nlmixr2 vpc not working correctly

[mattfidler]

  library(nlmixr2)
#> Loading required package: nlmixr2data

  library(ggPMX)
#> Registered S3 method overwritten by 'GGally':
#>   method from   
#>   +.gg   ggplot2

  one.cmt <- function() {
    ini({
      ## You may label each parameter with a comment
      tka <- 0.45 # Log Ka
      tcl <- 1 # 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)
      linCmt() ~ add(add.sd)
    })
  }

  fit <- nlmixr2::nlmixr2(one.cmt, nlmixr2data::theo_sd, est="saem", control=list(print=0))
#> ℹ parameter labels from comments will be replaced by 'label()'
#> → loading into symengine environment...
#> → pruning branches (`if`/`else`) of saem model...
#> ✔ done
#> → finding duplicate expressions in saem model...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> ✔ done
#> rxode2 2.0.7 using 4 threads (see ?getRxThreads)
#> Calculating covariance matrix
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → loading into symengine environment...
#> → pruning branches (`if`/`else`) of saem model...
#> ✔ done
#> → finding duplicate expressions in saem predOnly model 0...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → finding duplicate expressions in saem predOnly model 1...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → finding duplicate expressions in saem predOnly model 2...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> ✔ done
#> → Calculating residuals/tables
#> ✔ done
#> → compress origData in nlmixr2 object, save 5952
#> → compress phiM in nlmixr2 object, save 62352
#> → compress parHist in nlmixr2 object, save 9640
#> → compress saem0 in nlmixr2 object, save 24520

  ctr <- pmx_nlmixr(fit, ## VPC is turned on by default, can turn off
                    settings = pmx_settings(is.draft = FALSE))
#> → Add NPDE
#> ✔ done
#> Calculating -2LL by Gaussian quadrature (nnodes=3,nsd=1.6)
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00

  ctr %>% pmx_plot_vpc

  vpcPlot(fit)

  ct <- theophylline()

  ct %>% pmx_plot_vpc

^{Created on 2022-05-21 by the reprex package (v2.0.1)}

[mattfidler]

The default theo example works well, but nlmixr2 output looks wrong.

[mattfidler]

  library(nlmixr)

  library(ggPMX)
#> Registered S3 method overwritten by 'GGally':
#>   method from   
#>   +.gg   ggplot2

  one.cmt <- function() {
    ini({
      ## You may label each parameter with a comment
      tka <- 0.45 # Log Ka
      tcl <- 1 # 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)
      linCmt() ~ add(add.sd)
    })
  }

  fit <- nlmixr::nlmixr(one.cmt, nlmixr2data::theo_sd, est="saem", control=list(print=0))
#> ℹ parameter labels from comments will be replaced by 'label()'
#> → generate SAEM model
#> ✔ done
#> RxODE 1.1.5 using 4 threads (see ?getRxThreads)
#>   no cache: create with `rxCreateCache()`
#> Calculating covariance matrix
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → creating full model...
#> → pruning branches (`if`/`else`)...
#> ✔ done
#> → loading into symengine environment...
#> ✔ done
#> → compiling EBE model...
#> ✔ done
#> Calculating residuals/tables
#> done

  ctr <- pmx_nlmixr(fit, ## VPC is turned on by default, can turn off
                    settings = pmx_settings(is.draft = FALSE))
#> add npde
#> Compiling NPDE model...done
#> done
#> Compiling model...done
#> Compiling VPC model...done
#> done (0.52 sec)
#> Calculating -2LL by Gaussian quadrature (nnodes=3,nsd=1.6)
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00

  ctr %>% pmx_plot_vpc

  vpcPlot(fit)
#> Error in vpcPlot(fit): could not find function "vpcPlot"

  ct <- theophylline()

  ct %>% pmx_plot_vpc

^{Created on 2022-05-21 by the reprex package (v2.0.1)}

It doesn't work correctly with nlmixr either

[mattfidler]

I am stumped here, maybe drop it @biethbr1 @baltcir1 what do you think?

[mattfidler]

For now drop it.