as.nlmixr2 {babelmixr2}

Convert an object to a nlmixr2 fit object

Description

Convert an object to a nlmixr2 fit object

Usage

as.nlmixr2(
  x,
  ...,
  table = nlmixr2est::tableControl(),
  rxControl = rxode2::rxControl()
)

as.nlmixr(
  x,
  ...,
  table = nlmixr2est::tableControl(),
  rxControl = rxode2::rxControl()
)

Arguments

x

Object to convert

...

Other arguments

table

is the nlmixr2est::tableControl() options

rxControl

is the rxode2::rxControl() options, which is generally needed for how addl doses are handled in the translation

Value

nlmixr2 fit object

Author(s)

Matthew L. Fidler

Examples

# First read in the model (but without residuals)
mod <- nonmem2rx(system.file("mods/cpt/runODE032.ctl", package="nonmem2rx"),
                 determineError=FALSE, lst=".res", save=FALSE)

# define the model with residuals (and change the name of the
# parameters) In this step you need to be careful to not change the
# estimates and make sure the residual estimates are correct (could
# have to change var to sd).

 mod2 <-function() {
   ini({
     lcl <- 1.37034036528946
     lvc <- 4.19814911033061
     lq <- 1.38003493562413
     lvp <- 3.87657341967489
     RSV <- c(0, 0.196446108190896, 1)
     eta.cl ~ 0.101251418415006
     eta.v ~ 0.0993872449483344
     eta.q ~ 0.101302674763154
     eta.v2 ~ 0.0730497519364148
   })
   model({
     cmt(CENTRAL)
     cmt(PERI)
     cl <- exp(lcl + eta.cl)
     v <- exp(lvc + eta.v)
     q <- exp(lq + eta.q)
     v2 <- exp(lvp + eta.v2)
     v1 <- v
     scale1 <- v
     k21 <- q/v2
     k12 <- q/v
     d/dt(CENTRAL) <- k21 * PERI - k12 * CENTRAL - cl * CENTRAL/v1
     d/dt(PERI) <- -k21 * PERI + k12 * CENTRAL
     f <- CENTRAL/scale1
     f ~ prop(RSV)
   })
 }

# now we create another nonmem2rx object that validates the model above:

new <- as.nonmem2rx(mod2, mod)

# once that is done, you can translate to a full nlmixr2 fit (if you wish)

fit <- as.nlmixr2(new)

print(fit)