This shows an easy work-flow to create a VPC using a Monolix model:
Step 1: Convert the Monolix
model to
rxode2
:
library(babelmixr2)
library(monolix2rx)
# First we need the location of the monolix mlxtran file. Since we are
# running an example, we will use one of the built-in examples in
# `monolix2rx`
pkgTheo <- system.file("theo/theophylline_project.mlxtran", package="monolix2rx")
# You can use a control stream or other file. With the development
# version of `babelmixr2`, you can simply point to the listing file
mod <- monolix2rx(pkgTheo)
#> ℹ integrated model file 'oral1_1cpt_kaVCl.txt' into mlxtran object
#> ℹ updating model values to final parameter estimates
#> ℹ done
#> ℹ reading run info (# obs, doses, Monolix Version, etc) from summary.txt
#> ℹ done
#> ℹ reading covariance from FisherInformation/covarianceEstimatesLin.txt
#> ℹ done
#> Warning in .dataRenameFromMlxtran(data, .mlxtran): NAs introduced by coercion
#> ℹ imported monolix and translated to rxode2 compatible data ($monolixData)
#> ℹ imported monolix ETAS (_SAEM) imported to rxode2 compatible data ($etaData)
#> ℹ imported monolix pred/ipred data to compare ($predIpredData)
#> ℹ solving ipred problem
#> ℹ done
#> ℹ solving pred problem
#> ℹ done
Step 2: convert the rxode2
model to
nlmixr2
You can convert the model, mod
, to a nlmixr2 fit
object:
fit <- as.nlmixr2(mod)
#> → loading into symengine environment...
#> → pruning branches (`if`/`else`) of full model...
#> ✔ done
#> → finding duplicate expressions in EBE model...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → optimizing duplicate expressions in EBE model...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → compiling EBE model...
#> ✔ done
#> rxode2 4.0.0 using 2 threads (see ?getRxThreads)
#> no cache: create with `rxCreateCache()`
#> → Calculating residuals/tables
#> ✔ done
#> → compress origData in nlmixr2 object, save 7168
#> ℹ monolix parameter history integrated into fit object
fit
Step 3: Perform the VPC
From here we simply use vpcPlot()
in conjunction with
the vpc
package to get the regular and prediction-corrected
VPCs and arrange them on a single plot:
library(ggplot2)
p1 <- vpcPlot(fit, show=list(obs_dv=TRUE))
#> using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
p1 <- p1 + ylab("Concentrations") +
rxode2::rxTheme() +
xlab("Time (hr)") +
xgxr::xgx_scale_x_time_units("hour", "hour")
p1a <- p1 + xgxr::xgx_scale_y_log10()
## A prediction-corrected VPC
p2 <- vpcPlot(fit, pred_corr = TRUE, show=list(obs_dv=TRUE))
p2 <- p2 + ylab("Prediction-Corrected Concentrations") +
rxode2::rxTheme() +
xlab("Time (hr)") +
xgxr::xgx_scale_x_time_units("hour", "hour")
p2a <- p2 + xgxr::xgx_scale_y_log10()
library(patchwork)
(p1 * p1a) / (p2 * p2a)
#> Warning in transformation$transform(x): NaNs produced
#> Warning in ggplot2::scale_y_log10(..., breaks = breaks, minor_breaks =
#> minor_breaks, : log-10 transformation introduced infinite
#> values.
#> Warning in transformation$transform(x): NaNs produced
#> Warning in ggplot2::scale_y_log10(..., breaks = breaks, minor_breaks =
#> minor_breaks, : log-10 transformation introduced infinite
#> values.