similar to: list of distance matrices

Dear UseRs, MY PROBLEM IS A SMALL PIECE OF A REAL BIG AND A COMPLICATED PROBLEM. IF I DELIBERATE IN A VERY SIMPLE WAY THEN ALL I WANT IS TO PUT ALL THE POSSIBLE COMBINATIONS OF 75 DISTANCE MATRICES (BY TAKING 4 MATRICES, MORE COMMONLY 75C4), in the following equation. t<-as.matrix((MAT1)^2+(MAT2)^2+(MAT3)^2+(MAT4)^2+,upper=T,diag=T)) Then "1215450" values of "t"(one for

Hi all, I am trying to compare two distance matrices with R. I would like to create a XY plot of these matrices and do some linear regression on it. But, I am a bit new to R, so i have a few questions (I searched in the documentation with no success). The first problem is loading a distance matrix into R. This matrix is the output of a the Phylip program Protdist and lookes like this: 5

I am new at 'R' and not even sure whether I am contacting the appropriate forum!! However, I have carried out several mantel tests (using 'R') on genetic data and would like to plot the results in the form of a histogam of the distribution - and preferably use a procedure that shows the critical 'r' value. The tail end of my analysis is shown below. I just need help to dig

I'm trying to perform a mantel test that ignores specific pairs in my distance matrices. The reasoning is that some geographic distances below a certain threshold suffer from spatial autocorrelation, or perhaps ecological relationships become less relevant that stochastic processes above a certain threshold. The problem is that I can't find a way to do it. If I replace values in either or

Hi useRs, I am trying to compare several distance matrices obtained from subsets of variables from the same experiment. I put all the subsets in a list and then calculated the distance matrices with lapply. In order to do a mantel test between them I wrote a function the returns a list with the output of single tests. I would like to include the name of the tests, so I know what each element

Dear Sir/ Madam, I would like to ask you about mantel test in R. In ade4 package, if I want to use mantel.rtest, I get error massage "Object of class to "dist" expected". As I already have two dissimilarity matrices, shall I again compute distance measure using this function? If not, could you please let me know which function/command I can use to do? Thank you very much in

Dear all, I would like to compare two distance matrices to find the correlation between those and create a XY plot.could you please kindly help me and let me know how I can do that using R.(Mantel test?). Your help is very much appreciated!! Many thanks! Regards, Sima Fakheran ............................................................... Sima Fakheran Esfahani PhD Student Institute of

HI Elisa, You could use ?cut() vec1<-c(33,18,13,47,30,10,6,21,39,25,40,29,14,16,44,1,41,4,15,20,46,32,38,5,31,12,48,27,36,24,34,2,35,11,42,9,8,7,26,22,43,17,19,28,23,3,49,37,50,45) label1<-unlist(lapply(mapply(c,lapply(seq(0,45,5),function(x) x),lapply(seq(5,50,5),function(x) x),SIMPLIFY=FALSE),function(i) paste(i[1],"<x<=",i[2],sep="")))

Hi, i'm looking to test if two distance matrices are statistically different from each others. These two matrices have been computed on the same set of data (several population samples) 1. using a particular genetic distance 2. weighting that genetic distance with an extra factor (we can look at this as one set is computed before applying a treatment and the second one after applying

Hi, I have the following function that I want to apply to a list of 14 matrices (1536 x 170) of binary data: DRes <- function(x, nr = 10000, metric = "mixed", ...) { require(analogue) require(ade4) m <- c() for (i in 1:nr) { set.seed(i) x1 <- x[, sample(dimnames(x)[[2]], length(x[1,])/2)] x2 <- x[, !dimnames(x)[[2]] %in% dimnames(x1)[[2]]] d1 <-

Hi, I'm very new to R. I want to know if there is any way to write only the lower half of a distance matrix created in R to a csv file for example. I get the 'cannot coerce class "dist" into a data.frame' message when I try. I have used as.matrix and can write to a file this way, but as a full matrix. The reason I only want the lower half is that I've been doing some

Dear useRs, I have a very basic question. I have a distance matrix and i skipped the upper part of it deliberately. 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 elisa

dear useRs, i have a list containing 16 matrices. i want to calculate the column mean of each of them. i tried >sr <- lapply(s,function(x) colMeans(x, na.rm=TRUE)) but i am getting the following error >Error in colMeans(x, na.rm = TRUE) : 'x' must be numeric can it be done in any other way? and why i am getting this error?? thanks in advance.. elisa [[alternative

Hi there, I would like to find a more efficient way of permuting the rows and columns of a symmetrical matrix that represents ecological or actual distances between objects in space. The permutation is of the type used in a Mantel test. Specifically, the permutation has to accomplish something like this: Original matrix addresses: a11 a12 a13 a21 a22 a23 a31 a32 a33 Example

Hi everyone, I have two matrices of 2000x2000 size. They consist of a measurement of RMSD deviations of a protein structure. The basic question i want to answer is the following: are there a significant differences between the two matrices? I aim to use the Mantel test. I don't really know if this is a good idea or if there are better solutions for these mega matrices. Thanks [[alternative

dear useRs, i created a distance matrix, of certain voltage values. unfortunately, i lost the original values. i am only left with the distance matrix that i created from those values. i wanted to ask that is there a way in R to reverse distance matrix for the original values? thanks in advance eliza [[alternative HTML version deleted]]

Dear useRs, i want to split a matrix having 1116rows and 12 columns. i want to split that matrix into 36 small matrices each having 12 columns and 31 rows. The big matrix should be splitted row wise. which means that the first small matrix should copy values which are in first 31 rows and 12 columns of the big matrix. similarly 2nd small matrix should contain values from 32nd to 63rd row of the

Dear Users,I have two matrices A=15*365 and B=1*365. i want to calculate "Euclidean Distance" between these matrices in such a way that i should have euclidean distance of matrix B against all the columns of matrix A. More precisely, first i want euclidean dist. of column 1 of A against B, then column 2 against B, 3rd column of A against B and so on.is there a way in r to do it?your help

Hi Elisa, Try this: date1<-format(seq.Date(as.Date("1991.1.1",format="%Y.%m.%d"),as.Date("1996.12.31",format="%Y.%m.%d"),by="day"),"%Y.%m.%d") ?length(date1) #[1] 2192 mat1<-matrix(c(.314,.314,.273,.273,.236,.236,.236,.236,.273,.314,.403,.314),ncol=1) res1<-

Dear Elisa, Try this: el<- matrix(1:100,ncol=20) ?set.seed(25) ?el1<- matrix(sample(1:100,20,replace=TRUE),ncol=1) In the example you showed, there were no column names.? ?list(el[,sort(el1)[1:3]],sort(el1,index.return=TRUE)$ix[1:3]) #[[1]] ?# ?? [,1] [,2] [,3] #[1,]?? 31?? 61?? 71 #[2,]?? 32?? 62?? 72 #[3,]?? 33?? 63?? 73 #[4,]?? 34?? 64?? 74 #[5,]?? 35?? 65?? 75 # #[[2]] #[1] 9 5 3 A.K.