babelmixr2 (version 0.1.6)

bblDatToMonolix: Convert nlmixr2-compatible data to other formats (if possible)

Description

Convert nlmixr2-compatible data to other formats (if possible)

Usage

bblDatToMonolix(
  model,
  data,
  table = nlmixr2est::tableControl(),
  rxControl = rxode2::rxControl(),
  env = NULL
)
bblDatToNonmem(
  model,
  data,
  table = nlmixr2est::tableControl(),
  rxControl = rxode2::rxControl(),
  env = NULL
)
bblDatToRxode(
  model,
  data,
  table = nlmixr2est::tableControl(),
  rxControl = rxode2::rxControl(),
  env = NULL
)
bblDatToMrgsolve(
  model,
  data,
  table = nlmixr2est::tableControl(),
  rxControl = rxode2::rxControl(),
  env = NULL
)
bblDatToPknca(
  model,
  data,
  table = nlmixr2est::tableControl(),
  rxControl = rxode2::rxControl(),
  env = NULL
)

Value

With the function bblDatToMonolix() return a list with:

• Monolix compatible dataset ($monolix)

• Monolix ADM information ($adm)

With the function nlmixrDataToNonmem() return a dataset that is compatible with NONMEM.

With the function nlmixrDataToMrgsolve() return a dataset that is compatible with mrgsolve. Unlike NONMEM, it supports replacement events with evid=8 (note with rxode2 replacement evid is 5).

With the function nlmixrDataToRxode() this will normalize the dataset to use newer evid definitions that are closer to NONMEM instead of any classic definitions that are used at a lower level

Arguments

model

rxode2 model for conversion

data

Input dataset.

table

is the table control; this is mostly to figure out if there are additional columns to keep.

rxControl

is the rxode2 control options; This is to figure out how to handle the addl dosing information.

env

When NULL (default) nothing is done. When an environment, the function nlmixr2est::.foceiPreProcessData(data, env, model, rxControl) is called on the provided environment.

Author

Matthew L. Fidler

Examples

pk.turnover.emax3 <- function() {
  ini({
    tktr <- log(1)
    tka <- log(1)
    tcl <- log(0.1)
    tv <- log(10)
    ##
    eta.ktr ~ 1
    eta.ka ~ 1
    eta.cl ~ 2
    eta.v ~ 1
    prop.err <- 0.1
    pkadd.err <- 0.1
    ##
    temax <- logit(0.8)
    tec50 <- log(0.5)
    tkout <- log(0.05)
    te0 <- log(100)
    ##
    eta.emax ~ .5
    eta.ec50  ~ .5
    eta.kout ~ .5
    eta.e0 ~ .5
    ##
    pdadd.err <- 10
  })
  model({
    ktr <- exp(tktr + eta.ktr)
    ka <- exp(tka + eta.ka)
    cl <- exp(tcl + eta.cl)
    v <- exp(tv + eta.v)
    emax = expit(temax+eta.emax)
    ec50 =  exp(tec50 + eta.ec50)
    kout = exp(tkout + eta.kout)
    e0 = exp(te0 + eta.e0)
    ##
    DCP = center/v
    PD=1-emax*DCP/(ec50+DCP)
    ##
    effect(0) = e0
    kin = e0*kout
    ##
    d/dt(depot) = -ktr * depot
    d/dt(gut) =  ktr * depot -ka * gut
    d/dt(center) =  ka * gut - cl / v * center
    d/dt(effect) = kin*PD -kout*effect
    ##
    cp = center / v
    cp ~ prop(prop.err) + add(pkadd.err)
    effect ~ add(pdadd.err) | pca
  })
}

bblDatToMonolix(pk.turnover.emax3, nlmixr2data::warfarin)

bblDatToNonmem(pk.turnover.emax3, nlmixr2data::warfarin)

bblDatToMrgsolve(pk.turnover.emax3, nlmixr2data::warfarin)

bblDatToRxode(pk.turnover.emax3, nlmixr2data::warfarin)