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