[R] using var from bash in R script
Dear R users, This probably a really noob question, but I'm stuck. I'd like to pass some variables from bash to R as strings. I can successfully pass variables using commandArgs(), the problem is that I end up with an array. So, for example: Args - commandArgs(TRUE) Args [1] one two three Now, it just so happens that one, two, three are names of columns that I'd like to work with. I'd like to do something like this: print(summary(lm(Args[1] ~ Args[2]))) But, this doesn't work. The alternative would be to let bash write a number of R-scripts and then rm them when done, but that seems like an unnecessary step. Can this be done? Thanks -- View this message in context: http://r.789695.n4.nabble.com/using-var-from-bash-in-R-script-tp4262857p4262857.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] using var from bash in R script
On Jan 4, 2012, at 3:08 PM, dood wrote: Dear R users, This probably a really noob question, but I'm stuck. I'd like to pass some variables from bash to R as strings. I can successfully pass variables using commandArgs(), the problem is that I end up with an array. So, for example: Args - commandArgs(TRUE) Args [1] one two three Now, it just so happens that one, two, three are names of columns that I'd like to work with. I'd like to do something like this: print(summary(lm(Args[1] ~ Args[2]))) But, this doesn't work. The alternative would be to let bash write a number of R-scripts and then rm them when done, but that seems like an unnecessary step. Can this be done? Thanks See ?as.formula and ?paste Something along the lines of the following should work: Args - c(one, two, three) Args [1] one two three paste(Args[1], ~, Args[2]) [1] one ~ two as.formula(paste(Args[1], ~, Args[2])) one ~ two Then use: summary(lm(as.formula(paste(Args[1], ~, Args[2] If 'one', 'two' and 'three' are columns in a data frame (say 'DF'), you will want to use the data argument in the call to lm(): summary(lm(as.formula(paste(Args[1], ~, Args[2])), data = DF)) HTH, Marc Schwartz __ 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.
Re: [R] using var from bash in R script
On Jan 4, 2012, at 4:08 PM, dood wrote: Dear R users, This probably a really noob question, but I'm stuck. I'd like to pass some variables from bash to R as strings. I can successfully pass variables using commandArgs(), the problem is that I end up with an array. Huh? You should be getting a character vector. So, for example: Args - commandArgs(TRUE) Args [1] one two three Now, it just so happens that one, two, three are names of columns columns? Of what? Or perhaps ... in what? Does this what have a name in the R workspace? that I'd like to work with. I'd like to do something like this: print(summary(lm(Args[1] ~ Args[2]))) No 'data' argument to lm. You would be getting better answers if you provided more specifics. But, this doesn't work. The alternative would be to let bash write a number of R-scripts and then rm them when done, but that seems like an unnecessary step. Can this be done? require(fortunes) fortune(Yoda) Thanks -- View this message in context: http://r.789695.n4.nabble.com/using-var-from-bash-in-R-script-tp4262857p4262857.html Sent from the R help mailing list archive at Nabble.com. __ 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. David Winsemius, MD West Hartford, CT __ 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.
Re: [R] using var from bash in R script
Marc Schwartz-3 wrote See ?as.formula and ?paste Something along the lines of the following should work: Args - c(one, two, three) Args [1] one two three paste(Args[1], ~, Args[2]) [1] one ~ two as.formula(paste(Args[1], ~, Args[2])) one ~ two Then use: summary(lm(as.formula(paste(Args[1], ~, Args[2] If 'one', 'two' and 'three' are columns in a data frame (say 'DF'), you will want to use the data argument in the call to lm(): summary(lm(as.formula(paste(Args[1], ~, Args[2])), data = DF)) Thanks, that works! -- View this message in context: http://r.789695.n4.nabble.com/using-var-from-bash-in-R-script-tp4262857p4263235.html Sent from the R help mailing list archive at Nabble.com. __ 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.
