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