Hello, I am a R beginner and hoping to obtain some hints or suggestions about using permutations to sort a data set I have. Here is an example dataset: Ind1 11 00 12 15 28 Ind2 21 33 22 67 52 Ind3 22 45 21 22 56 Ind4 11 25 74 77 42 Ind5 41 32 67 45 22 This will be read into a variable using read.table. What I want to do is permute these individuals and every time pick 3 individuals and write them to a new variable. I want to do this 100 times so that in the end I will have 100 tables containing data for 3 individuals each. The data (for individuals) itself is not to be permuted, rather the selection of individuals. I am guessing this is probably trivial to do. But I would appreciate any advice on this matter. Thank you. Vikram
To pick random elements to sample, you can just use the sample function sample(1:5,3,replace=T/F) # pick true or false as needed for your data. If you replicate this, you should have no problem. replicate(100,function() return(sample(1:5,3,replace=T/F))) This will be plenty fast, but if you get into very large scale boot strapping, you might want to vectorize the whole thing. That's easily done with replace = T (just take 3*100 samples and then convert the output vector to a matrix) but I'm not sure its quite as easy with replace = F. Hope this helps, Michael On Wed, Aug 10, 2011 at 2:37 PM, Vikram Chhatre <crypticlineage@gmail.com>wrote:> Hello, > > I am a R beginner and hoping to obtain some hints or suggestions about > using permutations to sort a data set I have. > > Here is an example dataset: > > > Ind1 11 00 12 15 28 > Ind2 21 33 22 67 52 > Ind3 22 45 21 22 56 > Ind4 11 25 74 77 42 > Ind5 41 32 67 45 22 > > This will be read into a variable using read.table. What I want to do > is permute these individuals and every time pick 3 individuals and > write them to a new variable. I want to do this 100 times so that in > the end I will have 100 tables containing data for 3 individuals each. > The data (for individuals) itself is not to be permuted, rather the > selection of individuals. > > I am guessing this is probably trivial to do. But I would appreciate > any advice on this matter. > > Thank you. > Vikram > > ______________________________________________ > 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. >[[alternative HTML version deleted]]
Hi:
Your R terminology needs a little work, but I think this is what you're
after:
# read your example data from e-mail into an R session
dd <- read.table(textConnection("
Ind1 11 00 12 15 28
Ind2 21 33 22 67 52
Ind3 22 45 21 22 56
Ind4 11 25 74 77 42
Ind5 41 32 67 45 22"), header = FALSE)
closeAllConnections()
# generate a matrix whose rows yield three unique indices:
rows2sample <- t(replicate(100, sample(seq_len(nrow(dd)), 3, replace =
FALSE)))
# Generate a list, each component of which contains a sub-data frame.
# lapply() actually replaces a for loop in this case; the function simply
# samples the rows of dd that correspond to the indices in the i-th row
# of rows2sample.
# seq_len(nrow(rows2sample)) is a more long-winded, but safer, way
# to say 1:100.
subdataList <- lapply(seq_len(nrow(rows2sample)),
function(i) dd[rows2sample[i, ], ])
My results yielded the following:> head(rows2sample, 2) # first two rows of the index matrix
[,1] [,2] [,3]
[1,] 2 5 1
[2,] 4 1 3> length(subdataList)
[1] 100> subdataList[[1]]
V1 V2 V3 V4 V5 V6
2 Ind2 21 33 22 67 52
5 Ind5 41 32 67 45 22
1 Ind1 11 0 12 15 28> subdataList[[2]]
V1 V2 V3 V4 V5 V6
4 Ind4 11 25 74 77 42
1 Ind1 11 0 12 15 28
3 Ind3 22 45 21 22 56
...so it looks like it's doing the right thing. Now you need to learn
how to process lists, and for that the Introduction to R manual is a
good place to get started.
HTH,
Dennis
On Wed, Aug 10, 2011 at 11:37 AM, Vikram Chhatre
<crypticlineage at gmail.com> wrote:> Hello,
>
> I am a R beginner and hoping to obtain some hints or suggestions about
> using permutations to sort a data set I have.
>
> Here is an example dataset:
>
>
> Ind1 ? 11 ?00 ? 12 ?15 ?28
> Ind2 ?21 33 22 67 52
> Ind3 ?22 45 21 22 56
> Ind4 ?11 ?25 ? 74 ?77 ?42
> Ind5 ?41 32 67 45 22
>
> This will be read into a variable using read.table. ?What I want to do
> is permute these individuals and every time pick 3 individuals and
> write them to a new variable. ?I want to do this 100 times so that in
> the end I will have 100 tables containing data for 3 individuals each.
> ?The data (for individuals) itself is not to be permuted, rather the
> selection of individuals.
>
> I am guessing this is probably trivial to do. ?But I would appreciate
> any advice on this matter.
>
> Thank you.
> Vikram
>
> ______________________________________________
> R-help at 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.
>