Re: the first CRAN release of nlmixr
Thanks for the great work to make modeling in R more usable!
Quoted reply history
> On Nov 9, 2017, at 07:42, Wang, Wenping <[email protected]> wrote:
>
> The nlmixr team is very proud to announce the first CRAN release of nlmixr
> ( https://cran.r-project.org/web/packages/nlmixr/), an open source package for
> population PK and PKPD modelling. nlmixr builds on the RxODE package for
> simulation of nonlinear mixed effect models using ordinary differential
> equations, by implementing parameter estimation algorithms like nlme and SAEM
> (with gnlmm and FOCEi under active development). nlmixr greatly expands the
> utility of existing packages (like nlme) by providing an efficient and
> versatile way to specify pharmacometric models and dosing scenarios, with
> rapid execution due to compilation to C++.
>
> This new release features a unified user-interface. This user-interface
> provides PKPD modelers a minimalist, intuitive, expressive, domain-specific
> modeling language to compactly describe the model structure & efficiently
> explore the population data at hand. Below is an example of specifying the
> theophline data by this domain language:
>
> f <- function(){
> ini({
> lCl <- -3 # log Cl (L/hr)
> lVc <- -1 # log Vc (L)
> lKA <- 1 # log Ka (1/hr)
> add.err <- c(0, 0.2, 1)
> eta.Cl ~ 0.1 # BSV Cl
> eta.Vc ~ 0.1 # BSV Vc
> eta.KA ~ 0.1 # BSV Ka
> })
> model({
> ## First parameters are defined in terms of the initial estimates
> ## parameter names.
> Cl <- exp(lCl + eta.Cl)
> Vc <- exp(lVc + eta.Vc)
> KA <- exp(lKA + eta.KA)
> ## Next, the differential equations are defined
> d/dt(depot) = -KA*depot;
> d/dt(centr) = KA*depot-Cl/Vc*centr;
> ## And the concentration is then calculated
> cp = centr / Vc;
> ## Last, nlmixr is told that the plasma concentration follows
> ## an additive error (estimated by the parameter add.err)
> cp ~ add(add.err)
> })
> }
>
> fit <- nlmixr(f, theo_sd, est="saem")
> plot(fit)
>
> Get in touch, reach out to us and discuss ways you could contribute, or try
> it out for yourself, and experience the joy of exploring and modelling
> population data all within R! The nlmixr team is working hard to make this
> community based modeling tool even better. Our goal: Express your model in
> nlmixr, openly and freely.
>
> Wenping Wang, PhD
> Executive Director, Pharmacometrics
> Novartis Pharmaceuticals Corporation
> One Health Plaza, East Hanover, NJ 07936-1080, USA
> Phone +1 862 7789009; Fax +1 9737818265