search for: choleski

Hi everyone: I try to use r to do the Cholesky Decomposition,which is A=LDL',so far I only found how to decomposite A in to LL' by using chol(A),the function Cholesky(A) doesnt work,any one know other command to decomposte A in to LDL' My r code is: library(Matrix) A=matrix(c(1,1,1,1,5,5,1,5,14),nrow=3) > chol(A) [,1] [,2] [,3] [1,] 1 1 1 [2,] 0 2 2

Can we do Cholesky Decompositon in R for any matrix --------------------------------- [[alternative HTML version deleted]]

...>Da: p.dalgaard at biostat.ku.dk >Data: 21-nov-2009 18.56 >A: "Charles C. Berry"<cberry at tajo.ucsd.edu> >Cc: "simona.racioppi at libero.it"<simona.racioppi at libero.it>, <r-help at r- project.org> >Ogg: Re: [R] chol( neg.def.matrix ) WAS: Re: Choleski and Choleski with pivoting of matrix fails > >Charles C. Berry wrote: >> On Sat, 21 Nov 2009, simona.racioppi at libero.it wrote: >> >>> Hi Everyone, >>> >>> I need to take the square root of the following matrix: >>> >>>...

...of a model... Simona >----Messaggio originale---- >Da: RVaradhan at jhmi.edu >Data: 25-nov-2009 18.55 >A: <simona.racioppi at libero.it>, <P.Dalgaard at biostat.ku.dk> >Cc: <r-help at r-project.org> >Ogg: RE: [R] R: Re: R: Re: chol( neg.def.matrix ) WAS: Re: Choleski and Choleski with pivoting of matrix fails > >I do not understand what the problem is, as it works just fine for me: > >A <- matrix(c(0.5401984,-0.3998675,-1.3785897,-0.3998675,1.0561872, >0.8158639,-1.3785897, 0.8158639, 1.6073119), 3, 3, byrow=TRUE) > >eA <- eigen(A)...

...a: P.Dalgaard at biostat.ku.dk >Data: 23-nov-2009 14.09 >A: "simona.racioppi at libero.it"<simona.racioppi at libero.it> >Cc: "Charles C. Berry"<cberry at tajo.ucsd.edu>, <r-help at r-project.org> >Ogg: Re: R: Re: [R] chol( neg.def.matrix ) WAS: Re: Choleski and Choleski with pivoting of matrix fails > >simona.racioppi at libero.it wrote: >> It works! But Once I have the square root of this matrix, how do I convert it >> to a real (not imaginary) matrix which has the same property? Is that >> possible? > >No. That is t...

Dear R-devel members, I am looking for a fast Cholesky update/downdate. The matrix A being symmetric positive definite (n, n) and factorized as A = L %*% t(L), the goal is to factor the new matrix A +- C %*% t(C) where C is (n, r). For instance, C is 1-column when adding/removing an observation in a linear regression. Of special interest is the case where A is sparse. Looking at the

I have been playing around with sparse matrices in the Matrix package, in particularly with the Cholesky factorization of matrices of class dsCMatrix. And BTW, what a fantastic package. My problem is that I have to carry out repeated Cholesky factorization of a spares symmetric matrices, say Q_1, Q_2, ...,Q_n, where the Q's have the same non-zero pattern. I know in this case one does

Dear fellow R Users: I am doing a Cholesky decomposition on a correlation matrix and get error message the matrix is not semi-definite. Does anyone know: 1- a work around to this issue? 2- Is there any approach to try and figure out what vector might be co-linear with another in thr Matrix? 3- any way to perturb the data to work around this? Thanks for any suggestions.

Dear R-Users I used the nlme library to fit a linear mixed model (lme). The random effect standard errors and correlation reported are based on a Log-Cholesky parametrization. Can anyone tell me how to get the Covariance matrix of the random effects, given the above mentioned parameters based on the Log-Cholesky parametrization?? Thanks in advance Pryseley

I am trying to estimate a covariance matrix from the Hessian of a posterior mode. However, this Hessian is indefinite (possibly because of numerical/roundoff issues), and thus, the Cholesky decomposition does not exist. So, I want to use a modified Cholesky algorithm to estimate a Cholesky of a pseudovariance that is reasonably close to the original matrix. I know that there are R packages that

m <- matrix(nrow=5, ncol=5) m <- ifelse(row(m)==col(m), 1, 0.2) c <- chol(m) # Choleski decomposition u <- matrix(rnorm(2000*5), ncol=5) uc <- u %*% c cr <- pnorm(uc) cr <- qbinom(cr,1,0.5) cor(cr) I expected that the cor(cr) to be 0.2 as i set in m, but the result is around 0.1. Why is that? Thanks -- View this message in context: http://r.789695.n4.nabble.com/Ch...

Dear all, I made a simple test of the Cholesky decomposition in the package 'Matrix', by considering 2 variables 100% correlated. http://blogs.sas.com/content/iml/2012/02/08/use-the-cholesky-transformation-to-correlate-and-uncorrelate-variables/ The full code is below and can be simply copy&paste in the R prompt. After uncorrelation I still have a correlation of +-100%...

Hi there, Given a positive definite symmetric matrix, I can use chol(x) to obtain U where U is upper triangular and x=U'U. For example, x=matrix(c(5,1,2,1,3,1,2,1,4),3,3) U=chol(x) U # [,1] [,2] [,3] #[1,] 2.236068 0.4472136 0.8944272 #[2,] 0.000000 1.6733201 0.3585686 #[3,] 0.000000 0.0000000 1.7525492 t(U)%*%U # this is exactly x Does anyone know how to obtain L such

Dear R list members, I have a vector of Cholesky parameterization of a matrix let say A. I would like to compute the determinant and inverse of the original matrix A from the vector of cholesky parameters , would you suggest an R function to do the task. I have tried hard but unable to find anything like that. Please direct me any package or please share R code that can do the task. Thanks and

Hello Everyone I have a MCMC loop to calculate a time varying hierarchical Bayesian structure. This requires me to use around 5-6 matrix inversions in the loop. I use cholesky and chol2inv for the matrix decomposition. Because of the data I am working with I am required to invert a 167 by 167 matrix twice in one iteration. I need to run the iteration for 10000 times, but I get the error

Dear all: In what I am doing I sometimes get a (Hessian) matrix that has a couple of tiny negative eigenvalues (e.g. -6 * 10^-17). So, I can't run a Cholesky decomp on it - but I need to. Is there an established way to regularize my (Hessian) matrix (e.g., via some transformation) that would allow me to get a semi-positive definite matrix to be used in Cholesky decomp? Or should I try some

Dear All, My question is simple but I need someone to help me out. Suppose I have a positive definite matrix A. The funtion chol() gives matrix L, such that A = L'L. The inverse of A, say A.inv, is also positive definite and can be factorized as A.inv = M'M. Then A = inverse of (A.inv) = inverse of (M'M) = (inverse of M) %*% (inverse of M)' = ((inverse of

I've created some Splus code for a microarray problem that - needed to be in C, to take advantage of some sparse matrix properties - uses a cholesky decompostion as part of the computation For the cholesky, I used the cholesky2 routine, which is a part of the survival library. It does just what I want and I'm familiar with it (after all, I wrote it). In Splus, this all works

Hi: what I want to do is decompose the a symmetric matrix A into this form A=LDL' hence TAT'=D,T is inverse of (L)and T is a lower trangular matrix,and D is dignoal matrix for one case A=1 1 1 1 5 5 1 5 14 T=inverse(L)= 1 0 0 -1 1 0 0 -1 1 D=(1,4,9) I tried to use chol(A),but it returns only trangular, anyone know the function can return

The gchol function in library(kinship) does an LDL decomposition. An updated version has just recently been posted on Rforge, in the bdsmatrix library which is part of survival. > temp <- matrix(c(1,1,1,1,5,8,1,8,14), 3) > gt <- gchol(temp) > as.matrix(gt) # L [,1] [,2] [,3] [1,] 1 0.00 0 [2,] 1 1.00 0 [3,] 1 1.75 1 > diag(gt) # D [1]