rclg-demo.lisp

   1 ;; What is this talk of 'release'? Klingons do not make software
   2 ;; 'releases'.  Our software 'escapes' leaving a bloody trail of
   3 ;; designers and quality assurance people in it's wake.
   4
   5
   6
   7 ;;;#1 Load everything
   8
   9 ;; if needed...?  Shouldn't be, since rclg.asd ought to take care of
  10 ;; most of the issues that we have.
  11 (asdf:operate 'asdf:compile-op 'cffi :force t)
  12 (asdf:operate 'asdf:compile-op 'cffi)
  13 (asdf:operate 'asdf:compile-op 'rclg :force t)
  14 (asdf:operate 'asdf:compile-op 'rclg)
  15
  16 ;;(asdf:operate 'asdf:load-op 'cffi)
  17 (asdf:operate 'asdf:load-op 'rclg)
  18
  19 ;;;#2 Go to where the functions are
  20
  21 (in-package :rclg-user)
  22
  23 ;; Have we started yet?
  24 rclg-init::*r-started*
  25
  26 ;;;#3 Start R within Lisp
  27
  28 (start-rclg)
  29
  30 ;; but if it fails, it could be related to...
  31
  32
  33 ;; and now we make sure it's working
  34
  35 ;; rclg-init::*r-started*
  36
  37 (rclg-init::check-stack)
  38
  39 (r "Cstack_info")
  40
  41 ;; library problems can cause things to fail here.  libR.so needs to
  42 ;; be in the LD_LIBRARY_PATH prior to initialization of the common
  43 ;; lisp application.
  44
  45 ;; For example, on Debian, you will need to add "/usr/lib/R/lib" to
  46 ;; the LD_LIBRARY_PATH environmental variable, i.e. for sh/bash/zsh:
  47 ;;     export LD_LIBRARY_PATH=/usr/lib/R/lib:$LD_LIBRARY_PATH
  48 ;; or for csh/tcsh
  49 ;;     setenv LD_LIBRARY_PATH "/usr/lib/R/lib:$LD_LIBRARY_PATH"
  50 ;; (not sure about the above, but it's something like that).
  51 ;
  52
  53 ;;;#4 Demonstration of commands
  54
  55
  56
  57 ;; Basically, you now have three choices:
  58 ;;
  59 ;; r --- calls R, and converts the result back to CL as best as it
  60 ;;       can.  If it can't convert, returns an unprotected sexp
  61 ;;       (probably a bug, probably should be protected)
  62 ;;
  63 ;; rnb --- R no backconvert.  Calls R, and returns a protected
  64 ;;         unconverted R sexp.  Useful when you want to manipulate
  65 ;;         something on the R side and give it a CL name
  66 ;;
  67 ;; rnbi --- R no backconvert internal.  Calls R, returns a protected
  68 ;;          uncoverted R sexp.  However, it's tagged differently, and
  69 ;;          as soon as you use this as an argument to a function, it
  70 ;;          unprotects the sexp.  Useful for holding anonymous
  71 ;;          intermediate R results you don't want to backconvert.
  72 ;;
  73 ;; Protection/unprotection controls whether R can GC the sexp.
  74 ;;
  75 ;; Example:
  76 ;;
  77 ;; CL-USER> (defparameter *x* (r seq 1 10))
  78 ;; *X*
  79 ;; CL-USER> (defparameter *y* (rnbi rnorm 10))
  80 ;; *Y*
  81 ;; CL-USER> *y*
  82 ;; #<sexp at 0x89A0238, PROTECT=R-PROTECT-UNTIL-USED>
  83 ;; CL-USER> (r plot *x* *y*)
  84 ;; NIL
  85 ;; NIL
  86 ;; CL-USER> *y*
  87 ;; #<sexp at 0x89A0238, PROTECT=NIL>
  88
  89 ;; code used above
  90 (defparameter *x* (r seq 1 10))
  91 (defparameter *y* (rnbi rnorm 10))
  92 *y*
  93 (r plot *x* *y*)
  94 *y*
  95
  96 ;; This is for illustrative purposes only.  It is not a "good" use of rnbi.
  97 ;; Really, you'll want rnbi to hold anonymous intermeditae results, like:
  98
  99 (r plot *x* (rnbi rnorm 10))
 100
 101 ;; Notes:
 102 ;;
 103 ;; If the user protects the result of a call with rnb, it is the
 104 ;; user's responsibility to delete the sexp when it's no longer needed,
 105 ;; using rclg-control:unprotect-sexp.  (It might be better to use a
 106 ;; modification of the old safe version that's lying around.)
 107 ;;
 108 ;; There is no way to ask R whether an sexp is protected or not.
 109 ;; Therefore, there is no real way to enforce the protection.  If the user
 110 ;; goes around the API and calls %rf-unprotect-ptr or messes with the
 111 ;; description slot (slot-value sexp-holder 'protected), things can easily
 112 ;; get out of sync.
 113
 114
 115 ;; Examples of function use:
 116
 117
 118 (r "Sys.getenv" "LD_LIBRARY_PATH")
 119 (r "Sys.getenv" "LD_PRELOAD")
 120
 121 (r "ls")
 122 (r "search")
 123
 124 (r "geterrmessage")
 125
 126
 127 ;; These don't work if we have library problems.
 128 (r "library" "stats")
 129 (r library "MASS")
 130 (r "library" "Biobase")
 131
 132 (setf my.lib "Biobase")
 133 my.lib
 134 (r library my.lib)
 135
 136 (r "ls")
 137
 138 (r "print.default" 3)
 139 (r "rnorm" 10)
 140
 141 ;; Working in the R space
 142
 143 (r assign "x" 5)
 144 (r assign "x2" (list 1 2 3 5))
 145
 146 (r assign "x2" #(1 2 3 5 3 4 5))
 147 (r assign "z" "y") ;; unlike the above, this assigns character data
 148 (r "ls")
 149
 150 (setf my.r.x2 (r get "x2"))  ;; moving data from R to CL
 151 my.r.x2
 152 (r assign "x2" my.r.x2)  ;; moving data from CL to R
 153
 154 (r "get" "x")
 155 (r get "x2")
 156 (r "get" "z")
 157 (r get "z")
 158 (r "ls")
 159
 160
 161 (r assign "my.x" (r rnorm 10))
 162 (r assign "my.x" (rnb rnorm 10))
 163
 164 (r get "my.x")
 165
 166
 167
 168
 169 ;; More sophisticated computation
 170
 171 (r "plot" #(2 3 3 2 1) #(3 5 7 3 2))
 172
 173 (r plot (list 1 2 3 4 5) (list 1 2 3 4 5) :main "My title")
 174 (r plot :x (list 1 2 3 4 5) :y (list 5 4 3 4 5) :main "My title")
 175
 176 (r plot :y (list 5 4 3 4 5)  :x (list 1 2 3 4 5) :main "My title")
 177
 178 (r plot (rnb rnorm 10) (rnb rnorm 10)
 179    :main "silly" :xlab "xlabel" :ylab "ylabel")
 180
 181 (aref (r rnorm 10) 3) ;; pull out the 3rd value
 182
 183
 184 ;; create a CL function r-hist that calls the R function hist on a
 185 ;; sequence, returning no results.  The keywords :main and :xlab are
 186 ;; passed with default values nil, and the other keywords are passed with
 187 ;; the chosen values.
 188 (def-r-call (r-hist hist :no-result sequence) main
 189   xlab (breaks 50) (probability t) (col "blue"))
 190 ;; then the function can be called:
 191 (r-hist (rnbi rnorm 1000))
 192 ;; for instance.
 193
 194
 195 ;;;#5 Here is the TO MAKE WORK list (really, applications/tasks) that
 196 ;;;   need to work (i.e. be do-able).
 197
 198
 199 ;;; a. Need to be able to read in datasets and summarize
 200
 201 (r assign "my.df" (r read.table "testdata.csv"))
 202 (r get "my.df")
 203 (r summary "my.df")
 204
 205
 206 ;; however the following will work...
 207
 208 (rnb data.frame
 209      :x (r rnorm 10)
 210      :y (r rnorm 10)) ; fine
 211 (r data.frame
 212    :x (r rnorm 10)
 213    :y (r rnorm 10)) ; fine
 214
 215
 216 (r summary (r t (r data.frame
 217                    :x (r rnorm 10)
 218                    :y (r rnorm 10)))) ; fine ; fine ; no.
 219
 220 ;;; b. Need to be able to work with formulas as objects
 221
 222 (rnb as.formula "x ~ y") ; fine
 223 (rnbi as.formula "x ~ y") ; fine
 224 (r as.formula "x ~ y") ; barfs
 225
 226 ;;; c. and the last is important so that we can easily fit models, so
 227 ;;;    it needs to be fixed.
 228
 229 (r lm
 230    :formula (rnb as.formula "x ~ y")
 231    :data (rnb data.frame
 232             :x (r rnorm 10)
 233             :y (r rnorm 10)))
 234
 235 ;;; d. How to handle connections?
 236 ;;; e. How to handle S4 objects?
 237 ;;; f. Hooks and finishing up conversion tools?
 238
 239
 240 ;;; how do we terminate the R session?
 241 (r "q" "y") ;; fails.
 242
 243
 244 ;;; Local variables:
 245 ;;; mode: outline-minor
 246 ;;; outline-header-prefix: ";;;"
 247 ;;; End: