How can I read command line parameters from an R script

Question

I ve got a R script for which I d like to be able to supply several command-line parameters  rather than hardcode parameter values in the code itself    The script runs on Windows   I can t find info on how to read parameters supplied on the command-line into my R script   I d be surprised if it can t be done  so maybe I m just not using the best keywords in my Google search     Any pointers or recommendations

User · Answer

Try library getopt      if you want things to be nicer  For example   spec  lt - matrix c           in         i   1   character    file from fastq-stats -x  required             gc         g   1   character    input gc content file  optional             out        o   1   character    output filename  optional             help       h   0   logical      this help    ncol 5 byrow T   opt   getopt spec    if   is null opt help     is null opt in         cat paste getopt spec  usage T    n         q

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I just put together a nice data structure and chain of processing to generate this switching behaviour  no libraries needed  I m sure it will have been implemented numerous times over  and came across this thread looking for examples - thought I d chip in   I didn t even particularly need flags  the only flag here is a debug mode  creating a variable which I check for as a condition of starting a downstream function if   exists debug mode         else  print variables     The flag checking lapply statements below produce the same as   if   --debug   in  args  debug mode  lt - T if   -h   in  args     --help   in  args     where args is the variable read in from command line arguments  a character vector  equivalent to c  --debug   --help   when you supply these on for instance   It s reusable for any other flag and you avoid all the repetition  and no libraries so no dependencies   args  lt - commandArgs TRUE   flag details  lt - list   debug    list    def    Print variables rather than executing function XYZ        flag    --debug     output    debug mode  lt - T     help    list    def    Display flag definitions     flag   c  -h   --help      output    cat help prompt       flag conditions  lt - lapply flag details  function x      paste0 paste0     x flag       sep      in  args   collapse              flag truth table  lt - unlist lapply flag conditions  function x      if  eval parse text   x          return T      else return F       help prompts  lt - lapply names flag truth table   function x     joins 2-space-separatated flags with a tab-space to the flag description   paste0 c paste0 flag details x   1     flag     collapse          flag details x   1     def      collapse   t        help prompt  lt - paste c unlist help prompts      collapse   n n      The following lines handle the flags  running the corresponding  output  entry in flag details for any supplied flag output  lt - unlist lapply names flag truth table   function x     if  flag truth table x   return flag details x   1     output         eval parse text   flag output     Note that in flag details here the commands are stored as strings  then evaluated with eval parse text            Optparse is obviously desirable for any serious script  but minimal-functionality code is good too sometimes   Sample output     Rscript check mail Rscript --help --debug Print  variables rather than executing function XYZ     -h  --help  Display flag definitions

User · Answer

FYI    there is a function args    which retrieves the arguments of R functions  not to be confused with a vector of arguments named args

User · Answer

If you need to specify options with flags   like -h  --help  --number 42  etc  you can use the R package optparse  inspired from Python   http   cran r-project org web packages optparse vignettes optparse pdf   At least this how I understand your question  because I found this post when looking for an equivalent of the bash getopt  or perl Getopt  or python argparse and optparse

User · Answer

you need littler  pronounced  little r    Dirk will be by in about 15 minutes to elaborate

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Add this to the top of your script    args lt -commandArgs TRUE    Then you can refer to the arguments passed as args 1   args 2  etc   Then run   Rscript myscript R arg1 arg2 arg3   If your args are strings with spaces in them  enclose within double quotes

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In bash  you can construct a command line like the following     z 10   echo  z 10   Rscript -e  args lt -commandArgs TRUE  x args 1  args 2  x mean x  sd x   1  z   1   1  2  3  4  5  6  7  8  9 10  1  5 5  1  3 027650     You can see that the variable  z is substituted by bash shell with  10  and this value is picked up by commandArgs and fed into args 2   and the range command x 1 10 executed by R successfully  etc etc

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Since optparse has been mentioned a couple of times in the answers  and it provides a comprehensive kit for command line processing  here s a short simplified example of how you can use it  assuming the input file exists   script R   library optparse   option list  lt - list    make option c  -n    --count lines    action  store true   default FALSE      help  Count the line numbers  default       make option c  -f    --factor    type  integer   default 3      help  Multiply output by this number  default  default       parser  lt - OptionParser usage   prog  options  file   option list option list   args  lt - parse args parser  positional arguments   1  opt  lt - args options file  lt - args args  if opt count lines      print paste length readLines file     opt factor       Given an arbitrary file blah txt with 23 lines   On the command line   Rscript script R -h outputs  Usage  script R  options  file   Options          -n  --count lines                 Count the line numbers  default           -f FACTOR  --factor FACTOR                 Multiply output by this number  default 3           -h  --help                 Show this help message and exit   Rscript script R -n blah txt outputs  1   69   Rscript script R -n -f 5 blah txt outputs  1   115

User · Answer

A few points    Command-line parameters are accessible via commandArgs    so see help commandArgs  for an overview  You can use Rscript exe on all platforms  including Windows  It will support commandArgs    littler could be ported to Windows but lives right now only on OS X and Linux  There are two add-on packages on CRAN -- getopt and optparse -- which were both written for command-line parsing    Edit in Nov 2015   New alternatives have appeared and I wholeheartedly recommend docopt

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Dirk s answer here is everything you need  Here s a minimal reproducible example   I made two files  exmpl bat and exmpl R    exmpl bat   set R Script  C  Program Files R-3 0 2 bin RScript exe   R Script  exmpl R 2010-01-28 example 100  gt  exmpl batch 2 gt  amp 1   Alternatively  using Rterm exe   set R TERM  C  Program Files R-3 0 2 bin i386 Rterm exe   R TERM  --no-restore --no-save --args 2010-01-28 example 100  lt  exmpl R  gt  exmpl batch 2 gt  amp 1  exmpl R   options echo TRUE    if you want see commands in output file args  lt - commandArgs trailingOnly   TRUE  print args    trailingOnly TRUE means that only your arguments are returned  check    print commandArgs trailingOnly FALSE    start date  lt - as Date args 1   name  lt - args 2  n  lt - as integer args 3   rm args     Some computations  x  lt - rnorm n  png paste name   png  sep      plot start date  1L n   x  dev off    summary x     Save both files in the same directory and start exmpl bat  In the result you ll get    example png with some plot exmpl batch with all that was done   You could also add an environment variable  R Script     C  Program Files R-3 0 2 bin RScript exe    and use it in your batch scripts as  R Script   lt filename r gt   lt arguments gt   Differences between RScript and Rterm    Rscript has simpler syntax Rscript automatically chooses architecture on x64  see R Installation and Administration  2 6 Sub-architectures for details  Rscript needs options echo TRUE  in the  R file if you want to write the commands to the output file

[command-line] How can I read command line parameters from an R script?

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