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 rclg-init::*r-interactive*
  26
  27 ;;;#3 Start R within Lisp
  28
  29 (start-rclg) ; => 0 ; if works, nil otherwise.
  30
  31
  32 ;; but if it fails, it could be related to...
  33
  34
  35 ;; and now we make sure it's working
  36
  37 ;; rclg-init::*r-started*
  38 (setf  rclg-init::*r-interactive* 1) ; needed so that plot is interactive
  39
  40 (rclg-init::check-stack)
  41
  42 (r "Cstack_info")
  43
  44 ;; library problems can cause things to fail here.  libR.so needs to
  45 ;; be in the LD_LIBRARY_PATH prior to initialization of the common
  46 ;; lisp application.
  47
  48 ;; For example, on Debian, you will need to add "/usr/lib/R/lib" to
  49 ;; the LD_LIBRARY_PATH environmental variable, i.e. for sh/bash/zsh:
  50 ;;     export LD_LIBRARY_PATH=/usr/lib/R/lib:$LD_LIBRARY_PATH
  51 ;; or for csh/tcsh
  52 ;;     setenv LD_LIBRARY_PATH "/usr/lib/R/lib:$LD_LIBRARY_PATH"
  53 ;; (not sure about the above, but it's something like that).
  54 ;
  55
  56 ;;;#4 Demonstration of commands
  57
  58
  59
  60 ;; Basically, you now have three choices:
  61 ;;
  62 ;; r --- calls R, and converts the result back to CL as best as it
  63 ;;       can.  If it can't convert, returns an unprotected sexp
  64 ;;       (probably a bug, probably should be protected)
  65 ;;
  66 ;; rnb --- R no backconvert.  Calls R, and returns a protected
  67 ;;         unconverted R sexp.  Useful when you want to manipulate
  68 ;;         something on the R side and give it a CL name
  69 ;;
  70 ;; rnbi --- R no backconvert internal.  Calls R, returns a protected
  71 ;;          uncoverted R sexp.  However, it's tagged differently, and
  72 ;;          as soon as you use this as an argument to a function, it
  73 ;;          unprotects the sexp.  Useful for holding anonymous
  74 ;;          intermediate R results you don't want to backconvert.
  75 ;;
  76 ;; Protection/unprotection controls whether R can GC the sexp.
  77 ;;
  78 ;; Example:
  79 ;;
  80 ;; CL-USER> (defparameter *x* (r seq 1 10))
  81 ;; *X*
  82 ;; CL-USER> (defparameter *y* (rnbi rnorm 10))
  83 ;; *Y*
  84 ;; CL-USER> *y*
  85 ;; #<sexp at 0x89A0238, PROTECT=R-PROTECT-UNTIL-USED>
  86 ;; CL-USER> (r plot *x* *y*)
  87 ;; NIL
  88 ;; NIL
  89 ;; CL-USER> *y*
  90 ;; #<sexp at 0x89A0238, PROTECT=NIL>
  91
  92 ;; code used above
  93 (defparameter *x* (r seq 1 10))
  94 (defparameter *y* (rnbi rnorm 10))
  95 (defparameter *y* (r rnorm 10))
  96 *y*
  97 (r plot *x* *y*)
  98 *y*
  99
 100 ;; This is for illustrative purposes only.  It is not a "good" use of rnbi.
 101 ;; Really, you'll want rnbi to hold anonymous intermeditae results, like:
 102
 103 (r plot *x* (rnbi rnorm 10))
 104 (r hist (r rnorm 10))
 105 (r plot (list 1 2 3 2 3 4 5))
 106
 107 ;; Notes:
 108 ;;
 109 ;; If the user protects the result of a call with rnb, it is the
 110 ;; user's responsibility to delete the sexp when it's no longer needed,
 111 ;; using rclg-control:unprotect-sexp.  (It might be better to use a
 112 ;; modification of the old safe version that's lying around.)
 113 ;;
 114 ;; There is no way to ask R whether an sexp is protected or not.
 115 ;; Therefore, there is no real way to enforce the protection.  If the user
 116 ;; goes around the API and calls %rf-unprotect-ptr or messes with the
 117 ;; description slot (slot-value sexp-holder 'protected), things can easily
 118 ;; get out of sync.
 119
 120
 121 ;; Examples of function use:
 122
 123
 124 (r "Sys.getenv" "LD_LIBRARY_PATH")
 125 (r "Sys.getenv" "LD_PRELOAD")
 126
 127 (r "ls")
 128 (r "search")
 129
 130 (elt (r "search") 3)
 131
 132 (r "geterrmessage")
 133
 134
 135 ;; These don't work if we have library problems.
 136 (r "library" "stats")
 137 (r library "MASS")
 138
 139 ;; (r "library" "Biobase") ;; Terminates if doesn't exists -- need to try/catch!
 140
 141 (setf my.lib "Biobase")
 142 my.lib
 143 (r library my.lib)
 144
 145 (r "ls")
 146
 147 (r "print.default" 3)
 148 (r "rnorm" 10)
 149
 150 ;; Working in the R space
 151
 152 (r assign "x" 5)
 153 (r assign "x2" (list 1 2 3 5))
 154 (r plot "x2" "x2") ; BOMBO.
 155 (r assign "x2" #(1 2 3 5 3 4 5))
 156 (r assign "z" "y") ;; unlike the above, this assigns character data
 157 (r "ls")
 158 ;;(r "x2") ;halted "Error could not find function \"x2\""
 159
 160 (setf my.r.x2 (r get "x2"))  ;; moving data from R to CL
 161 my.r.x2
 162 (r assign "x2" my.r.x2)  ;; moving data from CL to R
 163
 164 (r "get" "x")
 165 (r get "x2")
 166 (r "get" "z")
 167 (r get "z")
 168 (r "ls")
 169
 170
 171 (r assign "my.x" (r rnorm 10))
 172 (r assign "my.x" (rnb rnorm 10))
 173
 174 (r get "my.x")
 175
 176
 177
 178
 179 ;; More sophisticated computation
 180
 181 (r "plot" #(2 3 3 2 1) #(3 5 7 3 2))
 182
 183 (r plot (list 1 2 3 4 5) (list 1 2 3 4 5) :main "My title")
 184 (r plot :x (list 1 2 3 4 5) :y (list 5 4 3 4 5) :main "My title")
 185
 186 (r plot :y (list 5 4 3 4 5)  :x (list 1 2 3 4 5) :main "My title")
 187
 188 (r plot (rnb rnorm 10) (rnb rnorm 10)
 189    :main "silly" :xlab "xlabel" :ylab "ylabel")
 190
 191 (aref (r rnorm 10) 3) ;; pull out the 3rd value
 192
 193
 194 ;; create a CL function r-hist that calls the R function hist on a
 195 ;; sequence, returning no results.  The keywords :main and :xlab are
 196 ;; passed with default values nil, and the other keywords are passed with
 197 ;; the chosen values.
 198 (def-r-call (r-hist hist :no-result sequence) main
 199   xlab (breaks 50) (probability t) (col "blue"))
 200 ;; then the function can be called:
 201 (r-hist (rnbi rnorm 1000))
 202 ;; for instance.
 203
 204
 205 ;;;#5 Here is the TO MAKE WORK list (really, applications/tasks) that
 206 ;;;   need to work (i.e. be do-able).
 207
 208
 209 ;;; a. Need to be able to read in datasets and summarize
 210
 211 (r assign "my.df" (r read.table "testdata.csv"))
 212 (r get "my.df")
 213 (r summary "my.df")
 214
 215
 216 ;; however the following will work...
 217
 218 (rnb data.frame
 219      :x (r rnorm 10)
 220      :y (r rnorm 10)) ; fine
 221 (r data.frame
 222    :x (r rnorm 10)
 223    :y (r rnorm 10)) ; fine
 224
 225
 226 (r summary (r t (r data.frame
 227                    :x (r rnorm 10)
 228                    :y (r rnorm 10)))) ; fine ; fine ; no.
 229
 230 ;;; b. Need to be able to work with formulas as objects
 231
 232 (rnb as.formula "x ~ y") ; fine
 233 (rnbi as.formula "x ~ y") ; fine
 234 (r as.formula "x ~ y") ; barfs
 235
 236 ;;; c. and the last is important so that we can easily fit models, so
 237 ;;;    it needs to be fixed.
 238
 239 (r lm
 240    :formula (rnb as.formula "x ~ y")
 241    :data (rnb data.frame
 242             :x (r rnorm 10)
 243             :y (r rnorm 10)))
 244
 245 ;;; d. How to handle connections?
 246 ;;; e. How to handle S4 objects?
 247 ;;; f. Hooks and finishing up conversion tools?
 248
 249
 250 ;;; how do we terminate the R session?
 251 (r "q" "y") ;; fails.
 252
 253
 254 ;;; Local variables:
 255 ;;; mode: outline-minor
 256 ;;; outline-header-prefix: ";;;"
 257 ;;; End: