[R] looping using combinatorics
Gabor Grothendieck
ggrothendieck at gmail.com
Fri Jul 14 20:01:28 CEST 2006
Use data.frame, not rbind, e.g. DF <- data.frame(a, b, c)
On 7/14/06, Jesse Albert Canchola <jesse.canchola.b at 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 at gmail.com>
> 07/13/2006 07:39 PM
>
> To
> "Jesse Albert Canchola" <jesse.canchola.b at bayer.com>
> cc
> r-help at 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 at 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 at Bayer.Com
> >
> >
> >
> >
> >
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