Create PowerPoint and Word documents using monolix2rx

Step 1: import the model into monolix2rx

library(monolix2rx)
library(babelmixr2)
#> Loading required package: nlmixr2
#> Loading required package: nlmixr2data
library(nlmixr2rpt)
library(onbrand)

library(nonmem2rx)

# 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 3.0.0 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

$$\begin{align*} cmt({depot}) \\ cmt({central}) \\ {ka} & = \exp\left({ka\_pop}+{omega\_ka}\right) \\ {V} & = \exp\left({V\_pop}+{omega\_V}\right) \\ {Cl} & = \exp\left({Cl\_pop}+{omega\_Cl}\right) \\ \frac{d \: depot}{dt} & = -{ka} {\times} {depot} \\ \frac{d \: central}{dt} & = +{ka} {\times} {depot}-\frac{{Cl}}{{V}} {\times} {central} \\ {Cc} & = \frac{{central}}{{V}} \\ {CONC} & = {Cc} \\ {CONC} & \sim add({a})+prop({b})+combined1() \end{align*}$$

Step 3: Create a PowerPoint file

A PowerPoint can be created from your own custom powerpoint templates, but in this example we will use the ones that come from nlmixr2rpt directly:

obnd_pptx = read_template(
  template = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.pptx"),
  mapping  = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.yaml"))

obnd_pptx = report_fit(
  fit     = fit,
  obnd    = obnd_pptx)
#> 
#> Attaching package: 'xpose'
#> The following object is masked from 'package:stats':
#> 
#>     filter
#> Registered S3 method overwritten by 'GGally':
#>   method from   
#>   +.gg   ggplot2
#> 
#> Attaching package: 'ggPMX'
#> The following object is masked from 'package:xpose':
#> 
#>     get_data
#> → Calculating residuals/tables
#> ✔ done
#> Warning in xpose.nlmixr2::xpose_data_nlmixr(fit): Added CWRES to fit (using
#> nlmixr2::addCwres)...
#> Skipping table: skip_table (NA found, not generated)
#> Skipping figure: res_vs_pred_idv (NA found, not generated)
#> Skipping figure: eta_cont (NA found, not generated)
#> Skipping figure: eta_cat (NA found, not generated)
#> Skipping figure: skip_figure (NA found, not generated)

save_report(obnd_pptx, "mod-PowerPoint.pptx")
#> $isgood
#> [1] TRUE
#> 
#> $msgs
#> NULL

Which gives the powerpoint here

Step 4: Create a Word file

Just like in PowerPoint, you can customizeown custom word templates, but in this example we will use the ones that come from nlmixr2rpt directly:

obnd_docx = read_template(
  template = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.docx"),
  mapping  = system.file(package="nlmixr2rpt", "templates","nlmixr_obnd_template.yaml"))

obnd_docx = report_fit(
  fit     = fit,
  obnd    = obnd_docx)
#> → Calculating residuals/tables
#> ✔ done
#> Warning in xpose.nlmixr2::xpose_data_nlmixr(fit): Added CWRES to fit (using
#> nlmixr2::addCwres)...
#> Skipping figure: res_vs_pred_idv (NA found, not generated)
#> Skipping figure: skip_figure (NA found, not generated)
#> Skipping figure: eta_cont (NA found, not generated)
#> Skipping figure: eta_cat (NA found, not generated)

save_report(obnd_docx, "mod-Word.docx")
#> $isgood
#> [1] TRUE
#> 
#> $msgs
#> NULL

Which gives the word document here