The document discusses the Getopt::Long module for parsing command line arguments in R. It provides an example of using Getopt::Long to parse arguments in an R script called getopt_long_sample.R, where the --save.path argument is parsed and assigned to the save.path variable. Getopt::Long allows defining argument types like strings, integers, and flags to parse command line options consistently in both Perl and R scripts.

1. R Getopt::Long
Tsukuba.R #9 (2011/11/12)
@a_bicky

14. parseArgs <- function() {
argv <- commandArgs(trailingOnly = TRUE)
argv <- strsplit(argv, "=")
argv <- sapply(argv, function(arg) {
ret <- ifelse(is.na(arg[2]), 1, arg[2])
names(ret) <- arg[1]
return(ret)
})
# show usage
# Not use 'existsFunction' because loading 'methods' package
takes about 60% of the startup time
if ("help" %in% names(argv)) {
tryCatch(usage(), error = function(e) cat("No usage for
this scriptn"))
quit()
}
# check arguments
# Not use 'existsFunction' because loading 'methods' package
takes about 60% of the startup time
try(checkArgs(argv), silent = TRUE)
return(argv)
}

15. orz

18. Getopt::Long

19. Perl parser
use Getopt::Long;
my $data = "file.dat";
my $length = 24;
my $verbose;
$result = GetOptions ("length=i" => $length, # numeric
"file=s" => $data, # string
"verbose" => $verbose); # flag
http://search.cpan.org/~jv/Getopt-Long-2.38/lib/Getopt/Long.pm
getopt_long_sample.pl
use Getopt::Long;
GetOptions('save_path=s' => $save_path);
print "$save_pathn";
$ perl getopt_long_sample.pl --save_path=hoge
hoge

21. …

24. http://d.hatena.ne.jp/a_bicky/20111020/1319061009

25. http://d.hatena.ne.jp/a_bicky/20111020/1319061009

26. http://d.hatena.ne.jp/a_bicky/20111020/1319061009

28. getopt_long_sample.R
source("GetoptLong.R")
GetOptions('save.path=s' = save.path)
print(save.path)
GetOptions('var1=s' = var1, #
'var2=i' = var2, #
'var3=f' = var3, #
'var4' = var4, #
'var5=s@' = var5, #
'var6=i%' = var6 #
)

29. getopt_long_sample.R
source("GetoptLong.R")
GetOptions('save.path=s' = save.path)
print(save.path)
use Getopt::Long;
GetOptions('save_path=s' => $save_path);
print "$save_pathn";

30. getopt_long_sample.R
source("GetoptLong.R")
GetOptions('save.path=s' = save.path)
print(save.path)
use Getopt::Long;
GetOptions('save_path=s' => $save_path);
print "$save_pathn";

32. getopt_long_sample.R
source("GetoptLong.R")
GetOptions('save.path=s' = save.path)
print(save.path)
$ RScript getopt_long_sample.R --save.path=hoge
[1] "hoge"

35. getopt_long_sample.R
source("GetoptLong.R")
GetOptions('save.path=s' = save.path)
print(save.path)

36. getopt_long_sample.R
source("GetoptLong.R")
GetOptions('save.path=s' = save.path)
print(save.path)

38. R
getopt_long_sample.R
source("GetoptLong.R")
GetOptions('save.path=s' = save.path)
print(save.path) save.path
# parent.frame
var.names <- as.character(match.call()[-1])
assign(var, ret[[var]], envir = parent.frame())

39. R
getopt_long_sample.R
source("GetoptLong.R")
GetOptions('save.path=s' = save.path)
print(save.path) save.path
# parent.frame
var.names <- as.character(match.call()[-1])
assign(var, ret[[var]], envir = parent.frame())
http://user.ecc.u-tokyo.ac.jp/~s105503/p02.html