Apply the fixed population estimated parameters
Arguments
- ui
rxode2 ui function
- returnNull
boolean for if unchanged values should return the original ui (
FALSE) or null (TRUE)
Value
when returnNull is TRUE, NULL if nothing was changed, or
the changed model ui. When returnNull is FALSE, return a ui no
matter if it is changed or not.
Examples
One.comp.transit.allo <- function() {
ini({
# Where initial conditions/variables are specified
lktr <- log(1.15) #log k transit (/h)
lcl <- log(0.15) #log Cl (L/hr)
lv <- log(7) #log V (L)
ALLC <- fix(0.75) #allometric exponent cl
ALLV <- fix(1.00) #allometric exponent v
prop.err <- 0.15 #proportional error (SD/mean)
add.err <- 0.6 #additive error (mg/L)
eta.ktr ~ 0.5
eta.cl ~ 0.1
eta.v ~ 0.1
})
model({
#Allometric scaling on weight
cl <- exp(lcl + eta.cl + ALLC * logWT70)
v <- exp(lv + eta.v + ALLV * logWT70)
ktr <- exp(lktr + eta.ktr)
# RxODE-style differential equations are supported
d/dt(depot) = -ktr * depot
d/dt(central) = ktr * trans - (cl/v) * central
d/dt(trans) = ktr * depot - ktr * trans
## Concentration is calculated
cp = central/v
# And is assumed to follow proportional and additive error
cp ~ prop(prop.err) + add(add.err)
})
}
m <- rxFixPop(One.comp.transit.allo)
#>
#>
#> ℹ parameter labels from comments will be replaced by 'label()'
m
#> ── rxode2-based free-form 3-cmt ODE model ──────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> lktr lcl lv prop.err add.err
#> 0.1397619 -1.8971200 1.9459101 0.1500000 0.6000000
#>
#> Omega ($omega):
#> eta.ktr eta.cl eta.v
#> eta.ktr 0.5 0.0 0.0
#> eta.cl 0.0 0.1 0.0
#> eta.v 0.0 0.0 0.1
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 depot
#> 2 2 central
#> 3 3 trans
#> ── μ-referencing ($muRefTable): ──
#> theta eta level
#> 1 lcl eta.cl id
#> 2 lv eta.v id
#> 3 lktr eta.ktr id
#>
#> ── Model (Normalized Syntax): ──
#> function() {
#> ini({
#> lktr <- 0.139761942375159
#> label("log k transit (/h)")
#> lcl <- -1.89711998488588
#> label("log Cl (L/hr)")
#> lv <- 1.94591014905531
#> label("log V (L)")
#> prop.err <- c(0, 0.15)
#> label("proportional error (SD/mean)")
#> add.err <- c(0, 0.6)
#> label("additive error (mg/L)")
#> eta.ktr ~ 0.5
#> eta.cl ~ 0.1
#> eta.v ~ 0.1
#> })
#> model({
#> cl <- exp(lcl + eta.cl + 0.75 * logWT70)
#> v <- exp(lv + eta.v + 1 * logWT70)
#> ktr <- exp(lktr + eta.ktr)
#> d/dt(depot) = -ktr * depot
#> d/dt(central) = ktr * trans - (cl/v) * central
#> d/dt(trans) = ktr * depot - ktr * trans
#> cp = central/v
#> cp ~ prop(prop.err) + add(add.err)
#> })
#> }
# now everything is already fixed, so calling again will do nothing
rxFixPop(m)
#> ── rxode2-based free-form 3-cmt ODE model ──────────────────────────────────────
#> ── Initalization: ──
#> Fixed Effects ($theta):
#> lktr lcl lv prop.err add.err
#> 0.1397619 -1.8971200 1.9459101 0.1500000 0.6000000
#>
#> Omega ($omega):
#> eta.ktr eta.cl eta.v
#> eta.ktr 0.5 0.0 0.0
#> eta.cl 0.0 0.1 0.0
#> eta.v 0.0 0.0 0.1
#>
#> States ($state or $stateDf):
#> Compartment Number Compartment Name
#> 1 1 depot
#> 2 2 central
#> 3 3 trans
#> ── μ-referencing ($muRefTable): ──
#> theta eta level
#> 1 lcl eta.cl id
#> 2 lv eta.v id
#> 3 lktr eta.ktr id
#>
#> ── Model (Normalized Syntax): ──
#> function() {
#> ini({
#> lktr <- 0.139761942375159
#> label("log k transit (/h)")
#> lcl <- -1.89711998488588
#> label("log Cl (L/hr)")
#> lv <- 1.94591014905531
#> label("log V (L)")
#> prop.err <- c(0, 0.15)
#> label("proportional error (SD/mean)")
#> add.err <- c(0, 0.6)
#> label("additive error (mg/L)")
#> eta.ktr ~ 0.5
#> eta.cl ~ 0.1
#> eta.v ~ 0.1
#> })
#> model({
#> cl <- exp(lcl + eta.cl + 0.75 * logWT70)
#> v <- exp(lv + eta.v + 1 * logWT70)
#> ktr <- exp(lktr + eta.ktr)
#> d/dt(depot) = -ktr * depot
#> d/dt(central) = ktr * trans - (cl/v) * central
#> d/dt(trans) = ktr * depot - ktr * trans
#> cp = central/v
#> cp ~ prop(prop.err) + add(add.err)
#> })
#> }
# if you call it with returnNull=TRUE when no changes have been
# performed, the function will return NULL
rxFixPop(m, returnNull=TRUE)
#> NULL