similar to: Plotting Upper triangle of Matrix with diagonal as the Base

Hi, nlme users, I am fitting a model for repeated measures, using gls(). The var-cov structure is UNSTRUCTURED in lower triangle and identical for the diagonal, for which I still have no idea how to fit using PROC MIXED. The error message is as follows: Error in "coef<-.corNatural"(*tmp*, value = log((cStNatPar + 1)/(1 - cStNatPar))) : NA/NaN/Inf in foreign function call

Hello and sorry that I still haven?t found a solution for my problem. I need to extract the lower and upper triangle from a square matrix including the diagonal. This diagonal is not zero in that special case. I tried with as.dist w<-as.dist(w, diag = TRUE) > w 1 2 3 4 5 1 0 2 2 0 3 3 8 0 4 4 9 14 0 5 5 10 15 20 0 but found no way to keep the diagonal that is in the

Hello, I am in need of help in putting histograms on the diagonal of a plot produced with splom(). The plot matrix I am trying to produce is to have standard scatterplots in the upper-left triangle, contour plots in the lower-right triangle, and histograms on the diagonal. I have a function that does the first two, but the histograms on the diagonal has been beyond my ability. Here is my

Hi, I want to compute the lower triangle of a square matrix (optionally, sans diagonal). With for() loops I can do something like this: ## 5 by 5 matrix rtn for (j in 1:5) { for (k in 1:j) { if (j != k) { ## optional rtn[j, k] <- my.func(j, k) } } } I'd like to do this with apply(). Is there some way I can do this kind of 'short-circuit'? Thanks, Mark Wilkinson

Hi, I am trying to use function pairs to plot the scatterplot, but I only want to keep the upper triangle, what's the argument to do this? Thanks, -Jack [[alternative HTML version deleted]]

Dear altogether, I want to blank the lower (or upper) part of a correlation matrix as it is done by dist() example: ( d <- cor(matrix(runif(12),nrow=4)) ) If I do the following d[lower.tri(d)] <- "" of course everything is changed to character - that's not what should be. Additionally, it does not work to assign "0" or anything else. The same is true for

Dear R Group I was trying to use the triangle.test function in SensoMineR and strangely i encounter a error in the output of preference matrix from the analysis. To illustrate, pl see the following dataframe of a design with the response and preference collected as shown below: design<-structure(list(`Product X` = c(3, 1, 4, 2, 4, 2, 1, 3, 4, 2, 4, 2, 1, 3, 4, 2, 4, 2, 3, 1), `Product Y` =

from ?eigen symmetric: if 'TRUE', the matrix is assumed to be symmetric (or Hermitian if complex) and only its lower triangle is used. If 'symmetric' is not specified, the matrix is inspected for symmetry. I think that could mislead a naive reader as it suggests that, with symmetric=TRUE, the result of eigen() (vectors and values) depends only on

Hello, I am using Mac OS X on a power book and R 2.5.0 I try to extract a diagonal from a dissimilarity matrix made with dsvdis, with this code: diag(DiTestRR) But I get this error message: Fehler in array(0, c(n, p)) : 'dim' spezifiziert ein zu großes Array english: Error in array(0, c(n, p)) : 'dim' specifies a too big array. Is there a limit to extract diagonals? I

I have output from a program which produces a distance matrix I want to read into a clustering program in R. The output is a .txt file and is 'almost' lower triangular in the sense that it is just the triangle below the diagonal. So for example a 4-by-4 distance matrix appears as, 1 2 3 4 5 6 i.e. it looks like a lower triangular of a 3-by3. I thought I might be able

Hi, Sorry if this is a repost. I searched but found no results. I am wondering if it is an easy way to construct the following matrix: r 1 0 0 0 r^2 r 1 0 0 r^3 r^2 r 1 0 r^4 r^3 r^2 r 1 where r could be any number. Thanks. Wen [[alternative HTML version deleted]]

Hi, I'd like to store large covariance matrices using Matrix classes. dsyMatrix seems like the right one, but I want to specify just the upper/lower triangle and diagonal and not have to instantiate a huge n^2 vector just for the sake of having half of it ignored: Dumb example: M <- new("dsyMatrix", uplo="U", x=rnorm(1e4), Dim=as.integer(c(100, 100))) diag(M) <- 1

> I am trying to produce a heatmap of pairwise correlations, but since the matrix is > symmetric, I only need either the upper or the lower triangle. I have scoured the > web and R documentation, but I have not been able to find a way to produce such a > figure. Is there a simple way to produce a heat map with only the part above or > below the diagonal? You might want to check

Hello, I need to chenge axes orirentation in triangle plot. (function triangle.plot in ade4 package) I want to plot elasticities of some species in demographic triangle, where axes values commnly increace "clockwise". If some better imangination is needed, see http://www.open.ac.uk/science/biosci/personalpages/j.silvertown/pdfs/Silvertown%20et%20al.%201993.pdf I am sorry if I just

Dear R-experts, I have found a splom-modification online which is given below. This works perfectly, but I would like to have a matrix of given correlation values to be used in the lower triangular part (lower.panel) of the splom-plot instead of calculated correlation values. Here is the matrix I would like to use (it can be any other convenient data structure):

Hello, everybody, I hope somebody could help me with a dist() function. I have a data frame of size 2*4087 (col*row), where col corresponds to the treatment and rows are species, values are Hellinger distances, I should reconstruct a distance matrix with a dist() function. I know that "euclidean" method should be used. When I type: dist(dframe,"euclidean") it gives me a

Hi, I am trying to create a triangular plot to show the 'composition' of a set of items with three variables (historically the percent sand, silt and clay in soil). So far I have tried the 'soil texture triangle plot' in the package plotrix and the 'ternary or triangular plots' in the package cwhtool (cwhmisc). Both have strengths and weaknesses, but neither has a

Suppose I have three numbers p1, p2, p3 with 0 <= p1,p2,p3 <= 1 and p1+p2+p3=1, and a function f=f(p1,p2,p3) = f(p1,p2,1-p1-p2). How to draw a contour plot of f() on the p1+p2+p3=1 plane, that is, an equilateral triangle? Functions triplot(), triangle.plot(), and ternaryplot() give only scatterplots, AFAICS -- Robin Hankin Uncertainty Analyst National Oceanography Centre,

Hello R users... how to align this Zmat (triangle image) in X axis? I would like that the triangle's base become in the X axis and the triangle's height become in the Y axis Is there some trick for make this? Thanks. Cleber ######################## my test and try f <- function(x,y){ z=1-x-y z[ z < (-1e-15) ] <- NA return( -100*x+0*y+100*z ) } x = seq( 1, 0,

Two questions about matrix indexing: Is is correct that V <- V[lower.tri(V, diag=TRUE)] returns the lower triangular of matrix V, that is: all elements above diagonal are set to zero? I understand that the triangle of matrix elements of V for which lower.tri is TRUE are returned while the others (above diagonal) are set to zero (or NA ???). If D and B are vectors of logicals, what