Version 0.89.0

A pharmacokinetics/pharmacodynamics library for Stan

Events specification

Torsten’s functions are prefixed with pmx_. For some of their arguments we adopt NM-TRAN format for events specification(Table 1).

Table 1: NM-TRAN compatible event specification arguments. All arrays should have the same length corresponding to the number of events.
Argument Name Definition Stan data type
time event time real[]
amt dosing amount real[]
rate infusion rate real[]
ii interdose interval real[]
evid event ID int[]
cmt event compartment int[]
addl additionial identical doses int[]
ss steady-state dosing flag int[]

All the real[] arguments above are allowed to be parameters in a Stan model. In addtion, Torsten functions support optional arguments and overloaded signatures. Optional arguments are indicated by surrounding square bracket []. Table below shows three commonly used PMX model arguments that support overloading. In the rest of this document we assume this convention unless indicated otherwise.

Table 2: PMX model parameter overloadings. One can use 1d array real[] to indicate constants of all events, or 2d array real[ , ] so that the \(i\)th row of the array describes the model arguments for time interval \((t_{i-1}, t_i)\), and the number of the rows equals to the size of time.
Argument Name Definition Stan data type Optional
theta model parameters real[] or real[ , ] N
biovar bioavailability fraction real[] or real[ , ] Y (default to 1.0)
tlag lag time real[] or real[ , ] Y (default to 0.0)
Last updated on 30 Jun 2021
Published on 25 Jun 2021
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