Thanks Ruben and John for replying to me. I am trying Rcgmin as suggested by
John Nash with numerical gradient but the result converged so for not close to
what I got in CG implemented in optim( ) and I have to find the analytical
gradient equation for multivariate Gaussian distribution. Is this
Dear list-members,
I have done optimization of 3 parameters by maximum likelihood method using
conjugate gradient as optimizer. Since I have the reported value of the
parameters from an article, I can validate the result of the optimized
parameters. The problem is that optimizer converges to t
:22 PM
To: Nataraj B (ORLL-Biotech)
Cc: kjetilbrinchmannhalvor...@gmail.com; r-help@r-project.org
Subject: Re: [R] Cholesky decomposition error
On Jun 20, 2012, at 06:17 ,
wrote:
> Dear Peter,
>
> Thanks for your reply, as per my last post; my current problem is not on
> posit
:07 PM
To: Nataraj B (ORLL-Biotech)
Cc: kjetilbrinchmannhalvor...@gmail.com; r-help@r-project.org
Subject: Re: [R] Cholesky decomposition error
On Jun 19, 2012, at 10:31 ,
wrote:
> Dear Kjetil, thanks for your time to detail the code. Sorry, I am still not
> able to grasp why you are cr
aj
-Original Message-
From: Kjetil Halvorsen [mailto:kjetilbrinchmannhalvor...@gmail.com]
Sent: Monday, June 18, 2012 10:07 PM
To: Nataraj B (ORLL-Biotech)
Cc: r-help@r-project.org
Subject: Re: [R] Cholesky decomposition error
see inline!
On Mon, Jun 18, 2012 at 12:38 AM, wrote:
> Thanks Kjeti
his my workflow.
Regards,
B.Nataraj
-Original Message-
From: Kjetil Halvorsen [mailto:kjetilbrinchmannhalvor...@gmail.com]
Sent: Sunday, June 17, 2012 4:10 AM
To: Nataraj B (ORLL-Biotech)
Cc: r-help@r-project.org
Subject: Re: [R] Cholesky decomposition error
see below.
On Fri,
om: Kjetil Halvorsen [mailto:kjetilbrinchmannhalvor...@gmail.com]
Sent: Friday, June 15, 2012 11:09 PM
To: Nataraj B (ORLL-Biotech)
Cc: gunter.ber...@gene.com; r-help@r-project.org
Subject: Re: [R] Cholesky decomposition error
see inline.
On Fri, Jun 15, 2012 at 4:33 AM, wrote:
> Thanks for you
the iteration process and if possible please help me to do that.
Regards,
B.Nataraj
-Original Message-
From: Bert Gunter [mailto:gunter.ber...@gene.com]
Sent: Friday, June 15, 2012 1:51 PM
To: Nataraj B (ORLL-Biotech)
Cc: r-help@r-project.org
Subject: Re: [R] Cholesky decomposition error
am confused and I am looking for some hints to introspect the problem
further.
Regards,
B.Nataraj
-Original Message-
From: Bert Gunter [mailto:gunter.ber...@gene.com]
Sent: Thursday, June 14, 2012 6:18 PM
To: Nataraj B (ORLL-Biotech)
Cc: r-help@r-project.org
Subject: Re: [R] Cholesky dec
Dear friends,
When I do Cholesky decomposition for a 15x15 matrix using the function chol(),
I get the following error for which I do not understand the meaning of the error
Error in chol.default(M_cov) :
the leading minor of order 10 is not positive definite
When I searched online for simila
Thanks for all who replied me to this topic. I have the "L" (cholesky
decomposed matrix)as a vector listed as columwise as mentioned in the article
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.31.494 and looking for
functions to convert the vector into inverse matrix ( but chol2inv m
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 any
will try my best to explain it more. But please do reply.
Regards,
B.Nataraj
-Original Message-
From: David Winsemius [mailto:dwinsem...@comcast.net]
Sent: Thursday, May 31, 2012 8:19 PM
To: Nataraj B (ORLL-Biotech)
Cc: r-help@r-project.org
Subject: Re: [R] Optimizing variables represented
Dear R-list members,
I have a matrix with non-numeric variables in it and I have to optimize the
variables of the matrix in a formula using optim routine of the stats4 package.
I know the matrix can only take numeric data and so I would like to know how
to store non-numeric variables inside a
Dear R-list members,
I have a problem of estimation of parameters represented in a covariance matrix
using maximum likelihood function. The problem is essentially a multivariate
Gaussian random field model. The maximum likelihood function is
L(m, *S2 , *N2 ; F1) =1/ (2* sqrt(det(*
Dear R help forum members,
I am modeling a gaussian distribution for a computational biology application
and I am working in the statistical package "R". In this regard, my problem is
that I have to construct a covariance matrix with variables (non-numeric) and
the covariance matrix is to be us
Dear list members,
I have installed R in Ubuntu successfully but issuing
command like R in terminal will able to see only the R
working in command mode, the regular GUI which I use to
have in my windows installation of R missing in linux..I am
new to linux and so clueless how I can go about that a
Dear all,
Sorry to post my query once again in the list, since I did
not get attention from anyone in my previous mail to this
list.
Now I make it simple here that please give me a code for
find out the columns of a dataframe whose correlation
coefficient is below a pre-determined threshold. (For
Dear all,
For removing correlated columns in a data frame,df.
I found a code written in R in the page
http://cheminfo.informatics.indiana.edu/~rguha/code/R/ of
Mr.Rajarshi Guha.
The code is
#
r2test <- function(df, cutoff=0.8) {
if (cutoff > 1 || cutoff <= 0) {
stop(" 0 <= c
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