nlmixr2_m3: An 'xp_xtra' example based on a nlmixr2 fit with M3 censoring

In xpose.xtras: Extra Functionality for the 'xpose' Package

An xp_xtra example based on a nlmixr2 fit with M3 censoring

Description

A modified version of the theophylline model fit with censoring added in to provoke M3 censoring. An additional output variable is added to use an an example in categorical DVs.

Usage

nlmixr2_m3

Format

An object of class xp_xtras (inherits from xpose_data, uneval) of length 10.

Source

https://github.com/nlmixr2/nlmixr2/issues/275#issuecomment-2445469327

See Also

xpdb_nlmixr2 catdv_vs_dvprobs()

Examples

## Not run: 
# This not-run block is to show how the dataset was generated
# This is also available in data-raw of the github repo
one.cmt <- function() {
  ini({
    ## You may label each parameter with a comment
    tka <- 0.45 # Ka
    tcl <- log(c(0, 2.7, 100)) # Log Cl
    ## This works with interactive models
    ## You may also label the preceding line with label("label text")
    tv <- 3.45; label("log V")
    ## the label("Label name") works with all models
    eta.ka ~ 0.6
    eta.cl ~ 0.3
    eta.v ~ 0.1
    add.sd <- 0.7
  })
  model({
    ka <- exp(tka + eta.ka)
    cl <- exp(tcl + eta.cl)
    v <- exp(tv + eta.v)
    # Not sure how one does this with linCmt(), if that has to be posthoc
    d/dt(depot) = -ka*depot
    d/dt(cent) = ka*depot - cl*cent/v
    cp = cent/v
    blqlike = pnorm( (LLOQ - cp)/add.sd  ) # blq likelihood for diagnostics
    cp ~ add(add.sd)
  })
}
theo_sdcens=nlmixr2data::theo_sd
good_lloq <- quantile(theo_sdcens[theo_sdcens$EVID==0,]$DV, 0.15)
theo_sdcens$CENS=ifelse(theo_sdcens$DV<good_lloq & theo_sdcens$EVID==0,1,0)
theo_sdcens$DV=ifelse(theo_sdcens$CENS==1,good_lloq,theo_sdcens$DV)
theo_sdcens$LLOQ=good_lloq # add lloq column
fitcens <- nlmixr2est::nlmixr2(one.cmt, theo_sdcens, "focei",
           control=nlmixr2est::foceiControl(print=0))
nlmixr2_m3 <- nlmixr2_as_xtra(obj = fitcens, .skip_assoc = TRUE)

## End(Not run)


nlmixr2_m3 %>% # modified from catdv_vs_dvprobs example
  set_var_types(catdv=CENS,dvprobs=BLQLIKE) %>%
  set_dv_probs(1, 1~BLQLIKE, .dv_var = CENS) %>%
  set_var_levels(1, CENS = lvl_bin()) %>%
  catdv_vs_dvprobs(xlab = "basic", quiet = TRUE)

xpose.xtras documentation built on April 19, 2026, 9:06 a.m.