Thanks. You might want to repost it as a text attachment since many of the lines wrapped around.
Another more permanent possibility would be to put it on the R wiki at http://rwiki.sciviews.org/doku.php Note that the gsubfn package has a facility for quasi-perl type string interpolation as well. Just preface any function with fn$ and the facility is applied to the arguments of the function (subject to certain heuristics which determine which args to apply it to). > library(gsubfn) > today <- format(Sys.Date()) > show <- list() > show$syntax <- 43 > Sys.setenv(AN_ENV_VAR="greetings (I'm an env var!)") > > fn$cat('Getting `Sys.getenv("AN_ENV_VAR")` from the environment, on $today, + `show$syntax` is also possible.\n') Getting greetings (I'm an env var!) from the environment, on 2010-03-29, 43 is also possible. On Mon, Mar 29, 2010 at 11:41 AM, Jason E. Aten <j.e.a...@gmail.com> wrote: > Dear R users, > > A colleague of mine asked me how to write a script (an executable text file > containing R code) in R. After I showed > him, he said that after extensive searching of the R archives, he had not > found anything like these techniques. > > He suggested that I share these methods to enable others to leverage R as a > better alternative to bash/perl scripts. > > So in the interest of giving back to the R community, and with all humility, > I offer the > following small demonstration of one method for creating scripts of R code > that are > executable from the (at least Linux) command line. > > I don't make any warrantees that this will work for you, but if it helps > somebody at least > get starting utilizing R effectively in scripts, then great! > > Best regards, > > Jason > > -- > Jason E. Aten, Ph.D. > > > # file: scriptdemo.rsh > > #!/bin/bash > exec R --vanilla -q --slave -e "source(file=pipe(\"tail -n +4 $0\"))" --args > $@ > #debug: exec R --vanilla --verbose -e "source(file=pipe(\"tail -n +4 $0\"))" > --args $@ > ### The above line starts R and then reads in this script, starting at line > 4: > # > # scriptdemo.rsh : a simple filter script to demonstrate how to write a > script in R that > # reads stdin and utilizes command line argv. Also shows how > to use ppp() to do > # bash scripting like variable substitution, which is really > just syntactic > # sugar. But sugar can be sweet. > # > # NB: Only tested on Linux, YMMV, and you may have to adapt to your OS. If > it breaks, you > # get to keep both pieces. > > # 1st point of note: notice the exec R invocation above, with the pipe and > tail combo. > # This file becomes the program read into R. If it is set chmod+x then you > can execute this file. > > pp=function(...) paste(sep="",...) > script="scriptdemo.rsh" > usage=pp(script,": put help info here") > > argv = commandArgs(trailingOnly=TRUE) > > > # --help > if(any(argv=="--help")) { > cat(usage) > quit(save="no",status=0) > } > > # 2nd point of note: this is how to read stdin inside a script: > # > > # slurp in all the input > r=readLines("stdin") > > bad=grep("^#",r) # remove comments > > # write out lines that didn't start with # > cat(r[setdiff(1:length(r),bad)],sep="\n") > > > # 3rd point of note: if you want nice bash shell scripting string > substitution and backticking > # you can use my ppp() function. Note it's not well vectorized at the > moment, so it will expect > # variables that are substituted from the environment to be of length 1. > # A bit hackish in places (sure the |@|@| and 34HERE43 stuff makes me > wince), but it gets the job done, > # as it's meant as a proof of concept. > > ########################## > # utility functions leading up to final definition of ppp() : shell > scripting like facilities for R > # Skip to the end of this file to see what ppp() does for you. > ########################## > > # delete one trailing whitespace > chomp=function(x) { > n=nchar(x) > a=substr(x,n,n) > w=which(a==" " | a == "\n" | a=="\t") > if (length(w)) { > x[w]=substr(x[w],1,n[w]-1) > } > x > } > > # delete one leading whitespace > prechomp=function(x) { > n=nchar(x) > a=substr(x,1,1) > w=which(a==" " | a == "\n" | a == "\t") > if (length(w)) { > x[w]=substr(x[w],2,n[w]) > } > x > } > > > # eliminate whitespace leading/trailing from a string > trim=function(x) { > y=chomp(x) > while(any(y!=x)) { > x=y > y=chomp(x) > } > > y=prechomp(x) > while(any(y!=x)) { > x=y > y=prechomp(x) > } > > x > } > > strsplit2=function(x,split,...) { > # detect trailing split : and add "" afterwards, so we know if it was > there. > a=strsplit(pp(x,"|@|@|"),split,...) > lapply(a,function(x) gsub("|@|@|","",x,fixed=TRUE)) > } > > strsplit3=function(x,split,keepsplit=FALSE,...) { > if (keepsplit) { > repstring="34HERE43" > if (length(grep(repstring,x))) { die(repstring, " repstring already > found. Arg! Aborting") } # sanity check > # note where we want to split, using \\1 backref to keep the original > a=gsub(pattern=pp("(",split,")") ,replacement=pp(repstring,"\\1"),x) > } else { > a=x > repstring=split > } > b=strsplit2(a,repstring,...) # split, keeping the original delimiters > } > > pp=function(...) paste(...,sep="") # pp() must be defined in outermost scope > for ppp() to work > > replacer=function(s,begin.string="${",end.string="}",keepend=FALSE,require.end=TRUE) > { > > translate.env=function(x) { > if (exists(x)) return(x) > a=Sys.getenv(x) > if (a!="") return(pp("\"",a,"\"")) > x > } > > parts=strsplit2(s,begin.string,fixed=T)[[1]] > if (length(parts) < 2 || all(parts=="")) return(s) > if (any(trim(parts[-1])=="")) { > warning(pp("ppp::replacer(): found begin.string '",begin.string,"' > in '",s,"' but had empty/blankspace/end of string following it.")) > return(s) > } > > collap=c() > collap[1]=parts[1] > for (i in 2:length(parts)) { > tmp=strsplit3(parts[i],end.string,keepsplit=keepend)[[1]] > if (length(tmp)==1) { > if (require.end) { > warning(pp("ppp::replacer(): could not find end.string > '",end.string,"' in string '",s,"' and require.end=TRUE, so karping.")) > collap[(i-1)*2]=parts[i] > collap[(i-1)*2+1]="" > } else { > collap[(i-1)*2]=pp("\",",translate.env(tmp[1]),",\"") # allow > newline to terminate as well, if end not required > collap[(i-1)*2+1]="" > } > } else { > collap[(i-1)*2]=pp("\",",translate.env(tmp[1]),",\"") > # collect the rest of parts[i] following tmp[1] and the end.string > (assumes end.string is only ever length 1) > > collap[(i-1)*2+1]=substr(parts[i],nchar(tmp[1])+1+(1-as.numeric(keepend)),nchar(parts[i])) > } > } > text=pp("pp(\"",pp(collap,collapse=""),"\")") > > # sys.frame(-2) is necessary to get definitions from calling function > before where we were defined. > if (sys.nframe() > 1) { > ftext=eval(parse(text=text),envir=sys.frame(-2)) > } else { > ftext=eval(parse(text=text)) > } > ftext > } > > pp=function(...) paste(...,sep="") # must be defined in outermost scope for > ppp() to work > > # shell like string interpolation... ppp("fill in ${myvar} here after > `hostname` is $myvar") > ppp=function(...) { > > sa=paste(sep="",...) > res=c() > for (j in 1:length(sa)) { > s=sa[j] > s2=replacer(s,"${","}") > terminators="\t| |\\.|`|\\$|\\{|\\}|\\(|\\)|<|>|\\|" > s3=replacer(s2,"$",terminators,keepend=TRUE,require.end=FALSE) # > !require.end allows end of line termination > res[j]=s3 > } > > do.sys.expecting.output=function(cmd) { > got=pp(system(intern=T,cmd),collapse="\n") > if (got=="") die("do.sys() on '",cmd,"' returned no output.") > got > } > > # now check for backtick system call requests as well, *after* variable > substitution is all finished. > bt=grep("`",res) > if(length(bt)) { > sa=res[bt] > for (j in 1:length(sa)) { > s=sa[j] > parts=strsplit2(s,"`",fixed=T)[[1]] > if (length(parts) < 3) { res[bt[j]]=s; next; } > > collap=c() > collap[1]=parts[1] > for (i in seq(2,length(parts)-1,2)) { > cmd=parts[i] > collap[i]=do.sys.expecting.output(cmd) > collap[i+1]=parts[i+1] > } > text=pp(collap,collapse="") > res[bt[j]]=text > } # for j > } #end if length(bt) > res > } > > > > # > # now demonstrate the use of ppp() in a scripting context: > # > > today="date" > month=3 > year=2010 > > show=list() > show$syntax = 43 > > Sys.setenv(AN_ENV_VAR="greetings (I'm an env var!)") > > demo=ppp("Getting $AN_ENV_VAR from the environment, on `$today`, > substituting ${show$syntax} in named lists is also possible. `cal $month > $year| head` ") > > cat("here's the demo output\n") > cat(demo,sep="\n") > > > ## # output of this demo script when run, show how to use stdin and ppp() > ## > ## > ## m...@host:~/uns/bin$ cat ~/tmp/test | template2.rsh > ## not comment 1 > ## not comment 2 > ## not comment 3 > ## not comment 4 > ## not comment 5 > ## here's the demo output > ## Getting greetings (I'm an env var!) from the environment, on Mon Mar 29 > 10:23:49 CDT 2010, substituting 43 in named lists is also possible. > March 2010 > ## Su Mo Tu We Th Fr Sa > ## 1 2 3 4 5 6 > ## 7 8 9 10 11 12 13 > ## 14 15 16 17 18 19 20 > ## 21 22 23 24 25 26 27 > ## 28 29 30 31 > ## > ## m...@host:~/uns/bin$ cat ~/tmp/test > ## # comment 1 > ## not comment 1 > ## not comment 2 > ## # comment 2 > ## not comment 3 > ## not comment 4 > ## not comment 5 > ## # comment 3 > ______________________________________________ R-help@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.
