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