There's also https://github.com/thk686/odeintr (use the devel version, not CRAN -- need to upload a bug fix).
THK http://www.keittlab.org/ On Wed, Jan 25, 2017 at 11:33 AM, Gibbons, Frank < frank.gibb...@astrazeneca.com> wrote: > Kyle, > > > > D’oh! You’re absolutely right. Embarrassing. :-} > > (I’m told that’s the emoticon for ‘sheepish grin’.) > > > > I did try going the way suggested by deSolve, but find that (for reasons > unknown to me), “R CMD SHLIB” compiles the object file but not the DLL > (error about not having permission). > > > > I wasn’t aware of RxODE at all (and only vaguely familiar with mrgsolve), > but installed it, read through the tutorial (from the journal CPT-PSP), and > within a few hours was in business. It won’t be for everyone of course, > since it’s specialized for PK/PD modeling, but it enabled me to get a 15x > performance improvement in my application (which requires repeated model > evaluation to optimize a study design). This is huge: over-lunchbreak vs > over-night. If the speedup reported by the authors in their tutorial > applies to my situation, this improvement factor will improve as the model > grows (currently just 2 ODEs). > > > > For those with similar goals as mine (PK/PD models), highly recommend it. > Much like Rcpp, it enables specification of both the compiled and > non-compiled parts of the code in a single file. But like SHLIB, it > compiles behind the scenes (few seconds), and while I don’t fully > understand what’s going on under the hood, it performs as if there’s a > minimum of back-and-forth between R and C. > > > > Many thanks to you both > > > > -Frank > > > > *From:* Kyle Baron [mailto:ky...@metrumrg.com] > *Sent:* Monday, January 23, 2017 1:35 PM > *To:* Dirk Eddelbuettel <e...@debian.org> > *Cc:* Gibbons, Frank <frank.gibb...@astrazeneca.com>; > rcpp-devel@lists.r-forge.r-project.org > *Subject:* Re: [Rcpp-devel] Using Rcpp to solve ODEs: LSODE (deSolve) > says "Confusion over the length of parms" > > > > Frank - > > > > In the code you provided, it looks like it is "poped.db.compiled.rcpp", > not "poped.db.compiled". > > > > I found that, after making the change to fix the error that Dirk pointed > out, the code appears to work with no error (attached). I don't know if > the results are what you were intending, however. > > > > Also: I would not set up the optimization like this. When you create > the one_comp_oral_ode function with cppFunction and hand that off to > deSolve, you are still passing along an R function to get called. Even if > the calculations are accomplished with Rcpp, it still an R function. So > every step the solver takes, it will have to call an R function. I don't > think this is what you want. When you write the ode function as suggested > by the deSolve package vignette, you pass off the name of a C function and > the solver calls that C function directly as the system advances. It will > be faster than what you are doing with cppFunction. > > > > Finally, I'll ask if you have looked at one of the more-modern simulation > packages for R that are designed for PK/PD work? > > I maintain mrgsolve: https://github.com/metrumresearchgroup/mrgsolve > > You could also look at RxODE: https://cran.r-project. > org/web/packages/RxODE/index.html > > > > Hope that helps ... > > Kyle > > > > > > > > On Sun, Jan 22, 2017 at 7:50 PM, Dirk Eddelbuettel <e...@debian.org> wrote: > > > Frank, > > That's a pretty long message and a lot of code. Can you try to distill it > down to a particular (smaller?) issue? > > And FWIW I cannot run. After saving your attachment, and installing PopED, > I > get > > R> source("/tmp/myExampleODE.compiled.R") > > Attaching package: ‘deSolve’ > > The following object is masked from ‘package:graphics’: > > matplot > > Elapsed time: 10.425 seconds. > Error in poped.db$settings$optsw[2] <- opt_xt : > object 'poped.db.compiled' not found > R> > > I also recommend the rbenchmark and microbenchmark packages over tic() and > toc(). > > Sorry that I have no quick fix. > > Dirk > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org > _______________________________________________ > Rcpp-devel mailing list > Rcpp-devel@lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel > > > > > > -- > > Kyle Baron > > Metrum Research Group > > 860-735-7043, Ext. 202 <(860)%20735-7043> > > ky...@metrumrg.com > > > ------------------------------ > > *Confidentiality Notice: *This message is private and may contain > confidential and proprietary information. If you have received this message > in error, please notify us and remove it from your system and note that you > must not copy, distribute or take any action in reliance on it. Any > unauthorized use or disclosure of the contents of this message is not > permitted and may be unlawful. > > > _______________________________________________ > Rcpp-devel mailing list > Rcpp-devel@lists.r-forge.r-project.org > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel >
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