similar to: using R's optimization routines from C

Hi, I have read R's Writing Extensions manual and am still confused about how to use some of the routines there when I call from C. Specifically, I am writing a little test function which I will optimize using the nmmin function which underlies R's optim() with Nelder-Mead. I guess I wonder what library/header files I should be using. I was using R_ext/Applic.h and linking with libR but I

My code is as follows: #include <iostream> #include <cmath> using namespace std; #define MATHLIB_STANDALONE 1 extern "C" { #include "R_ext/Applic.h" } typedef struct TT{ double ** tempX; double * tempY; int tempN; } TT, *MM; double fn(int N, double * beta, void * ex){ double total = 0; int i = 0,j = 0; double * betaFn = new double[N]; MM tmp = (MM)ex;

Dear list, I was trying to use the R API for optimization method "Simulated annealing" void samin(int n, double *x, double *Fmin, optimfn fn, int maxit, int tmax, double temp, int trace, void *ex); but I encountered the following problem: The implementation of the function samin (as seen in src/main/optim.c) passes its void * argument "ex" into the function

Hi, I'm trying to get a toy program making use of nmmin to run successfully. I've gotten to the point of compiling. However, when I attempt to run my executable, I guess a bus error. I see that someone else has asked about using nmmin before <http://tolstoy.newcastle.edu.au/R/help/06/03/23944.html>, but I haven't come across any replies. Is there some documentation on how to

Sorry, forgot to switch the header to the R group.... --- Globe Trotter <itsme_410 at yahoo.com> wrote: > Date: Thu, 2 Mar 2006 19:35:21 -0800 (PST) > From: Globe Trotter <itsme_410 at yahoo.com> > Subject: Re: [R] calling R's library using C > To: Dirk Eddelbuettel <edd at debian.org> > > Hi, Dirk: > > Thanks for all the help. I thought I would

I am trying to use the R API to call optim functions (nmmin, vmmin, lbfgsb, etc.) through a C program but I couldn't find the shared library to link under the R-2.6.0 build which is compiled under Linux (REL5). main.cpp:35: undefined reference to `Rf_initEmbeddedR(int, char**)' main.cpp:41: undefined reference to `nmmin' Thanks in advance for any help. ------------------------

I've searched to find examples of how to work with the C versions of optim. I've separated out the function just to test on it alone, and currently I'm attempting to use fmmin as follows: !~~CODE ~~! double optimfn(int n, double *par, void *ex) { double * lambda = (double*)malloc(sizeof(double)*n); double sum = 0; for(int i =0; i < n; i++) { lambda[i] =

Hi, This is Kotien Wu from NIH/NCI. We want to use R function for our web: http://cgap.nci.nih.gov It works for functions in R/R-1.9.1/src/nmath/standalone very well. We have function GetPvalueForT.c which has #define MATHLIB_STANDALONE 1 #include <Rmath.h> double GetPvalueForT ( double t, double deg ) { return 2 * pt(t, deg, 0, 0); } We create GetPvalueForT.i, which has /* File :

Hi, I am wondering where the library file for R's nmath routines are? Doing a search on libR gave me the following: /usr/lib/libRKC16.so.1.2.0 /usr/lib/libRKC.so.1.2.0 /usr/lib/R/lib/libRlapack.so /usr/lib/R/lib/libR.so /usr/lib/libRKC.so.1 /usr/lib/libRKC16.so.1 None of these have the functions in nmath. Any help? Many thanks and best wishes! GT

Hi, I'm seeing something that may be a bug in R's standalone math library, which is packaged by Debian as r-mathlib. I reported it to the Debian BTS as http://bugs.debian.org/657573 I'm using Debian squeeze, and the code was tested with r-mathlib 2.11.1-6 (default on stable) and 2.14.1-1 (from testing/unstable). I summarize this report below. The following code with the R math

Can anyone help me with lbfgsb (function for optimization)? It takes the following parameters: void lbfgsb (int n, int lmm, double *x, double *lower, double *upper, int *nbd, double *Fmin, optimfn fn, optimgr gr, int *fail, void *ex, double factr, double pgtol, int *fncount, int *grcount, int maxit, char *msg, int trace, int nREPORT); What do I put for parameter ex (11th parameter)? I looked at

Full_Name: c fillekes Version: Version 2.2.1 (2005-12-20 r36812) OS: Gentoo Linux kernel 2.6.12 Submission from: (NULL) (129.116.71.233) "Not Available" is of course not a numeric: R > is.numeric (NA) [1] FALSE But for some reason, all arithmetic operations on NA's are in fact numeric, even if it's with other NA's. > is.numeric (NA+NA) [1] TRUE >

On Wed, 2005-12-21 at 15:00 +0100, edd at debian.org wrote: > --CE+1k2dSO48ffgeK > Content-Type: text/plain; charset=us-ascii > Content-Disposition: inline > > Resend after type in mailheader. I have the bug on my system with > yesterday's R 2.2.1. A library mismatch is still a likely cause. > > Dirk <SNIP> > On 21 December 2005 at 01:50, Ethan

Hello, I can't link a c code with Mathlib according to introduction of R manual "Writing R Extensions", page 60. It is written : "It is possible to build Mathlib, the R set of mathematical functions documented in 'Rmath.h?, as a standalone library 'libRmath? under Unix and Windows. (This includes the functions documented in Section 5.7 [Numerical analysis

Hi, I'm trying to plot several lag.plots on a page, however the second plot replaces the first one (although it only takes up the upper half as it should): par(mfrow=c(2,1)) a<-sin(1:100) b<-cos(1:100) lag.plot(a) lag.plot(b) What's the trick to this? I'm using R 2.2.1 (2005-12-20 r36812) on Ubuntu Linux. Thanks, Gad -- Gad Abraham Department of Mathematics and

Hi, I wanted to use R's lbfgsb method for minimization from C. Unfortunately, my toy examples always crashes (segmentation fault). What's wrong with it? double eval(int n, double* par, void *ex) { double result = 0; for (int i=0; i<n; ++i) { result += par[i]*par[i]; } printf("result=%.2f\n", result); return result; } void grad(int n, double *par, double *gr,

dear R users not sure why I am not able to install tkrplot. > install.pacakges ("tkrplot", dependencies=TRUE) ... Configure: error: no acceptable C compiler found in $path ... well, I am using debian testing 2.6.15, R Version 2.2.1 (2005-12-20 r36812) #whereis gcc gcc: /usr/lib/gcc thank you --------------------------------- [[alternative HTML version

Full_Name: Lutz Prechelt Version: 2.2.1 OS: WinXP SP2 Submission from: (NULL) (130.133.8.114) This command plot(0, 0, xlim=c(3, 5), ylim=c(0, 10, 17)) should complain about 'ylim' (because it has three elements). However, it does in fact (in my german error message at least) complain about 'xlim' instead: Fehler in plot.window(xlim, ylim, log, asp, ...) : ung?ltiger

I started my laptop, opened a shell and get this error message: R : Copyright 2005, The R Foundation for Statistical Computing Version 2.2.1 (2005-12-20 r36812) ISBN 3-900051-07-0 lines deleted Error in fun(...) : couldn't find function "assignInNamespace" Error: .onLoad failed in 'loadNamespace' for 'Matrix' Fatal error: unable to restore saved data in .RData

hi I'm using the GDD package (in a 64bits fedora machine using R 2.3.0) to save in a png file some plots and i noticed that changing the lwd parameter does not change my line width I tried the same script in a Windows based R (2.2.1 r36812), using no GDD, and it worked. Does anybody has a clue? My testing script is something dumb like this: library(GDD) GDD("pres24.png",