TODO.lisp

   1 ;;; -*- mode: lisp -*-
   2
   3 ;;; Time-stamp: <2009-01-03 19:36:11 tony>
   4 ;;; Creation:   <2008-09-08 08:06:30 tony>
   5 ;;; File:       TODO.lisp
   6 ;;; Author:     AJ Rossini <blindglobe@gmail.com>
   7 ;;; Copyright:  (c) 2007-2008, AJ Rossini <blindglobe@gmail.com>.  BSD.
   8 ;;; Purpose:    Stuff that needs to be made working sits inside the progns...
   9
  10 ;;; What is this talk of 'release'? Klingons do not make software
  11 ;;; 'releases'.  Our software 'escapes', leaving a bloody trail of
  12 ;;; designers and quality assurance people in its wake.
  13
  14 ;;; This file contains the current challenges to solve, including a
  15 ;;; description of the setup and the work to solve....
  16
  17 ;;; SET UP
  18
  19 (in-package :cl-user)
  20 ;;(asdf:oos 'asdf:compile-op 'lispstat)
  21 ;;(asdf:oos 'asdf:load-op 'lispstat)
  22
  23
  24 (in-package :lisp-stat-unittests)
  25
  26 (describe (run-tests :suite 'lisp-stat-ut))
  27 (run-tests :suite 'lisp-stat-ut)
  28
  29 ;; tests = 54, failures = 7, errors = 3
  30
  31 (in-package :ls-user)
  32
  33 ;;; FIXME: Example: currently not relevant, yet
  34 #|
  35   (describe
  36     (lift::run-test
  37       :test-case  'lisp-stat-unittests::create-proto
  38       :suite 'lisp-stat-unittests::lisp-stat-ut-proto))
  39 |#
  40
  41 :;; FIXME: data frames and structural inheritance
  42 ;;
  43 ;; Serious flaw -- need to consider that we are not really well
  44 ;; working with the data structures, in that Luke created compound as
  45 ;; a base class, which turns out to be slightly backward if we are to
  46 ;; maintain the numerical structures as well as computational
  47 ;; efficiency.
  48
  49
  50 #+nil
  51 (progn ;; FIXME: Regression modeling
  52
  53   (defparameter m nil
  54     "holding variable.")
  55   ;; need to make vectors and matrices from the lists...
  56
  57   (def m (regression-model (list->vector-like iron)
  58                            (list->vector-like absorbtion) :print nil)) ;;Good
  59   (def m (regression-model (list->vector-like iron)
  60                            (list->vector-like absorbtion)))
  61
  62   (def m (regression-model (listoflists->matrix-like  (list iron aluminum))
  63                            (list->vector-like  absorbtion) :print nil))
  64
  65   (defparameter *indep-vars-1-matrix*
  66     (make-matrix 1 (length iron)
  67                  :initial-contents
  68                  (list (mapcar #'(lambda (x) (coerce x 'double-float))
  69                                iron))))
  70   ;; *indep-vars-1-matrix*
  71
  72   (defparameter *indep-vars-2-matrix*
  73     (make-matrix 2 (length iron)
  74                  :initial-contents
  75                  (list
  76                   (mapcar #'(lambda (x) (coerce x 'double-float))
  77                           iron)
  78                   (mapcar #'(lambda (x) (coerce x 'double-float))
  79                           aluminum))))
  80   ;; *indep-vars-2-matrix*
  81
  82
  83   ;; FAILS due to coercion issues; it just isn't lispy, it's R'y.
  84   ;; (defparameter *dep-var* (make-vector (length absorbtion)
  85   ;;                                 :initial-contents (list absorbtion)))
  86   ;; BUT this should be the right type.
  87   (defparameter *dep-var*
  88     (make-vector (length absorbtion)
  89                  :type :row
  90                  :initial-contents
  91                  (list
  92                   (mapcar #'(lambda (x) (coerce x 'double-float))
  93                           absorbtion))))
  94   ;; *dep-var*
  95
  96
  97   (defparameter *dep-var-int*
  98     (make-vector (length absorbtion)
  99                  :type :row
 100                  :element-type 'integer
 101                  :initial-contents (list absorbtion)))
 102
 103   (typep *dep-var* 'matrix-like)        ; => T
 104   (typep *dep-var* 'vector-like)        ; => T
 105
 106   (typep *indep-vars-1-matrix* 'matrix-like) ; => T
 107   (typep *indep-vars-1-matrix* 'vector-like) ; => T
 108   (typep *indep-vars-2-matrix* 'matrix-like) ; => T
 109   (typep *indep-vars-2-matrix* 'vector-like) ; => F
 110
 111   (def m1 (regression-model-new *indep-vars-1-matrix* *dep-var* ))
 112   (def m2 (regression-model-new *indep-vars-2-matrix* *dep-var* ))
 113
 114   iron
 115   ;; following fails, need to ensure that we work on list elts, not just
 116   ;; elts within a list:
 117   ;; (coerce iron 'real)
 118
 119   ;; the following is a general list-conversion coercion approach -- is
 120   ;; there a more efficient way?
 121   (mapcar #'(lambda (x) (coerce x 'double-float)) iron)
 122
 123   (coerce 1 'real)
 124
 125   (send m :compute)
 126   (send m :sweep-matrix)
 127   (format t "~%~A~%" (send m :sweep-matrix))
 128
 129   ;; need to get multiple-linear regression working (simple linear regr
 130   ;; works)... to do this, we need to redo the whole numeric structure,
 131   ;; I'm keeping these in as example of brokenness...
 132
 133   (send m :basis) ;; this should be positive?
 134   (send m :coef-estimates)  )
 135
 136 #+nil
 137 (progn ;; FIXME: Need to clean up data examples, licenses, attributions, etc.
 138   ;; The following breaks because we should use a package to hold
 139   ;; configuration details, and this would be the only package outside
 140   ;; of packages.lisp, as it holds the overall defsystem structure.
 141   (load-data "iris.lsp")  ;; (the above partially fixed).
 142   (variables)
 143   diabetes )
 144
 145 #+nil
 146 (progn ;; FIXME: Data.Frames probably deserve to be related to lists --
 147   ;; either lists of cases, or lists of variables.  We probably do not
 148   ;; want to mix them, but want to be able to convert between such
 149   ;; structures.
 150
 151   (defparameter *my-case-data*
 152     '((:cases
 153        (:case1 Y Med  3.4 5)
 154        (:case2 N Low  3.2 3)
 155        (:case3 Y High 3.1 4))
 156       (:var-names (list "Response" "Level" "Pressure" "Size"))))
 157
 158   *my-case-data*
 159
 160   (elt *my-case-data* 1)
 161   (elt *my-case-data* 0)
 162   (elt *my-case-data* 2) ;; error
 163   (elt (elt *my-case-data* 0) 1)
 164   (elt (elt *my-case-data* 0) 0)
 165   (elt (elt (elt *my-case-data* 0) 1) 0)
 166   (elt (elt (elt *my-case-data* 0) 1) 1)
 167   (elt (elt (elt *my-case-data* 0) 1) 2)
 168   (elt (elt *my-case-data* 0) 3))
 169
 170 #+nil
 171 (progn ;; FIXME: read data from CSV file.  To do.
 172
 173   ;; challenge is to ensure that we get mixed arrays when we want them,
 174   ;; and single-type (simple) arrays in other cases.
 175
 176   (defparameter *csv-num* (read-csv "Data/example-num.csv" :type 'numeric))
 177   (defparameter *csv-mix* (read-csv "Data/example-mixed.csv" :type 'data))
 178
 179   ;; The handling of these types should be compariable to what we do for
 180   ;; matrices, but without the numerical processing.  i.e. mref, bind2,
 181   ;; make-dataframe, and the class structure should be similar.
 182
 183   ;; With numerical data, there should be a straightforward mapping from
 184   ;; the data.frame to a matrix.   With categorical data (including
 185   ;; dense categories such as doc-strings, as well as sparse categories
 186   ;; such as binary data), we need to include metadata about ordering,
 187   ;; coding, and such.  So the structures should probably consider
 188
 189   ;; Using the CSV file:
 190
 191   (asdf:oos 'asdf:compile-op 'csv :force t)
 192   (asdf:oos 'asdf:load-op 'parse-number)
 193   (asdf:oos 'asdf:load-op 'csv)
 194   (fare-csv:read-csv-file "Data/example-numeric.csv")
 195
 196   ;; but I think the cl-csv package is broken, need to use the dsv-style
 197   ;; package.
 198   )