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README.md

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nlmixr: an R package for population PKPD modeling


Authors: Yuan Xiong, Rik Schoemaker, Justin Wilkins, Matthew Fidler, Wenping Wang

nlmixr is an R package for fitting general dynamic models, pharmacokinetic (PK) models and pharmacokinetic-pharmacodynamic (PKPD) models in particular, with either individual data or population data. nlmixr has five main modules: 1) dynmodel() and its mcmc cousin dynmodel.mcmc() for nonlinear dynamic models of individual data; 2) nlme_lin_cmpt()for one to three linear compartment models of population data with first order absorption, or i.v. bolus, or i.v. infusion using the nlme algorithm; 3) nlme_ode() for general dynamic models defined by ordinary differential equations (ODEs) of population data using the nlme algorithm; 4) saem_fit for general dynamic models defined by ordinary differential equations (ODEs) of population data by the Stochastic Approximation Expectation-Maximization (SAEM) algorithm; 5) gnlmm for generalized non-linear mixed-models (possibly defined by ordinary differential equations) of population data by the adaptive Gaussian quadrature algorithm.

A few utilities to facilitate population model building are also included in nlmixr.

For a brief Windows/OS X installation guide, please see: https://github.com/nlmixrdevelopment/nlmixr/blob/master/inst/Installing_nlmixr.pdf or https://github.com/nlmixrdevelopment/nlmixr/blob/master/inst/Installing_nlmixr.rtf

For a brief vignette, please see: https://github.com/nlmixrdevelopment/nlmixr/blob/master/inst/nlmixr-intro.pdf

The examples in the vignette can be run using VignetteDemo.R and the associated data files available at: https://github.com/nlmixrdevelopment/nlmixr/tree/master/vignettes

For PKPD modeling (with ODE and dosing history) with Stan, check out Yuan's package PMXStan: https://github.com/yxiong1/pmxstan