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 ky...@metrumrg.com
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