What s the best way to use R scripts on the command line terminal

Question

It s very convenient to have R scripts for doing simple plots from the command line   However  running R from bash scripts is not convenient at all   The ideal might be something like     path to R       or     usr bin env R       but I haven t been able to make either of those work   Another option is keeping the scripts purely in R  e g  script R  and invoking it with R --file script R or similar   However  occasionally a script will rely on obscure command line switches at which point part of the code exists outside the script   Example  sneaking things into R from bash via a local  Rprofile  the desired switches are then everything --vanilla implies except --no-init-file   Another option is a bash script to store the R flags and be painlessly executable  which then calls the R script   The problem is that this means a single program just got split into two files which now have to be keep in sync  transferred to new machines together  etc   The option I currently despise least is embedding the R in a bash script      bin bash       usage message to catch bad input without invoking R       any bash pre-processing of input       etc R --random-flags  lt  lt RSCRIPT   R code goes here RSCRIPT   Everything s in a single file   It s executable and easily handles arguments   The problem is that combining bash and R like this pretty much eliminates the possibility of any IDE not failing on one or the other  and makes my heart hurt real bad   Is there some better way I m missing

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Just a note to add to this post  Later versions of R seem to have buried Rscript somewhat   For R 3 1 2-1 on OSX downloaded Jan 2015 I found Rscript in    sw Library Frameworks R framework Versions 3 1 Resources bin Rscript   So  instead of something like     sw bin Rscript  I needed to use the following at the top of my script       sw Library Frameworks R framework Versions 3 1 Resources bin Rscript   The locate Rscript might be helpful to you

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path to R won t work because R is itself a script  so execve is unhappy   I use R --slave -f script

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Miguel Sanchez s response is the way it should be  The other way executing Rscript could be  env  command to run the system wide RScript      usr bin env Rscript

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You might want to use python s rpy2 module  However  the  right  way to do this is with R CMD BATCH  You can modify this to write to STDOUT  but the default is to write to a  Rout file  See example below     ramanujan    cat foo R print rnorm 10    ramanujan    R CMD BATCH foo R  ramanujan    cat foo Rout  R version 2 7 2  2008-08-25  Copyright  C  2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0  R is free software and comes with ABSOLUTELY NO WARRANTY  You are welcome to redistribute it under certain conditions  Type  license    or  licence    for distribution details   R is a collaborative project with many contributors  Type  contributors    for more information and  citation    on how to cite R or R packages in publications   Type  demo    for some demos   help    for on-line help  or  help start    for an HTML browser interface to help  Type  q    to quit R    Previously saved workspace restored        Rprofile loaded  Welcome at  Fri Apr 17 13 33 17 2009  gt  print rnorm 10     1   1 5891276  1 1219071 -0 6110963  0 1579430 -0 3104579  1 0072677 -0 1303165  0 6998849  1 9918643 -1 2390156  gt   Goodbye at  Fri Apr 17 13 33 17 2009  gt  proc time      user  system elapsed   0 614   0 050   0 721   Note  you ll want to try out the --vanilla and other options to remove all the startup cruft

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The following works for me using MSYS bash on Windows - I don t have R on my Linux box so can t try it there  You need two files - the first one called runr executes R with a file parameter    this is runr   following is path to R on my Windows machine   plus any R params you need c  r bin r --file  1   You need to make this executable with chmod  x runr   Then in your script file     runr   some R commands x   1 x   Note the    runr line may need to include the full path to runr  depending on how you are using the command  how your PATH variable is set etc   Not pretty  but it does seem to work

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If the program you re using to execute your script needs parameters  you can put them at the end of the    line      usr bin R --random --switches --f   Not knowing R  I can t test properly  but this seems to work   axa artemis    cat r test    usr bin R -q -f error axa artemis      r test  gt     usr bin R -q -f  gt  error Error  object  error  not found Execution halted axa artemis

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Content of script r      usr bin env Rscript  args   commandArgs trailingOnly   TRUE  message sprintf  Hello  s   args 1L      The first line is the shebang line  It   s best practice to use  usr bin env Rscript instead of hard-coding the path to your R installation  Otherwise you risk your script breaking on other computers   Next  make it executable  on the command line    chmod  x script r   Invocation from command line     script r world   Hello world

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Try littler  littler provides hash-bang  i e  script starting with    some path  capability for GNU R  as well as simple command-line and piping use

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Try smallR for writing quick R scripts in the command line   http   code google com p simple-r    r command in the directory   Plotting from the command line using smallR would look like this   r -p file txt

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If you are interested in parsing command line arguments to an R script try RScript which is bundled with R as of version 2 5 x  http   stat ethz ch R-manual R-patched library utils html Rscript html

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This works       usr bin Rscript   but I don t know what happens if you have more than 1 version of R installed on your machine   If you do it like this     usr bin env Rscript   it tells the interpreter to just use whatever R appears first on your path

[bash] What's the best way to use R scripts on the command line (terminal)?

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