~ubuntu-branches/ubuntu/edgy/ess/edgy

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<!ENTITY ess "ESS">
<!ENTITY intro SYSTEM "ess-cha-intro.xml">
<!ENTITY basic SYSTEM "ess-cha-basic.xml">
<!ENTITY advanced SYSTEM "ess-cha-advanced.xml">
<!ENTITY esslS SYSTEM "ess-cha-S.xml">
<!ENTITY esslSAS SYSTEM "ess-cha-SAS.xml">
<!ENTITY esslStata SYSTEM "ess-cha-Stata.xml">
<!ENTITY esslXLispStat SYSTEM "ess-cha-xlispstat.xml">
<!ENTITY essExS SYSTEM "ess-app-example-S.xml">

]>

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<book>
  <title>Emacs Speaks Statistics User Manual</title>
  <titleabbrev>ESS User Manual</titleabbrev>
  <bookinfo>
    <legalnotice>
      <para>
	This work is copyright A.J. Rossini, 
	<email>rossini@u.washington.edu</email> 
      </para>
    </legalnotice>
    <author>
      <firstname>Anthony</firstname>
      <surname>Rossini</surname>
      <affiliation>
	<orgname>
	  Department of Biostatistics, University of Washington
	</orgname> 
	<address format="linespecific">
	  Box 292731
	  Seattle, WA 98195
	</address>
      </affiliation>
    </author>
  </bookinfo>
  <dedication>
    <para>
      This is dedicated to free time.
    </para>
  </dedication>

  &intro;
  
  <!--  &basic; -->
  
  <appendix>
  <title>Examples for using S</title>

  <para>
    We present some basic suggestions for using ESS to interact with
    S.  These are just a subset of approaches, many better approaches
    are possible.  Contributions of examples of how you work with ESS
    are appreciated (especially since it helps us determine priorities
    on future enhancements)! (comments as to what should be happening
    are prefixed by "##").
  </para>

    <para>
      <literallayout format="linespecific" class="normal">
1:  ##    Data Analysis Example (source code is real)
    ## Load the file you want to work with
    C-x C-f myfile.s

    ## Edit as appropriate, and then start up S-PLUS 3.x
    M-x S+3

    ## A new buffer *S+3:1* will appear.  Splus will have been started
    ## in this buffer.  The buffer is in iESS [S+3:1] mode.

    ## Split the screen and go back to the file editing buffer.
    C-x 2 C-x b myfile.s

    ## Send regions, lines, or the entire file contents to S-PLUS. For regions,
    ## highlight a region with keystrokes or mouse and then send with:
    C-c C-r

    ## Re-edit myfile.s as necessary to correct any difficulties.  Add
    ## new commands here.  Send them to S by region with C-c C-r, or
    ## one line at a time with C-c C-n.

    ## Save the revised myfile.s with C-x C-s.

    ## Save the entire *S+3:1* interaction buffer with C-c C-s.  You
    ## will be prompted for a file name.  The recommended name is
    ## myfile.St.  With the *.St suffix, the file will come up in ESS
    ## Transcript mode the next time it is accessed from Emacs.
      </literallayout>
    </para>

    <para>
      <literallayout>
2:  ## Program revision example (source code is real)

    ## Start up S-PLUS 3.x in a process buffer (this will be *S+3:1*) 
    M-x S+3

    ## Load the file you want to work with
    C-x C-f myfile.s
    
    ## edit program, functions, and code in myfile.s, and send revised
    ## functions to S when ready with
    C-c C-f
    ## or highlighted regions with
    C-c C-r
    ## or individual lines with
    C-c C-n
    ## or load the entire buffer with 
    C-c C-l

    ## save the revised myfile.s when you have finished
    C-c C-s
</literallayout></para>

    <para>
      <literallayout>
3:  ## Program revision example (S object is real)

    ## Start up S-PLUS 3.x in a process buffer (this will be *S+3:1*) 
    M-x S+3

    ## Dump an existing S object my.function into a buffer to work with
    C-c C-d my.function
    ## a new buffer named yourloginname.my.function.S will be created with
    ## an editable copy of the object.  The buffer is associated with the
    ## pathname /tmp/yourloginname.my.function.S and will amlost certainly not
    ## exist after you log off.

    ## enter program, functions, and code into work buffer, and send
    ## entire contents to S-PLUS when ready
    C-c C-b

    ## Go to *S+3:1* buffer, which is the process buffer, and examine
    ## the results.
    C-c C-y
    ## The sequence C-c C-y is a shortcut for:  C-x b *S+3:1*

    ## Return to the work buffer (may/may not be prefixed)
    C-x C-b yourloginname.my.function.S
    ## Fix the function that didn't work, and resubmit by placing the
    ## cursor somewhere in the function and
    C-c C-f
    ## Or you could've selected a region (using the mouse, or keyboard 
    ## via setting point/mark) and 
    C-c C-r
    ## Or you could step through, line by line, using 
    C-c C-n
    ## Or just send a single line (without moving to the next) using
    C-c C-j
    ## To fix that error in syntax for the "rchisq" command, get help
    ## by
    C-c C-v rchisq
      </literallayout>
    </para>

    <para>
      <literallayout format="linespecific" class="normal">
4:  Data Analysis (S object is real)
    ## Start up S-PLUS 3.x, in a process buffer (this will be *S+3:1*) 
    M-x S+3

    ## Work in the process buffer.  When you find an object that needs 
    ## to be changed (this could be a data frame, or a variable, or a 
    ## function), dump it to a buffer:
    C-c C-d my.cool.function

    ## Edit the function as appropriate, and dump back in to the
    ## process buffer  
    C-c C-b

    ## Return to the S-PLUS process buffer
    C-c C-y
    ## Continue working.

    ## When you need help, use 
    C-c C-v rchisq
    ## instead of entering:   help("rchisq")
      </literallayout>
    </para>
  </appendix>

    <appendix>
      <title>Customization Examples and Solutions to Problems</title>
      <para>
	<literallayout format="linespecific" class="normal">
1. Suppose that you are primarily an SPLUS 3.4 user, occasionally
   using S version 4, and sick and tired of the buffer-name *S+3*
   we've stuck you with.  Simply edit the "ess-dialect" alist entry in 
   the essd-s+3.el and essd-s4.el files to be "S" instead of "S4" and
   "S+3".  This will insure that all the inferior process buffer names 
   are "*S*".
</literallayout>

	<literallayout format="linespecific" class="normal">
2. Suppose that you WANT to have the first buffer name indexed by
   ":1", in the same manner as your S-PLUS processes 2,3,4, and 5 (for
   you heavy simulation people).  Then uncomment the line in ess-site
   (or add after your (require 'ess-site) or (load "ess-site") command 
    in your .emacs file, the line:
       
       (setq ess-plain-first-buffername nil)
   )
</literallayout>

	<literallayout>3. Fontlocking sometimes fails to behave nicely upon errors.  When
   Splus dumps, a mis-matched "  (double-quote) can result in the
   wrong font-lock face being used for the remainder of the buffer.  

   Solution: add a " at the end of the "Dumped..." statement, to
   revert the font-lock face back to normal.
	</literallayout>
      </para>
    </appendix>
</book>

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