The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

rxode2lincmt

rxode2lincmt provides the analytic one, two and three compartment linear pharmacokinetic solutions and their parameter gradients that rxode2‘s linCmt() uses. The gradients come from ’stan’ automatic differentiation.

This code used to be compiled inside ‘rxode2’. It lives in its own package so that installing ‘rxode2’ does not compile ‘stan’: ‘rxode2’ imports rxode2lincmt and calls the compiled kernels through an external-pointer table. Most users never call rxode2lincmt directly; they write linCmt() in an ‘rxode2’ or ‘nlmixr2’ model.

The closed-form solutions follow the idea of the wnl package by Kyun-Seop Bae, though the implementation here is different.

Installation

You can install the development version of rxode2lincmt from GitHub with:

# install.packages("devtools")
devtools::install_github("nlmixr2/rxode2lincmt")

Compiling the ‘stan’-based solutions takes a while.

Examples

The eigenvalues and coefficient matrices of a two compartment model from its micro-constants:

library(rxode2lincmt)
solComp2(k10 = 0.1, k12 = 3, k21 = 1)
#> $L
#> [1] 4.07546291 0.02453709
#> 
#> $C1
#>            [,1]      [,2]
#> [1,]  0.7592000 0.2408000
#> [2,] -0.7405714 0.7405714
#> 
#> $C2
#>            [,1]      [,2]
#> [1,] -0.2468571 0.2468571
#> [2,]  0.2408000 0.7592000

The micro-constants of a two compartment model given clearance and volume parameters:

linCmtMicros(p1 = 2, v1 = 20, p2 = 3, p3 = 40, ncmt = 2)
#>      v      k    k12    k21 
#> 20.000  0.100  0.150  0.075

One step of the per-row kernel: the concentration one time unit after a 100-unit bolus into a one compartment model with clearance 2 and volume 20, which matches the closed form 100 / 20 * exp(-2 / 20):

step <- linCmtModelDouble(dt = 1, p1 = 2, v1 = 20, p2 = 0, p3 = 0, p4 = 0, p5 = 0,
                          ka = 0, alastNV = 100, rateNV = 0, ncmt = 1L, oral0 = 0L,
                          trans = 1L, deriv = FALSE, type = 0L, tau = 0, tinf = 0,
                          amt = 0, bolusCmt = 0L, ndiff = 0L)
step$val
#> [1] 4.524187
100 / 20 * exp(-2 / 20)
#> [1] 4.524187

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.