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) |