Displaying 20 results from an estimated 11000 matches similar to: "big databases"
2005 Dec 20
1
Problems in batch mode
Dear R-users,
I am trying to run some simulations in batch mode. In an older version
of the program, I used
rterm --vsize=100M --nsize=5000K --restore --save <input file> output file,
however, in the new version R 2.2.0 , the parameters vsize and nsize are
ignored.
I can use the command memory.limit to increase memory, but I am not sure if
this corresponds to vsize and nsize.
2005 Sep 23
4
books about MCMC to use MCMC R packages?
Dear list users,
I need to learn about MCMC methods, and since there are several packages in
R that deal with this subject, I want to use them.
I want to buy a book (or more than one, if necessary) that satisfies the
following requirements:
- it teaches well MCMC methods;
- it is easy to implement numerically the ideas of the book, and notation
and concepts are similar to the corresponding R
2005 Aug 13
2
monte carlo simulations/lmer
Hi - I am doing some monte carlo simulations comparing bayesian (using
Plummer's jags) and maximum likelihood (using lmer from package lme4
by Bates et al).
I would like to know if there is a way I can flag nonconvergence and
exceptions. Currently the simulations just stop and the output reads
things like:
Error in optim(.Call("lmer_coef", x, 2, PACKAGE = "Matrix"), fn,
2004 Sep 28
3
slow loops in Monte Carlo Simulations
Hi there,
I am running Monte Carlo Simulations in R using ordinary "while
(condition)" loops. Since the number of iterations is something like
100.000 and within each iteration a given subsample is extended
sequentially it takes hours to run the simulation.
Does anyone know if there is either a way to avoid using loops in
Monte Carlo Simulations or how to include possible faster
2020 Jul 14
1
dovecot 2.2.13
all, below command not reporting the actual usage report on dovecot 2.2.13.
please share your suggestion to how to fix this issue
doveadm -f flow mailbox status -A -t 'messages vsize' '*' is just showing
rkreddy messages=0 vsize=0
jcplho messages=0 vsize=0
planning messages=0 vsize=0
accounts messages=0 vsize=0
spam.notify messages=0 vsize=0
jsraju messages=0 vsize=0
amarnath
1998 Nov 30
1
[R] R functionality
> Date: Mon, 30 Nov 1998 12:07:10 -0500
> From: Paul Gilbert <pgilbert@bank-banque-canada.ca>
> To: Ed Kademan <kademan@phz.com>
>
> >Is there anything R can do that Splus can't?
>
> Problems which require lots of looping and cannot be re-coded as vector/matrix
> operations are theoretically possible but practically infeasible in S, unless
> they
2013 Mar 28
3
problem with plots with short example.
i am having problem running my own data. yesterday it was working just fine. today it is not. this is the code i was using as an example to follow. this code ALSO worked just fine yesterday, and is no longer working at all. i suspect it is a problem with either my computer or the software, at this point. if THIS won't even run.... something is wrong.
i can assure you this isn't
2010 Jan 19
2
Server hanging despite efforts to correct memory limits
My group is working with datasets between 100 Mb and 1 GB in size, using
multiple log ins. From the documentation, it appears that vsize is limited
to 2^30-1, which tends to prove too restrictive for our use. When we drop
that restriction (set vsize = NA) we end up hanging the server, which
requires a restart. Is there any way to increase the memory limits on R
while keeping our jobs from
2012 Jun 18
1
Problem with 'doveadm mailbox status -t' reporting cumulative vsizes after upgrading from v2.0.16 to v2.1.7
Hi,
I upgraded from Dovecot v2.0.16 to v2.1.7 over night and I noticed this
morning that one of my daily reports which lists summarised mailbox
sizes per user has started listing nonsense for vsizes.
The reporting script at its core calls :
doveadm -f flow mailbox status -A -t 'messages vsize' '*'
It appears that Dovecot 2.1.7 is not resetting the vsize after collating
the sum
2003 Oct 16
1
Improving efficiency in "outer"-like calculation
Hello,
I am doing mcmc=10000 simulations from a posterior distribution of the parameters
of a mixture of K=6 normal densities.
I have mcmc by K matrices simMeans, simVars and simWeights containing
the simulation output: one row for each simulation, one column for
each normal component of the mixture.
One thing I would like to do is a plot of the posterior predictive
density. In order to do that
1999 Apr 27
2
Memory management
Dear all,
I don't get it:
First of all, the help doesn't say what are the memory limits of
R. Say, what's the max heap size for instance ????
Secondly, I invoke R with the following commands each time:
rgui --vsize 30M --nsize 1000K
rgui --vsize 30M --nsize 2000K
rgui --vsize 30M --nsize 3000K
rgui --vsize 30M --nsize 4000K
I try to open a matrix 8000x8000 by issuing
2009 Nov 30
1
allocating vector memory > 1 GByte on Windows XP / Vista / 7
Let me begin stating that I read all help files and faq's on the subject
matter (there aren't more than about a dozen) but either did not find
solutions or found them not to work.
Here is the issue. I am trying to run a spatial regression on a
medium-sized dataset. Part of the functions in the spdep package I use
require me to allocate a vector of 1.1 Gb (mine is not a spatial SIG
2004 Oct 11
2
memory in R
Hi:
I am doing a MCMC algorithm which is well known to
consume much computer memory. And I have a problem
everytime I run my R program. It stopped at certain
iteration and says "can not allocate a vector of 19
kb".
It seems that the computer's memory has been
exhausted. However, it is said that after each
iteration the objects (such as a huge matrix) can be
set to NULL. And the
2010 May 20
1
ERROR: cannot allocate vector of size?
I've looked through all of the posts about this issue (and there are
plenty!) but I am still unable to solve the error. ERROR: cannot allocate
vector of size 455 Mb
I am using R 2.6.2 - x86_64 on a Linux x86_64 Redhat cluster system. When I
log in, based on the specs I provide [qsub -I -X -l arch=x86_64] I am
randomly assigned to a x86_64 node.
I am using package GenABEL. My data (~ 650,000
2006 Nov 29
2
--max-vsize option
The R memory docs say that the --*-vsize option takes an integer
argument and then 'G', 'M', 'K', or 'k'. When I start R using
R --max-vsize=10G
I receive the warning:
WARNING: --max-vsize=10G=10'M': too large and ignored
The system that I'm working on is a 64-bit Sun server with 40G of
memory. What is the correct syntax for this command?
Daniel
2011 Jul 21
1
--max-vsize
Hi,
In both R 2.13 and the SVN trunk, I observe odd behaviour with the
--max-vsize command-line argument:
1. passing a largeish value (about 260M or greater) makes mem.limits()
report NA for the vsize limit; gc() continues to report a value...
2. ...but that value (and the actual limit) is wrong by a factor of 8.
I attach a patch for issue 2, lightly tested. I believe that fixing
issue 1
2018 Jan 18
2
MCMC Estimation for Four Parametric Logistic (4PL) Item Response Model
Good day Sir/Ma'am! This is Alyssa Fatmah S. Mastura taking up Master of
Science in Statistics at Mindanao State University-Iligan Institute
Technology (MSU-IIT), Philippines. I am currently working on my master's
thesis titled "Comparing the Three Estimation Methods for the Four
Parametric Logistic (4PL) Item Response Model". While I am looking for a
package about Markov chain
2005 Nov 08
1
Hybrid Monte Carlo algorithm (MCMC)
Hi all,
I'm trying to estimate a nested model (purchase decision, cloglog formula, &
quantity bought given a purchase, truncated Poisson). Some of the parameters
are mixed (6) and 4 are fixed for all the respondent.
The simulated ML (500 simulations) method forwards highly correlated
estimates.
After some research, Hybrid Monte Carlo seems to be a good alternative to
estimate the model. I
2009 Jan 13
3
problem whit Geneland
I do the these passages:
library(Geneland)
set.seed(1)
data <- simdata(nindiv=200,
coord.lim=c(0,1,0,1) ,
number.nuclei=5 ,
allele.numbers=rep(10,20),
IBD=FALSE,
npop=2,
give.tess.grid=FALSE)
geno <- data$genotypes
coord <- t(data$coord.indiv)
path.mcmc <-
2012 Apr 05
1
reclaiming lost memory in R
Dear list,
I am trying to reclaim what I think is lost memory in R, I have been using gc(), rm() and also using Rprof to figure out where all the memory is going but I might be missing something.
I have the following situation
basic loop which calls memoryHogFunction:
for i in (1:N) {
dataset <- generateDataset(i)
fit <- try( memoryHogFunction(dataset, otherParameters))
}
and