Dear all,thanyou so very much. elisa > From: dcarl...@tamu.edu > To: dwinsem...@comcast.net > CC: eliza_bo...@hotmail.com; r-help@r-project.org > Subject: RE: [R] locating element in distance matrix > Date: Fri, 11 Jan 2013 16:41:13 -0600 > > If you really have a matrix to begin with, yes. But if you generated it from > dist() or its relations, you would have to convert it to a matrix (roughly > doubling the memory needed). The various hierarchical cluster functions > usually want a dist object. > > > dm <- dist(x, diag=TRUE, upper=TRUE) > > str(dm) > Class 'dist' atomic [1:45] 3.84 4.09 3.64 4.94 4.33 ... > ..- attr(*, "Size")= int 10 > ..- attr(*, "Diag")= logi TRUE > ..- attr(*, "Upper")= logi TRUE > ..- attr(*, "method")= chr "euclidean" > ..- attr(*, "call")= language dist(x = x, diag = TRUE, upper = TRUE) > > In dist(), diag=TRUE and upper=TRUE refer only to how the matrix is > displayed. It is still stored as a single vector: > > > round(dm, 3) > 1 2 3 4 5 6 7 8 9 10 > 1 0.000 3.843 4.094 3.643 4.935 4.328 4.288 6.205 6.197 2.181 > 2 3.843 0.000 5.085 5.171 5.067 3.788 4.384 5.770 7.113 2.830 > 3 4.094 5.085 0.000 3.571 4.548 4.103 3.532 3.917 6.470 3.734 > 4 3.643 5.171 3.571 0.000 3.821 3.843 3.667 5.513 5.176 3.294 > 5 4.935 5.067 4.548 3.821 0.000 4.815 3.465 5.918 6.138 4.764 > 6 4.328 3.788 4.103 3.843 4.815 0.000 2.794 3.937 5.475 3.023 > 7 4.288 4.384 3.532 3.667 3.465 2.794 0.000 4.075 5.251 4.010 > 8 6.205 5.770 3.917 5.513 5.918 3.937 4.075 0.000 5.511 5.152 > 9 6.197 7.113 6.470 5.176 6.138 5.475 5.251 5.511 0.000 6.168 > 10 2.181 2.830 3.734 3.294 4.764 3.023 4.010 5.152 6.168 0.000 > > dm[1] > [1] 3.843183 > > dm[2, 1] > Error in dm[2, 1] : incorrect number of dimensions > > ---------------------------------------------- > David L Carlson > Associate Professor of Anthropology > Texas A&M University > College Station, TX 77843-4352 > > > > > > -----Original Message----- > > From: David Winsemius [mailto:dwinsem...@comcast.net] > > Sent: Friday, January 11, 2013 4:21 PM > > To: dcarl...@tamu.edu > > Cc: 'eliza botto'; r-help@r-project.org > > Subject: Re: [R] locating element in distance matrix > > > > > > On Jan 11, 2013, at 1:51 PM, David L Carlson wrote: > > > > > If you have a dist object (created by dist()) or if you used > > lower.tri(x) to > > > extract the lower triangle of the matrix, which() will not work since > > the > > > matrix is now stored as a numeric vector with n(n-1)/2 elements where > > n is > > > the number of rows/columns. In that case you must compute the > > original > > > row/column values from the position along the vector: > > > > > >> dwhich <- function(d, indx) { > > > + i <- round((1+sqrt(1+8*length(d)))/2, 0) > > > + rowd <- unlist(sapply(2:i, function(x) x:i)) > > > + cold <- rep(1:(i-1), (i-1):1) > > > + return(data.frame(indx=indx, row=rowd[indx], col=cold[indx])) > > > + } > > > > Wouldn't it be easier to leave the distance matrix structure intact and > > just make the diagonal and upper.tri positions Inf? > > > > > dwhich <- function(d) { > > + d[row(d) <= col(d)] <- Inf > > + which(d == min(d,na.rm=FALSE), arr.ind=TRUE) > > + } > > > dwhich(dm) > > row col > > 10 10 1 > > > > -- > > > > >> set.seed(42) > > >> x <- matrix(rnorm(100), 10, 10) > > >> d <- dist(x) > > >> dm <- as.matrix(dist(x, diag=TRUE, upper=TRUE)) > > >> dm <- dm[lower.tri(dm)] > > >> dwhich(d, which(d==min(d))) > > > indx row col > > > 1 9 10 1 > > >> dwhich(dm, which(dm==min(dm))) > > > indx row col > > > 1 9 10 1 > > > > > > > > >> -----Original Message----- > > >> From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > > >> project.org] On Behalf Of David Winsemius > > >> Sent: Friday, January 11, 2013 12:37 PM > > >> To: eliza botto > > >> Cc: r-help@r-project.org > > >> Subject: Re: [R] locating element in distance matrix > > >> > > >> > > >> On Jan 11, 2013, at 9:55 AM, eliza botto wrote: > > >> > > >>> > > >>> Dear useRs, > > >>> I have a very basic question. I have a distance matrix and i > > skipped > > >>> the upper part of it deliberately. > > >> > > >> I have no idea what htat means. Code is always helpful in resolving > > >> ambiguities. > > >> > > >>> The distance matrix is 1000*1000. Then i used "min" command to > > >>> extract the lowest value from that matrix. Now i want to know what > > >>> is the location of that lowest element? More precisely, the row and > > >>> column number of that lowest element. > > >>> Thanks in advance > > >> > > >> ?which > > >> which( distmat == min(distmat), arr.ind=TRUE) > > >> > > >> (It's possible to have more than one match and it would be up to > > you > > >> to decide how to break ties.) > > >> > > >> -- > > >> > > >> David Winsemius, MD > > >> Alameda, CA, USA > > >> > > >> ______________________________________________ > > >> 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 > > Alameda, CA, USA > [[alternative HTML version deleted]]
______________________________________________ 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.
