R help - May 2009 - How to save R "clean" sessions in BATCH mode?

Thanks a lot for all of you that have reply me about opening and  
ending R workspaces in BATCH mode. However replies were a king general  
and I?m afraid I could not take the entire message from them.  
Therefore I chose to expose here a representative fraction of my work.

I have 50 Rdata files (F1,F2,F3,F4,
,F50) with objects inside.
I need to:

open F1:
    - perform some simple operations with the objects
    - export the solution with write.table
    - end F1 session
open F2
    repeat procedures as F1


open F50
    repeat procedures as F1



My difficulty here is to end a workspace and open one from the scratch  
to avoid mixing files from consecutive worksessions, and thus using R  
memory unnecessarily. I could use rm() to delete objects from the  
previous sessions but it seems not an efficient task.
Any suggestions on how to perform this in Batch Mode? An examplified  
help would be nice!

Diogo Andr? Alagador
http://www.biochange-lab.eu/people/diogo-alagador
Biodiversity and Global Change Lab, Museo Nacional de Ciencias  
Naturales, CSIC, Madrid, Espa?a
Forest Research Centre, Instituto Superior de Agronomia, UTL, Lisboa, Portugal

Would
rm(list=ls())
not be an easier solution, if I understand your question correctly?

Sarah

On Sat, May 16, 2009 at 11:21 AM,  <mcnda839 at mncn.csic.es>
wrote:
> Thanks a lot for all of you that have reply me about opening and ending R
> workspaces in BATCH mode. However replies were a king general and I?m
afraid
> I could not take the entire message from them. Therefore I chose to expose
> here a representative fraction of my work.
>
> I have 50 Rdata files (F1,F2,F3,F4,?,F50) with objects inside.
> I need to:
>
> open F1:
> ? - perform some simple operations with the objects
> ? - export the solution with write.table
> ? - end F1 session
> open F2
> ? repeat procedures as F1
> ?
> open F50
> ? repeat procedures as F1
> ?
>
> My difficulty here is to end a workspace and open one from the scratch to
> avoid mixing files from consecutive worksessions, and thus using R memory
> unnecessarily. I could use rm() to delete objects from the previous
sessions
> but it seems not an efficient task.
> Any suggestions on how to perform this in Batch Mode? An examplified help
> would be nice!
>
> Diogo Andr? Alagador
> http://www.biochange-lab.eu/people/diogo-alagador
> Biodiversity and Global Change Lab, Museo Nacional de Ciencias Naturales,
> CSIC, Madrid, Espa?a
> Forest Research Centre, Instituto Superior de Agronomia, UTL, Lisboa,
> Portugal
-- 
Sarah Goslee
http://www.functionaldiversity.org

On Sat, May 16, 2009 at 10:21 AM,  <mcnda839 at mncn.csic.es>
wrote:
> Thanks a lot for all of you that have reply me about opening and ending R
> workspaces in BATCH mode. However replies were a king general and I?m
afraid
> I could not take the entire message from them. Therefore I chose to expose
> here a representative fraction of my work.
>
> I have 50 Rdata files (F1,F2,F3,F4,?,F50) with objects inside.
> I need to:
>
> open F1:
> ? - perform some simple operations with the objects
> ? - export the solution with write.table
> ? - end F1 session
> open F2
> ? repeat procedures as F1
> ?
> open F50
> ? repeat procedures as F1
> ?
>
> My difficulty here is to end a workspace and open one from the scratch to
> avoid mixing files from consecutive worksessions, and thus using R memory
> unnecessarily. I could use rm() to delete objects from the previous
sessions
> but it seems not an efficient task.
> Any suggestions on how to perform this in Batch Mode? An examplified help
> would be nice!
First try either

Rcmd BATCH --help # for Windows

or

R CMD BATCH --help # for Mac OS X or for Linux

and note that there are optional arguments --no-save and --no-restore.
 Use them.
> Diogo Andr? Alagador
> http://www.biochange-lab.eu/people/diogo-alagador
> Biodiversity and Global Change Lab, Museo Nacional de Ciencias Naturales,
> CSIC, Madrid, Espa?a
> Forest Research Centre, Instituto Superior de Agronomia, UTL, Lisboa,
> Portugal
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

Le samedi 16 mai 2009 ? 17:21 +0200, mcnda839 at mncn.csic.es a ?crit
:
> Thanks a lot for all of you that have reply me about opening and  
> ending R workspaces in BATCH mode. However replies were a king general  
> and I?m afraid I could not take the entire message from them.  
> Therefore I chose to expose here a representative fraction of my work.
> 
> I have 50 Rdata files (F1,F2,F3,F4,
,F50) with objects inside.
> I need to:
> 
> open F1:
>     - perform some simple operations with the objects
>     - export the solution with write.table
>     - end F1 session
> open F2
>     repeat procedures as F1
> 
> open F50
>     repeat procedures as F1
> 
> 
> My difficulty here is to end a workspace and open one from the scratch  
> to avoid mixing files from consecutive worksessions, and thus using R  
> memory unnecessarily. I could use rm() to delete objects from the  
> previous sessions but it seems not an efficient task.
And re-loading R, rebuilding a whole process context, re-allocating
memory is an efficient one ?

Hah !
> Any suggestions on how to perform this in Batch Mode? An examplified  
> help would be nice!
Why not encapsulate your procedures in a function taking the filename as
its argument and loop?ng on the filenames list ? Anything created in the
function, being local to the function, will be (efficiently) cleaned up
at the function exit. Magic...

Exemple :
> ls()
character(0)
> Foo<-runif(10,0,1)
> ls()
[1] "Foo"
> ?save.image
> save.image("Foo1.RData")
> ls()
[1] "Foo"
> rm(list=ls())
> Foo<-letters[round(runif(10,min=1,max=26))]
> Foo
 [1] "v" "m" "b" "y" "g"
"u" "r" "f" "y"
"q"
> save.image("Foo2.RData")
> rm(list=ls())
> bar<-edit()
bar<-edit()
Waiting for Emacs...
> bar
function(filename) {
  load(file=filename)
  print(ls())
  print(Foo)
  invisible(NULL)
}
> ls()
[1] "bar"
> bar("Foo1.RData")
[1] "filename" "Foo"     # Note : by default, ls() list the
function's
# environment, not the global one... **> no "bar" here...
 [1] 0.8030422 0.6326055 0.8188481 0.6161665 0.5917206 0.6631358
0.7290200
 [8] 0.2970315 0.2016259 0.4473244
> ls()
[1] "bar"	# Bar is still in the global
environment...
> bar("Foo2.RData")
[1] "filename" "Foo"     
 [1] "v" "m" "b" "y" "g"
"u" "r" "f" "y"
"q"
> ls()
[1] "bar"
> 
Good enough for you ?

HTH,

					Emmanuel Charpentier