as.nlmixr2: Convert an object to a nlmixr2 fit object

In nlmixr2/babelmixr: Use 'nlmixr2' to Interact with Open Source and Commercial Software

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(),
  ci = 0.95
)

as.nlmixr(
  x,
  ...,
  table = nlmixr2est::tableControl(),
  rxControl = rxode2::rxControl(),
  ci = 0.95
)

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
ci	is the confidence interval of the residual differences calculated (by default 0.95)

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)

nlmixr2/babelmixr documentation built on Nov. 21, 2024, 3:16 a.m.