some long-running MCMC
calculations. And, I would like the C++ code to store the
results every, say, 1 iterations. Of course, I could do
this in a loop from R. But, I want to be sure that is really
necessary before I re-write my R code ;o)
--
Rodney Sparapani, PhD
Manager of Statistical
On 07/19/2013 07:32 AM, Dirk Eddelbuettel wrote:
Oh, and stop using the hidous '=' for assignment in R;-)
Dirk
And, real names are mandatory mystery guest ;o)
--
Rodney Sparapani, PhD
Manager of Statistical & Computational Operations
Center for Patient Care and Outcomes
On 05/23/2013 03:01 PM, Rodney Sparapani wrote:
possibly, just add ".cpp" to any file that does not already have it
before copying it to TEMP.
Actually, this latter suggestion is rather easy to implement
and, I believe, simplifies life for spaces in filenames, etc.
It adds 5
Hi!
As the original bugbear, I would also like to see this feature. Or
possibly, just add ".cpp" to any file that does not already have it
before copying it to TEMP.
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
Sr. Biostatistician http://www
guys!
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
Sr. Biostatistician http://www.mcw.edu/pcor
4 wheels good, 2 wheels better! Medical College of Wisconsin (MCW)
WWLD?: What Would Lombardi Do? Milwaukee, WI, USA
On 05/22/2013 12:23 PM, Dirk Eddelbuettel wrote:
Methinks there may be something particular to your box.
Dirk
Possible, but I don't think it is likely. I found this issue
on the following OSes: RHEL 5, Oracle 6, CentOS 6 and OS X ML...
with various versions of GCC
--
Rodney Sparapani
[1] RcppArmadillo_0.3.800.1 Rcpp_0.10.3 Matrix_1.0-12
[4] lattice_0.20-15
loaded via a namespace (and not attached):
[1] grid_2.15.3 tools_2.15.3
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
Sr. Biostatistician http://www.mcw.edu/pcor
4 wheels good, 2 whe
D0G/sourcecpp_f97a2e266e27/sourceCpp_930.so")
(from arma-sp.cxx.R#1) :
unable to load shared object
'/tmp/RtmpSgRD0G/sourcecpp_f97a2e266e27/sourceCpp_930.so':
/tmp/RtmpSgRD0G/sourcecpp_f97a2e266e27/sourceCpp_930.so: cannot open
shared object file: No such file or directory
--
Rodney Sparap
ch-r-workshop/
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
Sr. Biostatistician http://www.mcw.edu/pcor
4 wheels good, 2 wheels better! Medical College of Wisconsin (MCW)
WWLD?: What Would Lombardi Do? Milwaukee, WI,
th Rcpp? Pointers to the relevant docs/files/etc. are very
welcome. Thanks
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
Sr. Biostatistician http://www.mcw.edu/pcor
4 wheels good, 2 wheels better! Medical College of Wisconsin (MCW)
WWLD?: What Would Lom
Rcpp/inline? I've played around with f2c to convert the
Fortran code to C (but it makes me nervous ;o) Should I be working
from a package skeleton? Basically, any advice is welcome. Thanks!
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
Sr. Biostatistician
march=amdfam10"
CXX="g++"
CXXFLAGS="-g -O2 -march=amdfam10"
With these settings...
MCMC Code SwitchesRelative Time
R none or -O2 1.0
RcppEigen none or -O2 0.09
R -O2 -march=amdfam10
ct on
these benchmarks. Is that because it is ignoring them or it
just has no benefit?
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
Sr. Biostatistician http://www.mcw.edu/pcor
4 wheels good, 2 wheels better! Medical Coll
return wrap(rn);',
includes="using namespace Rcpp;\n", plugin="Rcpp")
funk2()
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
Sr. Biostatistician http://www.mcw.edu/pcor
4 wheels good, 2 wheels better! Medical College of Wis
I
can't seem to see a pattern. Or should you just use it all
of the time whether it is needed or not? Thanks!
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
Sr. Biostatistician http://www.mcw.edu/pcor
4 wheels good, 2 wheels better! Medical College
On 09/17/2012 02:26 PM, Rodney Sparapani wrote:
Hi Gang:
For me, the following returns a 1 instead of a 2. Any ideas?
mcmc <- list(names=list("M", "burnin", "thin", "save"),
save=list("beta", "rho", "mu", "theta&q
0, thin=1)
check1 <- NULL
check1 <- cxxfunction(signature(arg1="list", arg2="list", arg3="list"),
body='
List list3(arg3), save=list3["save"];
const int burnin=list3["burnin"], M=list3["M"], thin=list3["t
On 09/13/2012 12:25 PM, Dirk Eddelbuettel wrote:
We are getting rather off-topic now discussing R assignments and IDEs etc.
Dirk
Hi Gang:
I would agree that we are a bit off-topic. But, I have lots of
questions (that's why they call me whiskers: I'm curious like a
cat ;o) Is there some plac
& object)".
That's very nice! However, if I place it at qnorm(, then all I get is:
"Rmath.h: const extern "C" qnorm".
Thanks
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
Sr. Biostatistician http://www.mcw.edu/pcor
4 wheel
sor macro and C++ template code (AKA magic pixie dust) in
PREFIX/lib64/R/library/Rcpp/include/Rcpp/stats/dpq/dpq.h
Bravo!
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
Sr. Biostatistician http://www.mcw.edu/pcor
4 wheels good, 2 wheels better! Medical Colle
s I can see,
there is nothing in Rcpp nor Rmath.h that actually specifies the
prototypes like the example above (and I did look, hence my initial
confusion about the syntax of qnorm). Were these written simply by
looking at the R help itself like ?qnorm or were they automated in
some way? Thank
very nice! However, if I place it at qnorm(, then all I get is:
"Rmath.h: const extern "C" qnorm". Not very helpful. Could you share
with us what you see in Eclipse?
Thanks!
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
Sr. Biostatistician
x27;s weird. I thought Step 2 went well ;o) The hard copy of steps
that I was looking at was incomplete for Step 3; do web browsers not
wrap long lines? Now, I have that complete description.
But, I guess I should go back to the beginning and start all over
again. Thanks
--
Rodney Sparapani, PhD C
nment preferences of the Workspace are invalid.
I'm trying to install this on Eclipse Juno with StatET
from http://download.walware.de/eclipse-3.8 Any suggestions
will be appreciated.
Thanks!
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
Sr. Biostatistician
rning message:
running command '/opt/local/lib64/R/bin/R CMD SHLIB file1a785d3ff187.cpp
2> file1a785d3ff187.cpp.err.txt' had status 1
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
Sr. Biostatistician http://www.mcw.edu/pcor
4 wheels good, 2 whe
27;
make: *** [file33b64e743def.o] Error 1
In addition: Warning message:
running command '/opt/local/lib64/R/bin/R CMD SHLIB file33b64e743def.cpp
2> file33b64e743def.cpp.err.txt' had status 1
Am I doing something stupid? Thanks
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Rese
ng it!
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
Sr. Biostatistician http://www.mcw.edu/pcor
4 wheels good, 2 wheels better! Medical College of Wisconsin (MCW)
WWLD?: What Would Lombardi Do? Milwaukee, WI
Everything that
RcppEigen needs is provided (I should have checked the source
immediately). Thanks
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
Sr. Biostatistician http://www.mcw.edu/pcor
4 wheels good, 2 wheels better! Medical College of Wisconsin (
frustration). Replace line 9 of
PREFIX/include/Eigen/CholmodSupport with
#ifdef RcppEigen__RcppEigen__h
#include
#else
#include
#endif
Thanks for all of your help!
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
Sr. Biostatistician http://www.mcw.edu/pcor
l/lib64/R/library/Rcpp/include" -I../inst/include ...
Shouldn't -I../inst/include be first? In src/Makevars,
there is just PKG_CXXFLAGS=-I../inst/include. So, I guess that
should have been prepended to the CXXFLAGS rather than
appended. Am I making sense?
--
Rodney Sparapani, PhD Cen
On 08/30/2012 03:24 PM, Rodney Sparapani wrote:
# R CMD INSTALL RcppEigen_0.3.1.tar.gz
* installing to library '/opt/local/lib64/R/library'
* installing *source* package 'RcppEigen' ...
** package 'RcppEigen' successfully unpacked and MD5 sums checked
** libs
g++ -I
igenForward.h:31,
from ../inst/include/RcppEigen.h:25,
from RcppEigen.cpp:22:
/opt/local/include/Eigen/CholmodSupport:9:23: error: cholmod.h: No such
file or directory
Something is pulling in the Eigen header file
/opt/local/include/Eigen/CholmodSupport
--
Rodney Sparap
defined and act accordingly. If you guys think I'm on the
right track, then I could probably figure this out (since I am the
one that can replicate the issue that no one else seems to see).
If not, then please advice. Thanks
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
tached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RcppEigen_0.2.0 Rcpp_0.9.10 inline_0.3.8
loaded via a namespace (and not attached):
[1] compiler_2.14.2 grid_2.14.2 lattice_0.20-6 Matrix_1.0-5
[5] tools_2.14.2
yum install suite
On 08/14/2012 09:38 AM, Douglas Bates wrote:
I think you want to move the RNGScope declaration before the calls to
rcauchy and runif.
That's it! Thank you Doug.
--
Rodney Sparapani, PhD Center for Patient Care and Outcomes Research
Sr. Biostatistician http://www.mcw.edu/p
NA
LinkingTo Suggests
NA "RUnit, inline, rbenchmark"
Enhances OS_type
NA NA
License
36 matches
Mail list logo
