Re: [NMusers] the first CRAN release of nlmixr

From: William Denney <wdenney_at_humanpredictions.com>
Date: Thu, 9 Nov 2017 09:29:31 -0500

Thanks for the great work to make modeling in R more usable!

> On Nov 9, 2017, at 07:42, Wang, Wenping <wenping.wang_at_novartis.com> 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 f=
or population PK and PKPD modelling. nlmixr builds on the RxODE package for s=
imulation of nonlinear mixed effect models using ordinary differential equat=
ions, by implementing parameter estimation algorithms like nlme and SAEM (wi=
th gnlmm and FOCEi under active development). nlmixr greatly expands the uti=
lity of existing packages (like nlme) by providing an efficient and versatil=
e way to specify pharmacometric models and dosing scenarios, with rapid exec=
ution due to compilation to C++.
>
> This new release features a unified user-interface. This user-interface p=
rovides PKPD modelers a minimalist, intuitive, expressive, domain-specific m=
odeling language to compactly describe the model structure & efficiently exp=
lore the population data at hand. Below is an example of specifying the the=
ophline 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 estim=
ates
> ## 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 tr=
y it out for yourself, and experience the joy of exploring and modelling pop=
ulation data all within R! The nlmixr team is working hard to make this comm=
unity based modeling tool even better. Our goal: Express your model in nlmix=
r, 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

Received on Thu Nov 09 2017 - 09:29:31 EST

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