To add transit compartments to the model
Usage
addTransit(
model,
transit,
central = "central",
depot = "depot",
transitComp = "transit",
ktr = "ktr"
)Arguments
- model
The model as a function
- transit
the number of transit compartments to be added
- central
a character vector representing the central compartment
- depot
a character vector representing the depot compartment
- transitComp
the transit compartment prefix
- ktr
the parameter name for the transit compartment rate
Examples
readModelDb("PK_1cmt_des") |>
addTransit(3)
#>
#>
#> ℹ promote `lktr` to population parameter with initial estimate 0.05
#> ℹ change initial estimate of `lktr` to `0.05`
#> ── rxode2-based free-form 5-cmt ODE model ──────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> lka lcl lvc propSd lktr
#> 0.45 1.00 3.45 0.50 0.05
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 depot
#> 2 2 transit1
#> 3 3 transit2
#> 4 4 transit3
#> 5 5 central
#> ── Model (Normalized Syntax): ──
#> function() {
#> description <- "One compartment PK model with linear clearance using differential equations"
#> ini({
#> lka <- 0.45
#> label("Absorption rate (Ka)")
#> lcl <- 1
#> label("Clearance (CL)")
#> lvc <- 3.45
#> label("Central volume of distribution (V)")
#> propSd <- c(0, 0.5)
#> label("Proportional residual error (fraction)")
#> lktr <- 0.05
#> })
#> model({
#> ktr <- exp(lktr)
#> ka <- exp(lka)
#> cl <- exp(lcl)
#> vc <- exp(lvc)
#> kel <- cl/vc
#> d/dt(depot) <- -ka * depot
#> d/dt(transit1) <- ka * depot - ktr * transit1
#> d/dt(transit2) <- ktr * transit1 - ktr * transit2
#> d/dt(transit3) <- ktr * transit2 - ktr * transit3
#> d/dt(central) <- ktr * transit3 - kel * central
#> Cc <- central/vc
#> Cc ~ prop(propSd)
#> })
#> }