You can use the set-oriented functions setdiff(), union(), and intersect().
E.g., setdiff(colnames(data2), colnames(data1)) gives the names of columns
of data2 that are not  names of columns of data1.  The following might be
what you want
    merge(data1, data2[, c("id", setdiff(colnames(data2),colnames(data1)))], 
by="id")
You didn't give an example of the data nor the desired result so I made some up:
   > data1 <- data.frame(id=c(1,1,2,3), Name=c("Joe","Joe","Ken","Leo"))
   > data2 <- data.frame(id=c(2,3), Name=c("Melody","Nell"), Age=c(45,49))
   > merge(data1, data2, by="id")
     id Name.x Name.y Age
   1  2    Ken Melody  45
   2  3    Leo   Nell  49
   > merge(data1, data2[, c("id", setdiff(colnames(data2),colnames(data1)))], 
by="id")
     id Name Age
   1  2  Ken  45
   2  3  Leo  49

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com


> -----Original Message-----
> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
> Behalf
> Of Dan Abner
> Sent: Monday, March 11, 2013 2:02 PM
> To: Ista Zahn
> Cc: r-help@r-project.org
> Subject: Re: [R] merge function while obviating duplicate columns XXXX
> 
> Ok, let's say I only want the common columns from data1. Is there a
> succinct way of doing this for potentially hundreds of "in common"
> columns?
> 
> 
> 
> On Mon, Mar 11, 2013 at 3:25 PM, Ista Zahn <istaz...@gmail.com> wrote:
> > On Mon, Mar 11, 2013 at 3:17 PM, Dan Abner <dan.abne...@gmail.com> wrote:
> >> Hi everyone,
> >>
> >> I have the following call to the merge() function. How does one
> >> prevent duplicate columns in the resulting data frame that the 2
> >> parent data frames have in common but are not true key or "by"
> >> variables?
> >>
> >>
> >> data3<-merge(data1,data2,by="id")
> >> data3
> >>
> >> id total.x total.y balance
> >> 1 78  78 90
> >> 2 91  91 63
> >> 3 74  74 57
> >> 4 89  89 58
> >> 5 90  90 27
> >>
> >>
> >> In this example, total is not a true key or "by" variable that
> >> uniquely identifies rows suitable for matching purposes, but instead
> >> just happens to be common to both sets.
> >
> > Well, which one do you want? Or do you want to exclude total from the 
> > result?
> >
> >>
> >> In reality, I have hundreds for these "in common" variables, so I need
> >> a solution that is tractable for a large number of "in common"
> >> columns.
> >>
> >> Thanks!
> >>
> >> Dan
> >>
> >> ______________________________________________
> >> 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.
> 
> ______________________________________________
> 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.

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