[Rcpp-devel] Beginner Question: Two misc. questions on usage of Rcpp

[Sunny Srivastava]

Thanks again!

On Sun, Jan 30, 2011 at 4:16 PM, Dirk Eddelbuettel <edd at debian.org> wrote:

>
> Howdy,
>
> Thanks for posting here, and the kind words below.
>
> On 30 January 2011 at 15:49, Sunny Srivastava wrote:
> | Dear Rcpp-List:
> |
> | I have been working on speeding my R code. A while ago, I realized that
> no
> | further vectorization would help and interacting R with C/C++/.. was
> absolutely
> | necessary. I don't program in C/C++ extensively, so the transition was a
> | difficult process. I tried to use the R API but the error messages were
> | intimidating. A few weeks ago I saw Professor Chambers presentation (pdf
> from
> | David Smith's website) about R in Stanford. I saw him mentioning Rcpp
> which
> | motivated me to try Rcpp (I confess, I am lazy to try new stuff). And I
> haven't
> | been dissapointed. Thank you very much Dirk and Romain (and other
> developers,
> | including Professor Chambers and Professor Bates).
> |
> | Rcpp reduced the length of my code considerably (like: I didn't need to
> bother
> | about PROTECT .. ) and the informative syntax (like: Rcpp::IntegerMatrix
> ..)
> | made my code more readable. These are great advantages, but the best part
> was
> | testing and compiling with the Inline package. I am a statistician;
> writing a C
> | program and then using dyn.load was the way I learned to do it in grad
> school.
> | Rcpp + inline makes this process way easier.
> |
> | Thank you for the great documentation on your webpage Dirk. It helped me
> a lot.
> |
> | I am still a beginner in using Rcpp and friends (2 weeks old) and have a
> few
> | miscellaneous questions. The answer to these questions may be very basic
> or
> | obvious, so please bear with me. (Dirk showed me a simple way to test
> things
> | using Rcpp + inline here --
> http://stats.stackexchange.com/questions/6690/
> |
> what-is-the-difference-between-rf-dpois-in-rmath-h-and-the-dpois-that-i-use-direc
> | )
> |
> | 1. I have been using Rcpp + inline to test if the faster implementation
> gives
> | the right results (which is obtained from R code). I was wondering if
> there are
> | other strategies which people use to test their Rcpp code? (sorry, if
> this
> | doesn't make sense.)
>
> No, that is precisely the best way about it: write code, and then test and
> profile it.
>
> A few times in the past users have posted things here that lead us to
> improve
> things down the road.  One only finds bottlenecks by testing for them.
>
> | 2. I have a MCMC simulation (say: foo) which uses several functions (say:
> fun1,
> | fun2). These functions (fun1, fun2) are themselves computation intensive
> and I
> | used Rcpp to speed them. Until now I do something like this:
> |
> | In R file:
> |
> | foo <- function (...){
> |
> |     src1 <- paste(readLines("fun1-rcpp.cpp"), collapse="\n")
> |     RcppFun1 <- cxxfunction( .., plugin="Rcpp",body=src1)
>
> You probably want to write a package. That way the 'compilation cost' is
> borne just once when you install the package, rather than each time its
> run.
>
> Doing a package may be a new step, but we try to help with documentation
> and
> existing packages. Give it a try!
>
> |    ## similar cpp code for fun2
> |
> |     for (i in 1:10000){
> |           ## use RcppFun1, RcppFun2 here
> |     }
> | }
>
> It's a bit hard to say based on just this, but yes, you may be able to
> 'refactor' this and regroup functions.  But no need to obsess over it.
>
> | I was wondering if this is OK (it already speeds up my code by zillion
> times)
> | or is there a more elegant way of doing this. I am thinking about using
> Rcpp to
> | increase the speed of foo (for more speed) but I am not too sure on how
> to do
> | this. Towards this end, I checked a few packages mentioned on Dirk's
> website
> | namely, pcaMethods. I am thinking RcppExport and .Call is the way to do
> this?
>
> Yes. Give it try, look at some small packages and try to copy whatever
> package structure you may find useful.
>
> Cheers, Dirk
>
>
> | Thank you for your answers or pointers.
> |
> | S.
> |
> | ----------------------------------------------------------------------
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>
> --
> Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
>
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