the first CRAN release of nlmixr
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