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