Templated Word and PowerPoint reporting for nlmixr2
The purpose of this package is to automate the reporting of analyses
performed in the nlmixr2 package in both PowerPoint and
Word. This is accomplished with a yaml file that contains specifications
for report elements (figures and tables) as well as the contents of Word
and PowerPoint documents. Internal templates for both the documents and
the report yaml file are included. These can be customized: The format
of the document templates can be customized for your organization by
using the onbrand package. The report contents can be
customized by creating a copy of the included yaml file and modifying it
to suite your needs (see the vignette below).
To install off of CRAN:
install.packages("nlmixr2rpt", dependencies = TRUE)To install the development version from GitHub
#install.packages("devtools")
devtools::install_github("nlmixr2/nlmixr2rpt", dependencies=TRUE)Assuming you have the results of an nlmixr analysis in the object
fit you can dump those results into a PowerPoint document
by doing the following:
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)
save_report(obnd_pptx, "report.pptx")This creates an onbrand reporting object obnd_pptx. You
can add other reporting elements using onbrand or
officer. Next the command report_fit() will
append the results in the fit object to an onbrand report.
After calling report_fit() you can append other reporting
elements. Finally you just need to save the document using
save_report().
The process for a Word document is the same. You simply need to use a Word onbrand template instead of a PowerPoint.
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)
save_report(obnd_docx, "report.docx")If you want to learn more about customizing the outputs or using your own organizational templates in reporting, be sure to browse through the documentation and check out the vignettes: