TODO.lisp

   1 ;;; -*- mode: lisp -*-
   2
   3 ;;; Time-stamp: <2010-06-15 09:59:40 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
   9 ;;;          progns... This file contains the current challenges to
  10 ;;;          solve, including a description of the setup and the work
  11 ;;;          to solve....
  12
  13 ;;; What is this talk of 'release'? Klingons do not make software
  14 ;;; 'releases'.  Our software 'escapes', leaving a bloody trail of
  15 ;;; designers and quality assurance people in its wake.
  16
  17 ;;; SET UP
  18
  19 (in-package :cl-user)
  20
  21 (progn
  22   (defun init-CLS ()
  23
  24     ;; core system
  25     ;;(asdf:oos 'asdf:load-op 'lisp-matrix)
  26     ;;(asdf:oos 'asdf:compile-op 'cls :force t)
  27     (asdf:oos 'asdf:load-op :cls)
  28
  29     ;; visualization
  30     ;;  (asdf:oos 'asdf:load-op 'cl-cairo2-x11)
  31     ;;  (asdf:oos 'asdf:compile-op 'iterate :force t)
  32     (asdf:oos 'asdf:load-op 'iterate)
  33     ;;  (asdf:oos 'asdf:compile-op :cl-2d :force t)
  34     (asdf:oos 'asdf:load-op 'cl-2d)
  35
  36     ;; doc reporting
  37     (asdf:oos 'asdf:load-op 'cl-pdf)
  38     (asdf:oos 'asdf:load-op 'cl-typesetting))
  39
  40   ;;INFRA
  41   ;; (asdf:oos 'asdf:compile-op 'asdf-system-connections :force t)
  42   ;; (asdf:oos 'asdf:compile-op 'lisp-matrix)
  43   ;; (asdf:oos 'asdf:load-op 'xarray)
  44
  45   ;;DOCS
  46   ;;; (asdf:oos 'asdf:compile-op 'metatilities-base :force t)
  47   ;;; (asdf:oos 'asdf:load-op 'metatilities-base)
  48   ;;; (asdf:oos 'asdf:load-op 'anaphora)
  49   ;;; (asdf:oos 'asdf:load-op 'tinaa)
  50   ;;; (asdf:oos 'asdf:load-op 'cl-ppcre)
  51   ;; (asdf:oos 'asdf:load-op 'cl-markdown) ;; just need this and the next...
  52   ;; (asdf:oos 'asdf:load-op 'docudown)
  53
  54   ;;use of extension packages supporting versioning and validation of
  55   ;;CLOS objects?
  56   ;; (asdf:oos 'asdf:compile-op 'versioned-objects :force t)
  57   ;; (asdf:oos 'asdf:load-op 'versioned-objects)
  58   ;; (asdf:oos 'asdf:compile-op 'validations :force t)
  59   ;; (asdf:oos 'asdf:load-op 'validations)
  60
  61   ;;VIZ
  62   ;; (asdf:oos 'asdf:compile-op 'cffi :force t)
  63   ;; (asdf:oos 'asdf:load-op 'cl-opengl)
  64   ;; (asdf:oos 'asdf:load-op 'cl-glu)
  65   ;; (asdf:oos 'asdf:load-op 'cl-glut)
  66   ;; (asdf:oos 'asdf:load-op 'cl-glut-examples)
  67
  68   ;; (asdf:oos 'asdf:load-op 'cells)
  69   (asdf:oos 'asdf:load-op 'bordeaux-threads)
  70   ;; (asdf:oos 'asdf:load-op 'cells-gtk)
  71
  72   (init-CLS))
  73
  74 (in-package :lisp-stat-unittests)
  75
  76 ;; tests = 78, failures = 7, errors = 20
  77 (run-tests :suite 'lisp-stat-ut)
  78
  79 (asdf:oos 'asdf:test-op 'cls)
  80 ;; which runs (describe (run-tests :suite 'lisp-stat-ut))
  81
  82 (describe 'lisp-stat-ut)
  83 (documentation 'lisp-stat-ut 'type)
  84
  85 ;; FIXME: Example: currently not relevant, yet
  86 ;;   (describe (lift::run-test :test-case  'lisp-stat-unittests::create-proto
  87 ;;                             :suite 'lisp-stat-unittests::lisp-stat-ut-proto))
  88
  89 (describe (lift::run-tests :suite 'lisp-stat-ut-dataframe))
  90 (lift::run-tests :suite 'lisp-stat-ut-dataframe)
  91
  92 (describe (lift::run-test
  93            :test-case  'lisp-stat-unittests::create-proto
  94            :suite 'lisp-stat-unittests::lisp-stat-ut-proto))
  95
  96 (in-package :ls-user)
  97
  98 ;;; Tasks working on...
  99
 100 #+nil
 101 (progn )
 102
 103 #+nil
 104 (progn
 105   ;; Syntax examples using lexical scope, closures, and bindings to
 106   ;; ensure a clean communication of results
 107   (with-data dataset ((dsvarname1 [usevarname1])
 108                       (dsvarname2 [usevarname2]))
 109       @body))
 110
 111 (defparameter *df-test*
 112   (make-instance 'dataframe-array
 113                  :storage #2A (('a "test0" 0 0d0)
 114                                ('b "test1" 1 1d0)
 115                                ('c "test2" 2 2d0)
 116                                ('d "test3" 3 3d0)
 117                                ('e "test4" 4 4d0))
 118                  :doc "test reality"
 119                  :case-labels (list "0" "1" 2 "3" "4")
 120                  :var-labels (list "symbol" "string" "integer" "double-float")
 121                  :var-types (list 'symbol 'string 'integer 'double-float)))
 122
 123 *df-test* ; but with SBCL, ints become floats?
 124
 125 (defun check-var (df colnum)
 126   (let ((nobs (xdim (dataset df) 0)))
 127     (dotimes (i nobs)
 128       (check-type (xref df i colnum) (elt (var-types df) i)))))
 129
 130 (xdim (dataset *df-test*) 1)
 131 (xdim (dataset *df-test*) 0)
 132
 133 (check-var *df-test* 0)
 134
 135 (class-of
 136   (xref *df-test* 1 1))
 137
 138 (check-type (xref *df-test* 1 1)
 139             string) ;; => nil, so good.
 140 (check-type (xref *df-test* 1 1)
 141             vector) ;; => nil, so good.
 142 (check-type (xref *df-test* 1 1)
 143             real) ;; => simple-error type thrown, so good.
 144
 145 ;; How to nest errors within errors?
 146 (check-type (check-type (xref *df-test* 1 1) real) ;; => error thrown, so good.
 147             simple-error)
 148 (xref *df-test* 1 2)
 149
 150
 151 (check-type)
 152
 153
 154 (integerp (xref *df-test* 1 2))
 155 (floatp (xref *df-test* 1 2))
 156 (integerp (xref *df-test* 1 3))
 157 (type-of (xref *df-test* 1 3))
 158 (floatp (xref *df-test* 1 3))
 159
 160 (type-of (vector 1 1d0))
 161 (type-of *df-test*)
 162
 163
 164 (xref *df-test* 2 1)
 165 (xref *df-test* 0 0)
 166 (xref *df-test* 1 0)
 167 (xref *df-test* 1 '*)
 168
 169 ;;; Experiments with cl-variates
 170
 171 ;; (asdf:oos 'asdf:compile-op 'cl-variates :force t)
 172 ;; (asdf:oos 'asdf:compile-op 'cl-variates-test :force t)
 173 ;; (asdf:oos 'asdf:load-op 'lift)
 174 ;; (asdf:oos 'asdf:load-op 'cl-variates)
 175 (asdf:oos 'asdf:load-op 'cl-variates-test)
 176
 177 (in-package :cl-variates-test)
 178 ;; check tests
 179 (run-tests :suite 'cl-variates-test)
 180 (describe (run-tests :suite 'cl-variates-test))
 181
 182 (in-package :cl-variates-user)
 183 ;; example usage
 184 (defparameter state (make-random-number-generator))
 185 (setf (random-seed state) 44)
 186 (random-seed state)
 187 (loop for i from 1 to 10 collect
 188                   (random-range state 0 10))
 189 ;; => (1 5 1 0 7 1 2 2 8 10)
 190 (setf (random-seed state) 44)
 191 (loop for i from 1 to 10 collect
 192                   (random-range state 0 10))
 193 ;; => (1 5 1 0 7 1 2 2 8 10)
 194
 195 (setf (random-seed state) 44)
 196 (random-seed state)
 197 (loop for i from 1 to 10 collect
 198                   (normal-random state 0 1))
 199 ;; =>
 200 ;; (-1.2968656102820426 0.40746363934173213 -0.8594712469518473 0.8795681301148328
 201 ;;  1.0731526250004264 -0.8161629082481728 0.7001813608754809 0.1078045427044097
 202 ;;  0.20750134211656893 -0.14501914108452274)
 203
 204 (setf (random-seed state) 44)
 205 (loop for i from 1 to 10 collect
 206                   (normal-random state 0 1))
 207 ;; =>
 208 ;; (-1.2968656102820426 0.40746363934173213 -0.8594712469518473 0.8795681301148328
 209 ;;  1.0731526250004264 -0.8161629082481728 0.7001813608754809 0.1078045427044097
 210 ;;  0.20750134211656893 -0.14501914108452274)
 211
 212
 213 ;;; experiments with LLA
 214 (in-package :cl-user)
 215 (asdf:oos 'asdf:load-op 'lla)
 216 (in-package :lla-user)
 217
 218
 219
 220 (in-package :cls-user)
 221 ;;;; PFIM notes
 222
 223 ;; PFIM 3.2
 224
 225 ;; population design eval and opt
 226 #|
 227 issues:
 228 - # individuals
 229 - # sampling times
 230 - sampling times?
 231
 232 constraints:
 233 number of samples/cost of lab analysis and collection
 234 expt constraints
 235 |#
 236
 237 (defun pfim (&key model ( constraints ( summary-function )
 238
 239   (list num-subjects num-times list-times))))
 240
 241 #|
 242 N individuals i
 243 Each individal has a deisgn psi_i
 244    nubmer of samples n_i and sampling times t_{i{1}} t_{i{n_1}}
 245    individuals can differ
 246
 247 Model:
 248
 249 individual-level model
 250 |#
 251
 252 (=model y_i (+ (f \theta_i \psi_i) epsilion_i ))
 253 (=var \epsilion_i \sigma_between \sigma_within  )
 254
 255 ;; Information Matrix for pop deisgn
 256
 257 (defparameter IM (sum  (i 1 N) (MF \psi_i \phi_i)))
 258
 259 #|
 260 For nonlinear structureal models, expand around RE=0
 261
 262 Cramer-Rao : MF^{-1} is lower bound for estimation variance.
 263
 264 Design comparisons:
 265
 266 - smallest SE, but is a matrix, so
 267 - criteria for matrix comparison
 268 -- D-opt, (power (determinant MF) (/ 1 P))
 269
 270
 271 find design maxing D opt, (power (determinant MF) (/ 1 P))
 272 Design varialables
 273  -- contin vars for smapling times within interval or set
 274  -- number of groups for cat vars
 275
 276 Stat in Med 2009, expansion around post-hoc RE est, not necessarily zero.
 277
 278 Example binary covariate C
 279 |#
 280
 281 (if (= i reference-class)
 282     (setf (aref C i) 0)
 283     (setf (aref C i) 1))
 284
 285 ;; Exponential RE,
 286 (=model (log \theta) (  ))
 287
 288 ;; extensions
 289
 290 ;; outputs
 291
 292 #|
 293 PFIM provides for a given design and values of \beta:
 294  compute extended FIM
 295  SE/RSE for \beta of each class of each covar
 296  eval influence of design on SE(\beta)
 297
 298 inter-occassion variability (IOV)
 299 - patients sampled more than once, H occassions
 300 - RE for IOV
 301 - additional vars to estimate
 302
 303 |#
 304
 305 ;;; comparison criteria
 306
 307 functional of conc/time curve which is used for comparison, i.e.
 308 (AUC conc/time-curve)
 309 (Cmax conc/time-curve)
 310 (Tmax conc/time-curve)
 311
 312 where
 313
 314 (defun conc/time-curve (t)
 315   ;; computation
 316 #|
 317   (let ((conc (exp (* t \beta1))))
 318      conc)
 319 |#
 320   )
 321
 322 ;;See
 323 (url-get "www.pfim.biostat.fr")
 324
 325 ;;; Thinking of generics...
 326 (information-matrix model parameters)
 327 (information-matrix variance-matrix)
 328 (information-matrix model data)
 329 (information-matrix list-of-individual-IMs)
 330
 331
 332 (defun IM (loglikelihood parameters times)
 333   "Does double work.  Sum up the resulting IMs to form a full IM."
 334   (let ((IM (make-matrix (length parameters)
 335                          (length parameters)
 336                          :initial-value 0.0d0)))
 337     (dolist (parameterI parameters)
 338       (dolist (parameterJ parameters)
 339         (setf (aref IM I J)
 340               (differentiate (differentiate loglikelihood parameterI) parameterJ))))))
 341
 342
 343
 344 ;; difference between empirical, fisherian, and ...? information.
 345
 346 ;;; Docudown...
 347
 348 ;;; CL-genomic
 349 (asdf:oos 'asdf:compile-op :ironclad)
 350
 351 (in-package :cl-user)
 352 (asdf:oos 'asdf:load-op :cl-genomic)
 353
 354 (in-package :bio-sequence)
 355 (make-dna "agccg") ;; fine
 356 (make-aa "agccg")  ;; fine
 357 (make-aa "agc9zz") ;; error
 358
 359