Displaying 20 results from an estimated 5000 matches similar to: "LDL' Cholesky decomposition"
2011 Dec 16
0
Rd error message
I get the following error from one of my Rd files in R CMD check (R
2-14.0)
* checking Rd files ... WARNING
Error in switch(attr(block, "Rd_tag"), TEXT = if (!grepl("^[[:space:]]*
$", :
EXPR must be a length 1 vector
problem found in ?backsolve.Rd?
This is likely something that will be glaringly obvious once it's
pointed out, but without a line number I can't
2005 Jan 21
1
Cholesky Decomposition
Can we do Cholesky Decompositon in R for any matrix
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2018 Jan 09
1
resolving a names conflict
The survival package uses a generalized cholesky decompostition throughout.? If A is a
symmetric matrix A= LDL' where L is lower triangular with 1s on the diagonal, D is
diagonal, and D[i,i] =0 if column i of A is redundant.? Being able to read the rank and
dependencies directly off of D is very handy.
The bdsmatrix package uses the same, but exposes it to the user as gchol and solve
2004 Oct 18
1
installing package 'kinship'
Dear All,
I have problem installing the 'kinship' package. I used the
'install.packages' from R command line and had no problem installing other
packages before.
Here is what I get:
* Installing *source* package 'kinship' ...
** libs
gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include
-I/usr/local/include -fno-common -g -O2 -c agfit6b.c -o agfit6b.o
2010 Jul 27
0
AIC from coxme
Hi,
I am running the following model:
fit1.full <- coxme(Surv(age_sym1, sym1) ~ sex + lifedxm*sex + (1|famid),
data=bip.surv)
I would like to extract the AIC from that object to calculate the AICC.
However, when I look at str(fit1.full) and summary(fit1.full) (pasted
below) I don't see anything that would allow me to get pull the AIC out
from that object.
Is there a way to retrieve the
2009 Aug 13
2
CMD check error (bug?)
R version 2.9.0 running on Centos (Red Hat linux).
I have a pair of packages coxme and bdsmatrix. The latter is installed
in my local library (I don't have permission for global install at
work.) That is, it is in the location pointed to in R_LIBS_USER. In R,
the command library(bdsmatrix) works fine.
Coxme depends on bdsmatrix, in fact uses some cross-calls to it's C
routines, which
2009 Mar 05
3
Package issue
I've converted the bdsmatrix package (used by coxme) to the newer style of
S4, and uploaded it. It is in the pkg directory of survival, on r-forge.
I'm stuck on something that is almost certainly a namespace issue. I've
borrowed liberally from Matrix (a big help) and read the documentation, and
just upgraded to 2.8.1 - but still stuck.
All the tests work when I run them "by
2012 May 03
0
Modified Cholesky decomposition for sparse matrices
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
2013 Jun 19
0
Simple example of variables decorrelation using the Cholesky decomposition
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%...
2009 Apr 01
2
Need Advice on Matrix Not Positive Semi-Definite with cholesky decomposition
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.
2009 Mar 11
0
anyone can help me with Cholesky Decomposition
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
2010 Apr 23
2
Deferred Default Marker
I've finally narrowed down a puzzling problem: here is the short test
case.
tmt34% R --vanilla
R version 2.10.0 (2009-10-26)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
> temp <- matrix(runif(50), ncol=2)
> t(temp) %*% temp
[,1] [,2]
[1,] 7.916016 6.049698
[2,] 6.049698 7.650694
> library(kinship)
Loading required package:
2009 Mar 10
5
Cholesky Decomposition in R
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
2008 Dec 28
1
Random coefficients model with a covariate: coxme function
Dear R users:
I'm new to R and am trying to fit a mixed model
Cox regression model with coxme function.
I have one two-level factor (treat) and one
covariate (covar) and 32 different groups
(centers). I'd like to fit a random coefficients model, with treat and covar
as fixed factors and a random intercept, random
treat effect and random covar slope per center.
I haver a couple of
2008 Mar 05
1
coxme - fitting random treatment effect nested within centre
Dear all,
I am using "coxme" function in Kinship library to fit random treatment effect nested within centre. I got 3 treatments (0,1,2) and 3 centres. I used following commands, but got an error.
> ugroup=paste(rep(1:3,each=3),rep(0:2,3),sep='/')
> mat1=bdsmatrix(rep(c(1,1,1,1,1,1,1,1,1),3),blocksize=rep(3,3),dimnames=list(ugroup,ugroup))
>
2009 Aug 05
1
inheriting C symbols
The package coxme depends heavily on bdsmatrix, to the point of needing
access to some of its C calls. The kinship package (in progress) uses
the R level functions in bdsmatrix, but not the C calls. That is, I
don't want to always export the symbols.
For testing I can use an explicit dyn.load('somepath/bsdmatrix.so',
local=F). How do I incorporate such a dependency in the
2007 Jun 11
0
lmekin() function in kinship package
Hi,
I had a problem with the lmekin() in kinship package:
lmekin() can not be wrapped into another function
library(kinship)
#creat an example dataset
xx<-rnorm(100)
yy<-rnorm(100)
id<-1:100
test.dat<-as.data.frame(cbind(xx,yy,id))
rm(xx,yy,id)
a<-bdsmatrix(rep(10,10),rep(block,10),dimnames=list(c(1:100),c(1:100)))
#100x100 block (n=10) diagonal matrix to indicate the
2009 Nov 23
1
R: Re: chol( neg.def.matrix ) WAS: Re: Choleski and Choleski with pivoting of matrix fails
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?
Best,
Simon
>----Messaggio originale----
>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
2011 Dec 05
2
class extension and documentation
I've added a "backsolve" method to the bdsmatrix library.
Per the Extending manual section 7.1 I've also added the following 3
lines along with my setMethod definitions for 2 classes.
backsolve <- function(r, ...) UseMethod("backsolve")
backsolve.default <- base:::backsolve
formals(backsolve.default) <- c(formals(backsolve.default), alist(...
= ))
I've
2017 Dec 29
0
winbuilder warning message wrt function pointers
You can legally cast a function pointer to another function pointer, where
the signatures differ. (It is not legal to cast between data and function
pointers.)
I would make typedefs for the various signatures, as the casting syntax is
more
readable then.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Fri, Dec 29, 2017 at 10:13 AM, Therneau, Terry M., Ph.D. <
therneau at mayo.edu> wrote: