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

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

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
)

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.

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

Author(s)

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)

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