From: Gabor Grothendieck <ggrothendieck_at_gmail.com>

Date: Sat 15 Jul 2006 - 04:01:28 EST

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Sat Jul 15 04:04:08 2006

Date: Sat 15 Jul 2006 - 04:01:28 EST

Use data.frame, not rbind, e.g. DF <- data.frame(a, b, c)

On 7/14/06, Jesse Albert Canchola <jesse.canchola.b@bayer.com> wrote:

*> Many thanks, Gabor. This is very close to what would be ideal. You gave
**> me an idea as follows:
**>
**> Rather than combine pairs of data vectors/frames AFTER the "combn"
**> function, combine all data before (though I belive this would be less
**> efficient) and add an index then use that index to choose your pairs (or
**> whatever combinatorics you are using; e.g., 8 choose 4 so all
**> combinations of 4 out of 8 for a total of 70 combinations.)
**>
**> Example data frames with variable names:
**>
**> Data frame "a" where I add an "index":
**> id measure index
**> 1 1.1 1
**> 2 1.2 1
**> 3 1.3 1
**>
**> Data frame "b" where I add an "index":
**> id measure index
**> 4 2.1 2
**> 5 2.2 2
**> 6 2.3 2
**>
**> Data frame "c" where I add an index:
**> id measure index
**> 7 3.1 3
**> 8 3.2 3
**> 9 3.3 3
**>
**> If we combine all these data at once using rbind, we get:
**> id measure index
**> 1 1.1 1
**> 2 1.2 1
**> 3 1.3 1
**> 4 2.1 2
**> 5 2.2 2
**> 6 2.3 2
**> 7 3.1 3
**> 8 3.2 3
**> 9 3.3 3
**>
**> We can then use something similar to your code and the index to choose the
**> required pairs as derived from the "combn" function.
**> For example, the "combn" function will choose the data pairs
**> (1,2)
**> (1,3)
**> (2,3)
**>
**> where, for example, the pairs (1,2) will have data from frames "a" and
**> "b":
**> 1 1.1 1
**> 2 1.2 1
**> 3 1.3 1
**> 4 2.1 2
**> 5 2.2 2
**> 6 2.3 2
**>
**> so that we can go down the list subsetting what we need and doing
**> operations on each combined pair as we go.
**>
**> Is there an easy way in R to do this operation?
**>
**> For the above, an attempt might be:
**>
**> ########## STAB CODE #########
**> DF <- rbind(a,b,c)
**> DF
**> for(index in as.data.frame(combn(3,2))) print(DF[,index])
**> ######## END STAB CODE ######
**>
**> but this is choosing 3 choose 2 COLUMNS within the combined file rather
**> than 3 choose 2 ROWS.
**>
**>
**> Best regards and TIAA,
**> Jesse
**>
**>
**>
**>
**>
*

> "Gabor Grothendieck" <ggrothendieck@gmail.com>

*> 07/13/2006 07:39 PM
**>
**> To
**> "Jesse Albert Canchola" <jesse.canchola.b@bayer.com>
**> cc
**> r-help@stat.math.ethz.ch
**> Subject
**> Re: [R] looping using combinatorics
**>
**>
**>
**>
**>
**>
**> I assume your question is given 3 vectors of the same length: a, b and c
**> how do we loop over pairs of them. In the following each iteration
**> displays
**> one pair:
**>
**> library(combinat)
**> DF <- data.frame(a = 1:4, b = 5:8, c = 9:12)
**> for(idx in as.data.frame(combn(3,2))) print(DF[,idx])
**>
**> On 7/13/06, Jesse Albert Canchola <jesse.canchola.b@bayer.com> wrote:
**> > I have a problem where I need to loop over the total combinations of
**> > vectors (combined once chosen via combinatorics). Here is a
**> > simplification of the problem:
**> >
**> > STEP 1: Define three vectors a, b, c.
**> > STEP 2: Combine all possible pairwise vectors (i.e., 3 choose 2 = 3
**> > possible pairs of vectors: ab,ac, bc)
**> > NOTE: the actual problem has 8 choose 4, 8 choose 5 and 8 choose 6
**> > combinations.
**> > STEP 3: Do the same math on each pairwise combination and spit out
**> > answers each time
**> >
**> > ####### BEGIN CODE #######
**> > #STEP 1
**> > a1 <- c(1,2,3,4,5,6,7,8,9,10,11,12)
**> > a <- matrix(a1,2,3,byrow=T)
**> > a
**> >
**> > b1 <- c(13,14,15,16,17,18,19,20,21,22,23,24)
**> > b <- matrix(b1,2,3,byrow=T)
**> > b
**> >
**> > c1 <- c(25,26,27,28,29,30,31,32,33,34,35,36)
**> > c <- matrix(b1,2,3,byrow=T)
**> > c
**> >
**> > # example: combine the first two vectors "a" and "b"
**> > combab <- rbind(a,b)
**> >
**> > # the a,b combined data from the algorithm later below should look like
**> > # something like the following:
**> > combab
**> >
**> > # use the combinatorics "combn" function found in the "combinat" package
**> > on CRAN
**> > m <- combn(3,2) # three choose two combinations
**> > m
**> >
**> > # the first assignment below should be numeric and then subsequent
**> > # assignments as character since the first time you assign a number to
**> > # a character in a matrix the rest of the numbers in the matrix are
**> > coerced to character
**> > m[m==1]='a'; m[m=='2']='b'; m[m=='3']='c'
**> > m
**> >
**> > #STEP 2: combine pairwise vectors into a matrix or frame
**> > for (i in dim(m)[1])
**> > for (j in dim(m)[2])
**> > {
**> > combined <-
**> > rbind(cat(format(m[i]),"\n"),cat(format(m[j]),"\n")) #cat/format removes
**> > the quotes
**> > combined
**> > }
**> > traceback()
**> >
**> >
**> > #STEP 3: {not there yet}
**> > ################# END CODE ################
**> >
**> > The problem is that in STEP 2 (not complete), the results in the rbind
**> are
**> > not recognized as the objects they represent (i.e., the "a" without
**> quotes
**> > is not recognized as the data object we defined in STEP 1. Perhaps this
**> > is a parsing problem. Perhaps there is an alterative way to do this. I
**> > looked pretty long and hard in the CRAN libraries but alas, I am stuck.
**> > BTW, I picked up R about a month ago (I used primarily SAS, Stata and
**> > SPSS).
**> >
**> > Regards and TIA,
**> > Jesse
**> >
**> >
**> >
**> >
**> >
**> >
**> > Jesse A. Canchola
**> > Biostatistician III
**> > Bayer Healthcare
**> > 725 Potter St.
**> > Berkeley, CA 94710
**> > P: 510.705.5855
**> > F: 510.705.5718
**> > E: Jesse.Canchola.b@Bayer.Com
**> >
**> >
**> >
**> >
**> >
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*

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