Create PowerPoint and Word documents using nonmem2rx
Source:vignettes/articles/create-office.Rmd
create-office.Rmd
Step 1: import the model into nonmem2rx
library(nonmem2rx)
library(babelmixr2)
#> Loading required package: nlmixr2
#> Loading required package: nlmixr2data
library(nlmixr2rpt)
library(onbrand)
library(nonmem2rx)
# First we need the location of the nonmem control stream Since we are running an example, we will use one of the built-in examples in `nonmem2rx`
ctlFile <- system.file("mods/cpt/runODE032.ctl", package="nonmem2rx")
# You can use a control stream or other file. With the development
# version of `babelmixr2`, you can simply point to the listing file
mod <- nonmem2rx(ctlFile, lst=".res", save=FALSE)
#> ℹ getting information from '/home/runner/work/_temp/Library/nonmem2rx/mods/cpt/runODE032.ctl'
#> ℹ reading in xml file
#> ℹ done
#> ℹ reading in ext file
#> ℹ done
#> ℹ reading in phi file
#> ℹ done
#> ℹ reading in lst file
#> ℹ abbreviated list parsing
#> ℹ done
#> ℹ done
#> ℹ splitting control stream by records
#> ℹ done
#> ℹ Processing record $INPUT
#> ℹ Processing record $MODEL
#> ℹ Processing record $gTHETA
#> ℹ Processing record $OMEGA
#> ℹ Processing record $SIGMA
#> ℹ Processing record $PROBLEM
#> ℹ Processing record $DATA
#> ℹ Processing record $SUBROUTINES
#> ℹ Processing record $PK
#> ℹ Processing record $DES
#> ℹ Processing record $ERROR
#> ℹ Processing record $ESTIMATION
#> ℹ Ignore record $ESTIMATION
#> ℹ Processing record $COVARIANCE
#> ℹ Ignore record $COVARIANCE
#> ℹ Processing record $TABLE
#> ℹ change initial estimate of `theta1` to `1.37034036528946`
#> ℹ change initial estimate of `theta2` to `4.19814911033061`
#> ℹ change initial estimate of `theta3` to `1.38003493562413`
#> ℹ change initial estimate of `theta4` to `3.87657341967489`
#> ℹ change initial estimate of `theta5` to `0.196446108190896`
#> ℹ change initial estimate of `eta1` to `0.101251418415006`
#> ℹ change initial estimate of `eta2` to `0.0993872449483344`
#> ℹ change initial estimate of `eta3` to `0.101302674763154`
#> ℹ change initial estimate of `eta4` to `0.0730497519364148`
#> ℹ read in nonmem input data (for model validation): /home/runner/work/_temp/Library/nonmem2rx/mods/cpt/Bolus_2CPT.csv
#> ℹ ignoring lines that begin with a letter (IGNORE=@)'
#> ℹ applying names specified by $INPUT
#> ℹ subsetting accept/ignore filters code: .data[-which((.data$SD == 0)),]
#> ℹ done
#> ℹ read in nonmem IPRED data (for model validation): /home/runner/work/_temp/Library/nonmem2rx/mods/cpt/runODE032.csv
#> ℹ done
#> ℹ changing most variables to lower case
#> ℹ done
#> ℹ replace theta names
#> ℹ done
#> ℹ replace eta names
#> ℹ done (no labels)
#> ℹ renaming compartments
#> ℹ done
#> ℹ solving ipred problem
#> ℹ done
#> ℹ solving pred problem
#> ℹ done
Step 2: convert the rxode2
model to
nlmixr2
In this step, you convert the model to nlmixr2
by
as.nlmixr2(mod)
; You may need to do a little manual work to get the residual
specification to match between nlmixr2 and NONMEM.
Once the residual specification is compatible with a nlmixr2 object,
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 3.0.2.9000 using 2 threads (see ?getRxThreads)
#> no cache: create with `rxCreateCache()`
#> → Calculating residuals/tables
#> ✔ done
#> → compress origData in nlmixr2 object, save 204016
#> → compress parHistData in nlmixr2 object, save 2184
fit
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
#> → loading into symengine environment...
#> → pruning branches (`if`/`else`) of full model...
#> ✔ done
#> → calculate jacobian
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → calculate sensitivities
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → calculate ∂(f)/∂(η)
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → calculate ∂(R²)/∂(η)
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → finding duplicate expressions in inner model...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → optimizing duplicate expressions in inner model...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → finding duplicate expressions in EBE model...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → optimizing duplicate expressions in EBE model...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → compiling inner model...
#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
#> ✔ done
#> → finding duplicate expressions in FD model...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → optimizing duplicate expressions in FD model...
#> [====|====|====|====|====|====|====|====|====|====] 0:00:00
#> → compiling EBE model...
#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
#> ✔ done
#> → compiling events FD model...
#> using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
#> ✔ done
#> → 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