RxODE
Modeling SyntaxThis vignette briefly describes the syntax used to define models
that RxODE
will translate into R-callable compiled code. It also
describes the communication of variables between R
and the
RxODE
modeling specification.
# An RxODE model specification (this line is a comment).
if(comed==0){ # concomitant medication (con-med)?
F = 1.0; # full bioavailability w.o. con-med
}
else {
F = 0.80; # 20% reduced bioavailability
}
C2 = centr/V2; # concentration in the central compartment
C3 = peri/V3; # concentration in the peripheral compartment
# ODE describing the PK and PD
d/dt(depot) = -KA*depot;
d/dt(centr) = F*KA*depot - CL*C2 - Q*C2 + Q*C3;
d/dt(peri) = Q*C2 - Q*C3;
d/dt(eff) = Kin - Kout*(1-C2/(EC50+C2))*eff;
An RxODE
model specification consists of one or more
statements terminated by semi-colons ;
and
optional comments (comments are delimited by #
and an
end-of-line).
A block of statements is a set of statements delimited by
curly braces, { ... }
.
Statements can be either assignments or conditional if
statements. Assignment statements can be either simple
assignments, where the left hand is an identifier (i.e., variable), or
special time-derivative assignments, where the left hand
specifies the change of the amount in the corresponding state
variable (compartment) with respect to time
e.g., d/dt(depot)
:
# simple assignment
C2 = centr/V2;
# time-derivative assignment
d/dt(centr) = F*KA*depot - CL*C2 - Q*C2 + Q*C3;
Expressions in assignment and if
statements can be numeric or logical,
however, no character nor integer expressions are currently supported.
Numeric expressions can include the following numeric operators
+, -, *, /, ^
and those mathematical functions defined in the C or the
R math libraries (e.g., fabs
, exp
, log
, sin
).
Notice that the modulo operator %
is currently unsupported.
The RxODE
syntax is case-sensitive, i.e., ABC
is different
than abc
, Abc
, ABc
, etc.
Identifiers (variable names) may consist of one or more alphanumeric
and underscore _
characters, but the first character cannot be a digit.
NB: The dot .
character may not be used as part of an identifier.
Identifiers in a model specification can refer to:
t
(time), tlast
(last time point), and
podo
(oral dose, in the undocumented case of absorption transit
models).ka
rate of absorption, CL
clearance, etc.)Currently, the RxODE
modeling language only recognizes system state
variables and “parameters”, thus, any values that need to be passed
from R to the ODE model (e.g., age
) should be passed in the params
argument of the integrator function solve()
.
Users specify which variables are the dynamic system's state variables
via the d/dt(identifier)
operator as part of the model specification,
and which are model parameters via the params=
argument in RxODE
solve()
method:
m1 <- RxODE(model = ode, modName = "m1")
# model parameters -- a named vector is required
theta <-
c(KA=0.29, CL=18.6, V2=40.2, Q=10.5, V3=297, Kin=1, Kout=1, EC50=200)
# state variables and their amounts at time 0 (the use of names is
# encouraged, but not required)
inits <- c(depot=0, centr=0, peri=0, eff=1)
# qd1 is an eventTable specification with a set of dosing and sampling
# records (code not shown here)
m1$solve(theta, event = qd1, inits = inits)
The values of these variables at pre-specified time points are
saved during model fitting/integration and returned as part of the
fitted values (see the function eventTable
, in particular its
member function add.sampling
function to define a set of time points when
to capture the values of these variables) and returned as
part of the modeling output.
Comments are not allowed inside statements, therefore the following code is syntactically incorrect:
# incorrect syntax (comments not allowed inside statements)
S2 = 1.0 # scaler for the central compartment ;
# correct syntax
S2 = 1.0; # scaler for the central compartment
The modulo operator %
is currently unsupported.
Similarly, the old-style exponentiation operator **
is unsupported
(use ^
).