Compartment

Defines name and volume of a compartment.

compartment(name, volume = 1)

cmp(name, volume = 1)

Arguments

name	Name of the compartment
volume	Volume as a number, formula or parameter name

Value

A building block of type 'compartment'

Details

In most applications, compartments contain kinetically homogeneous amount of drug (applications where the compartment content represents other quantities are also possible). In assemblerr, a compartment is defined by providing a a name and the compartment volume.

Compartment names

Every compartment must have a valid name. A compartment name can contain letters, numbers as well as the underscore character, and needs to start with a letter. Adding a compartment with an already existing name will replace the definition of the compartment.

Compartment volumes

The compartment volume can be provided as a number, R formula, or a parameter name. It will be used by assemblerr to replace references to the compartment concentration (e.g., ~C["central"]) with the corresponding amount divided by volume (e.g., ~A["central]/vc).

See also

flow for how to describe compartment kinetics

Examples

# model with depot and central compartment
m <- model() +
 compartment("depot", volume = 1) +
 compartment("central", volume = "vc") +
 flow(~ka*A, from = "depot", to = "central") +
 flow(~cl*C, from = "central") +
 prm_log_normal("ka") +
 prm_log_normal("cl") +
 prm_log_normal("vc") +
 obs_additive(conc~C["central"])

render(
  model = m,
  options = assemblerr_options(
    ode.use_special_advans = FALSE,
    ode.use_general_linear_advans = FALSE
   )
)
#> $PROBLEM
#> $INPUT ID TIME DV AMT
#> $DATA data.csv IGNORE=@
#> $SUBROUTINES ADVAN13 TOL=6
#> $MODEL COMP=(DEPOT) COMP=(CENTRAL)
#> $PK
#> KA = THETA(1) * EXP(ETA(1))
#> CL = THETA(2) * EXP(ETA(2))
#> VC = THETA(3) * EXP(ETA(3))
#> $DES
#> DADT(1) = -(KA * A(1))
#> DADT(2) = KA * A(1) - CL * (A(2)/VC)
#> $ERROR
#> CONC = A(2)/VC
#> Y = CONC + EPS(1)
#> $ESTIMATION METHOD=COND MAXEVAL=999999 
#> $THETA (0, 1, Inf) ; POP_KA
#> $THETA (0, 1, Inf) ; POP_CL
#> $THETA (0, 1, Inf) ; POP_VC
#> $OMEGA 0.1 ; IIV_KA
#> $OMEGA 0.1 ; IIV_CL
#> $OMEGA 0.1 ; IIV_VC
#> $SIGMA 1; RUV_ADD