The nlmixr team is very proud to announce a major public release of 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 prop.err)
cp ~ add(add.err)
})
}
fit <- nlmixr(f, theo_sd, est="saem")
plot(fit)
On Tuesday, 17 October, 2017, 7:30-9:30 am, Rik Schoemaker will present an
nlmixr poster at ACoP (T-012): nlmixr: an open-source package for
pharmacometric modelling in R. Get in touch, see us at ACoP to discuss ways you
could contribute (Matt Fidler, Rik Schoemaker, Yuan Xiong, Justin Wilkins,
Mirjam Trame and Wenping Wang will all be there), or try it out for yourself,
and experience the joy of a population modelling package within R! The source
is available at
https://github.com/nlmixrdevelopment/nlmixr<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_nlmixrdevelopment_nlmixr&d=DwMGaQ&c=ZbgFmJjg4pdtrnL2HUJUDw&r=gxBd80D9lXamwrJ3yb-JDV55-1nopV0qFcyswak8yoI&m=XMBmM8Z2cx7XobeGoFY5DDdh9C6aG42NH_ZsFeDHbUU&s=MW3xpu6AQIRVD2gUNA4p0Ii_Dc8A-4vGp5GzGqpFA8c&e=>,
and the nlmixr team is in the process of submitting the package to CRAN, and
working hard to further improve this community based modeling tool. 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
