oddp
557 < <= = /= >= > ;; complex
558 conjugate realpart imagpart phase
559 min max logand logior logxor lognot ffloor fceiling
560 ftruncate fround signum cis
)
561 (:export run-lisp-stat-tests run-lisp-stat-test scoreboard
; exec
562 almost
= almost
=lists numerical
=)) ; compare
564 (defpackage :cls-dataframe-example
566 :lift
:lisp-stat-unittests
567 :lisp-stat-data-examples
569 (:export absorbtion aluminum iron
))
572 (defpackage :lisp-stat-optimize
577 :lisp-stat-object-system
579 :lisp-stat-compound-data
585 :lisp-stat-linalg-data
589 (:shadowing-import-from
:lisp-stat-object-system
590 call-method call-next-method
)
591 (:shadowing-import-from
:lisp-stat-math
592 expt
+ -
* / ** mod rem abs
1+ 1- log exp sqrt sin cos tan
593 asin acos atan sinh cosh tanh asinh acosh atanh float random
594 truncate floor ceiling round minusp zerop plusp evenp oddp
595 < <= = /= >= > complex conjugate realpart imagpart phase
596 min max logand logior logxor lognot ffloor fceiling
597 ftruncate fround signum cis
)
603 newtonmax nelmeadmax
))