That's awesome!! I was trying to use the tri function, but not successfully.
-----Original Message----- From: jim holtman [mailto:[EMAIL PROTECTED] Sent: Monday, July 21, 2008 10:10 AM To: Jon Hak Cc: r-help@r-project.org Subject: Re: [R] manipulate a matrix2 Will this do it for you: > ?print.default > x [,1] [,2] [,3] [,4] [,5] [1,] 1 6 11 16 21 [2,] 2 7 12 17 22 [3,] 3 8 13 18 23 [4,] 4 9 14 19 24 [5,] 5 10 15 20 25 > x[upper.tri(x)] <- NA > x [,1] [,2] [,3] [,4] [,5] [1,] 1 NA NA NA NA [2,] 2 7 NA NA NA [3,] 3 8 13 NA NA [4,] 4 9 14 19 NA [5,] 5 10 15 20 25 > print(x, na.print='.') [,1] [,2] [,3] [,4] [,5] [1,] 1 . . . . [2,] 2 7 . . . [3,] 3 8 13 . . [4,] 4 9 14 19 . [5,] 5 10 15 20 25 > On Mon, Jul 21, 2008 at 11:47 AM, Jon Hak <[EMAIL PROTECTED]> wrote: > The vegan matrix produces values of similarity between sample sites. > Because the matrix uses the same samples for the row names and the > column header it has duplicates on either side of the base diagonal > (below). > > 3 7 8 11 12 > 3 0 0.6 1 0.3 0.85 > 7 0.66 0 1 0.65 0.95 > 8 1 1 0 1 1 > 11 0.3 0.65 1 0 0.9 > 12 0.85 0.95 1 0.9 0 > > Ideally, the matrix should look like; > > 3 7 8 11 12 > 3 0 > 7 0.66 0 > 8 1 1 0 > 11 0.3 0.65 1 0 > 12 0.85 0.95 1 0.9 0 > > This is probably a question for the Vegan developers, but I really > appreciate your (and the lists) insight. > > -----Original Message----- > From: jim holtman [mailto:[EMAIL PROTECTED] > Sent: Monday, July 21, 2008 9:18 AM > To: Jon Hak > Cc: r-help@r-project.org > Subject: Re: [R] manipulate a matrix2 > > I am not familiar with the vegdist function. What defines a duplicate > in the matrix? There are ways if identifying if more than one row > meets the criteria duplicates and then removing them. Can you give an > illustration of what you mean with a before/after data representation. > > On Mon, Jul 21, 2008 at 10:22 AM, Jon Hak <[EMAIL PROTECTED]> > wrote: >> Thanks Jim, that was exactly what I was after. >> >> On a second note, do you have any insight into pulling out the >> duplicates in this type of matrix? >> I thought that was what the upper=FALSE is in: >> csv.dis <- vegdist(csv.m, method='jaccard', binary=FALSE, diag=FALSE, >> upper=FALSE). I just need either the lower or upper portion, with the >> zeros (,3 & ,3) being the dividing line. >> >> [,3] [,5] [,6] [,9] [,11] >> >> [3,] 0 2 3 4 5 >> >> [5,] 2 0 8 9 10 >> >> [6,] 3 8 0 14 15 >> >> [9,] 4 9 14 0 20 >> >> [11,] 5 10 15 20 0 >> >> Thanks again, >> >> Jon >> >> >> >> -----Original Message----- >> From: jim holtman [mailto:[EMAIL PROTECTED] >> Sent: Friday, July 18, 2008 9:56 AM >> To: Jon Hak >> Cc: r-help@r-project.org >> Subject: Re: [R] manipulate a matrix2 >> >> Is this what you want: >> >>> x >> [,3] [,5] [,6] [,9] [,11] >> [,3] 1 6 11 16 21 >> [,5] 2 7 12 17 22 >> [,6] 3 8 13 18 23 >> [,9] 4 9 14 19 24 >> [,11] 5 10 15 20 25 >>> library(reshape) >>> melt(x) >> X1 X2 value >> 1 [,3] [,3] 1 >> 2 [,5] [,3] 2 >> 3 [,6] [,3] 3 >> 4 [,9] [,3] 4 >> 5 [,11] [,3] 5 >> 6 [,3] [,5] 6 >> 7 [,5] [,5] 7 >> 8 [,6] [,5] 8 >> 9 [,9] [,5] 9 >> 10 [,11] [,5] 10 >> 11 [,3] [,6] 11 >> 12 [,5] [,6] 12 >> 13 [,6] [,6] 13 >> 14 [,9] [,6] 14 >> 15 [,11] [,6] 15 >> 16 [,3] [,9] 16 >> 17 [,5] [,9] 17 >> 18 [,6] [,9] 18 >> 19 [,9] [,9] 19 >> 20 [,11] [,9] 20 >> 21 [,3] [,11] 21 >> 22 [,5] [,11] 22 >> 23 [,6] [,11] 23 >> 24 [,9] [,11] 24 >> 25 [,11] [,11] 25 >>> >> >> >> On Fri, Jul 18, 2008 at 11:10 AM, Jon Hak <[EMAIL PROTECTED]> >> wrote: >>> Building upon Jim's answer below (Thanks Jim, that helped a lot), I >> need >>> to pickup where this thread left off. I'm using Vegan to calculate >> the >>> Jaccard's Index and the Row.Names and column names are represented in >> my >>> matrix as seen here. >>> >>> [,3] [,5] [,6] [,9] [,11] >>> >>> [3,] 0 6 11 16 21 >>> >>> [5,] 2 0 12 17 22 >>> >>> [6,] 3 8 0 18 23 >>> >>> [9,] 4 9 14 0 24 >>> >>> [11,] 5 10 15 20 0 >>> >>> >>> >>> When I use the command; >>> xy <- cbind(row=as.vector(row.names(x)), col=as.vector(colnames(x)), >>> value=as.vector(x)) >>> >>> I get the list (the column value is the issue); >>> >>> row col value >>> [1,] 3 1 0 >>> [2,] 5 1 2 >>> [3,] 6 1 3 >>> [4,] 9 1 4 >>> [5,] 11 1 5 >>> [6,] 3 2 6 >>> [7,] 5 2 0 >>> [8,] 6 2 8 >>> [9,] 9 2 9 >>> [10,] 11 2 10 >>> [11,] 3 3 11 >>> [12,] 5 3 0 >>> >>> I would really like the col value to equal the actual name, not the >>> column number. What am I missing? The analysis is very large, 6k > x6k >>> matrix so automating the process is a high priority. >>> >>> Thanks, >>> Jon >>> >>> >>> >>> From: jim holtman <jholtman_at_gmail.com >>> >> > <mailto:jholtman_at_gmail.com?Subject=Re:%20%5BR%5D%20manipulate%20a%20m >>> atrix> > >>> Date: Mon, 25 Jun 2007 12:39:46 -0400 >>> >>> Is this what you want? >>> >>>> x >>> >>> [,1] [,2] [,3] [,4] [,5] >>> >>> [1,] 1 6 11 16 21 >>> [2,] 2 7 12 17 22 >>> [3,] 3 8 13 18 23 >>> [4,] 4 9 14 19 24 >>> [5,] 5 10 15 20 25 >>> >>> >>> >>> cbind(row=as.vector(row(x)), col=as.vector(col(x)), >> value=as.vector(x)) >>> >>> >>> row col value >>> [1,] 1 1 1 >>> [2,] 2 1 2 >>> [3,] 3 1 3 >>> [4,] 4 1 4 >>> [5,] 5 1 5 >>> [6,] 1 2 6 >>> [7,] 2 2 7 >>> [8,] 3 2 8 >>> [9,] 4 2 9 >>> [10,] 5 2 10 >>> [11,] 1 3 11 >>> [12,] 2 3 12 >>> [13,] 3 3 13 >>> [14,] 4 3 14 >>> [15,] 5 3 15 >>> [16,] 1 4 16 >>> [17,] 2 4 17 >>> [18,] 3 4 18 >>> [19,] 4 4 19 >>> [20,] 5 4 20 >>> [21,] 1 5 21 >>> [22,] 2 5 22 >>> [23,] 3 5 23 >>> >>> >>> [24,] 4 5 24 >>> [25,] 5 5 25 >>>> >>> >>> On 6/25/07, Jon Hak <Jon_Hak_at_natureserve.org> wrote: >>>> >>>> I have read everything I can find on how to manipulate a results >>> matrix in >>> >> > <http://tolstoy.newcastle.edu.au/R/e2/help/07/06/19875.html#19887qlink1> >>> >>>> R and I have to admit I'm stumped. I have set up a process to > extract >>> a >>>> dataset from ArcGIS to compute a similarity index (Jaccards) in >> Vegan. >>> The >>>> dataset is fairly simple, but large, and consists of rows = sample >>> area, and >>>> columns = elements. I've been able to view the results in R, but I >>> want to >>>> get the results out to a database and a matrix that is 6000-rows x >>>> 6000-columns can be very difficult to manipulate in Windows XP. I >>> would to >>>> rotate the matrix so that the output would look like the old >> condensed >>> >>>> format in programs like Conoco. Ideally, I would like format to look >>>> something like this; >>>> >>>> >>>> Site-row Site-col Jaccard >>>> 1 1 1 >>>> 1 2 .9 >>>> 1 3 .6 >>>> 2 1 .9 >>>> 2 2 1 >>>> 2 3 .75 >>>> >>>> Thanks for any help, >>>> >>>> >>>> >>>> >>>> *********************************************************** >>>> John Hak >>>> Senior GIS Analyst/Sr. Ecologist >>>> NatureServe >>>> 4001 Discovery Drive >>>> Boulder, CO 80303 >>>> (703) 797-4809 >>>> >>>> There is perhaps no better demonstration of the folly of human >>> conceits >>>> than this distant image of our tiny world. To me, it underscores our >>>> responsibility to deal more kindly with one another, and to preserve >>> and >>>> cherish the pale blue dot, the only home we've ever known. --Carl >>> Sagan >>>> >>>> >>>> ______________________________________________ >>>> R-help_at_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 >>>> and provide commented, minimal, self-contained, reproducible code. >>>> >>> >>> -- >>> Jim Holtman >>> Cincinnati, OH >>> +1 513 646 9390 >>> >>> What is the problem you are trying to solve? >>> >>> [[alternative HTML version deleted]] >>> >>> >>> >>> >>> >>> >>> [[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. >>> >> >> >> >> -- >> Jim Holtman >> Cincinnati, OH >> +1 513 646 9390 >> >> What is the problem you are trying to solve? >> > > > > -- > Jim Holtman > Cincinnati, OH > +1 513 646 9390 > > What is the problem you are trying to solve? > -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? ______________________________________________ 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.
