similar to: removing of memory - optim()?

Hi, my name is Marcel R. Lopes. My problem is, I made a code to calculate the estimates of a Cox model with random effects. Used to optimize the R command for this. The estimates were calculated correctly, but the Hessian matrix does not have good values. The same thing was done in SAS and gave good results for the Hessian Matrix. Where is the problem in R? As the Hessian is calculated?. How

Dear all I'm having some trouble with a bound-constrained optimization using optim(...,method="L-BFGS-B"). Usually, everything works fine, but for some simulations, the algorithm just gets stuck. When I let my function (+gradient) evaluation print out the function value, I see that L-BFGS-B keeps calling the function with arguments giving the same function value (up to at least

Dear R users, I am trying to minimise a function using "nlm". I am getting the following error message: "Error: function is too long to keep source" The function is really very long (about 100 A4 pages). Is there anything I could do to solve this problem? At the moment I am using "nlmin" in S-Plus with no problems but I'd prefer to use R. Thank you very

Hi everyone, I have two questions: I would like to get confidence intervals on the coefficients derived from the optim() function. I apply optim() to a given function f > res <- optim(c(0.08,0.04,1.),f,NULL,method="L-BFGS-B",lower=c(0.,0.,0.)) And I would like to get the p-value and confidence intervals associated with > res$par My second question deals with error message. I

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

Dear RUsers, I am new to R. I am learning how to use R. I am a PC user and run R on windows. I would appreciate if some one could guide me on a few questions I have: 1) I have 4 cel files (2 replicates for NORM and Disease resp). I have been able to run siggenes on this dataset where I have 4 labels in the class file groupsnhi.cl op-> (0,0,1,1) and my data has been read into datrmanhi after

Dear Group I'm still trying to bring many data into R (see older postings). After solving some troubles with the database I do most of the work in MySQL. But still I could be nice to work on some data using R. Therefore I can use a dedicated Server with Gentoo Linux as OS hosting only R. This Server is a nice machine with two CPU and 4GB RAM which should do the job: Dual Intel XEON 3.06 GHz

Some naive questions: 1) How to remove a column in a data frame? I expected that rm would work but this is not the case (e.g. rm(dat$yyy) gives Warning message: remove: variable dat$yyy was not found). I only found to assign NULL value (e.g.: dat$yyy<-NULL). Is it the right way? 2) Is the place formerly occupied by dat$yyy automatically gained by R for other uses? 3) If t1 and t2 are 2 only

On May 24, 2008, at 11:43 AM, Marcel Moolenaar wrote: > All, > > So far I've tried LLVM on amd64, i386, ia64 and powerpc under FreeBSD > and aside for ia64, things look pretty good for a first try. There > are 2 unexpected failures for PowerPC, which appear to be caused by > uninitialized memory. I'm still working on a fix for that (need to > brush up on my C++

All, So far I've tried LLVM on amd64, i386, ia64 and powerpc under FreeBSD and aside for ia64, things look pretty good for a first try. There are 2 unexpected failures for PowerPC, which appear to be caused by uninitialized memory. I'm still working on a fix for that (need to brush up on my C++ skills). [sidenote: In FreeBSD -current, the memory allocator initializes memory with 0xa5

I'd like to be able to test linear hypotheses after setting up and running a model using optim or perhaps nlm. One hypothesis I need to test are that the average of several coefficients is less than zero, so I don't believe I can use the likelihood ratio test. I can't seem to find a provision anywhere for testing linear combinations of coefficients after max. likelihood. Cheers

Hi, in part of my code I need to optimize a function from within Rcpp (I followed the 2nd answer here https://stackoverflow.com/questions/48348079/applying-the-optim-function-in-r-in-c-with-rcpp). However, I found that the function leaks memory (very little, but it compounds if it's a part of repeatedly running simulation). I created a minimal reproducible example, but I have no idea where

Dear all, I am trying to make some matrix operations (whose size I think is smaller than what R allows) but the operations are not feasible when they run in one session but it is feasible if they run separately while each operation is totally independent of the other. I run the code in one session the error that appears is: Error: cannot allocate vector of size 915.5 Mb R(16467,0xa0421540)

Hi, ever since I have switched my server from Centos 7 to Fedora 32, asterisk is showing memory issues and no calls are possible. I'm using the asterisk that comes with Fedora; before that, I used a self-compiled version on Centos. The hardware is still the same. Asterisk shows the following message when trying to make a call: WARNING[92530]: pbx.c:4644 increase_call_count: Available

On May 24, 2008, at 12:12 PM, Bill Wendling wrote: > Let us know if you would like extra eyes on the two PPC failures. Many > of us have a lot of experience with C++. :-) Do you know where these > allocations are? I don't mind if people help out, so here's some information: FAIL: /nfs/llvm/src/llvm/test/Transforms/PredicateSimplifier/ 2006-11-04-ReplacingZeros.ll Failed with

Hi, I am learning R by reading R source code. Here is one question I have about the optim function in R. The context : In the optim.R, after all the prep steps, the main function call call is made via : .External2(C_optim, par, fn1, gr1, method, con, lower, upper). So, it seems to me, to follow what is going on from here, that I should read the optim function in \src\library\stats\src\optim.c

Hello, I wonder why the control parameter REPORT is not supported by method SANN. Looking into optim.c I found an internal constant: #define STEPS 100 ... and decreasing this to 10 helped me fine-tuning the annealing parameters in an actual problem. Is there any reason why not passing nREPORT to samin and setting something like: STEPS = nREPORT / tmax Thomas P. -- Thomas Petzoldt

Hello! I am getting the following errors when running optim() [I tried optim() with 3 different methods as you can see]: Error in optim(c(0.66, 0.999, 0.064), pe, NULL, method = "L-BFGS-B") : objective function in optim evaluates to length 6 not 1 > out <- optim( c(0.66, 0.999, 0.064), pe, NULL, method = "Nelder-Mead") Error in optim(c(0.66, 0.999, 0.064),

> hi all, > I am using optim. I am getting the following error message: > > Error in optim(par = start.vals[, h], fn = post.func.pois, gr = post.grad. > pois, : > L-BFGS-B needs finite values of fn > > If I look at optim typing '> optim' it seems that the error comes from > inside .Internal(optim), so I wonder how can I see the code for .Internal(

Hi all, I?m using the arima() function to study a time series but it gives me the following error: Error en optim(init[mask], armafn, method = "BFGS", hessian = TRUE, control = optim.control, : non-finite finite-difference value [3] I know that I can change the method of the arima() to "CSS" instead of "ML" but I'm specially interested in using