nlmixr2rpt
Templated Word and PowerPoint reporting for nlmixr2
Overview
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).
Installation
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)Getting Started
PowerPoint
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().
Word
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")Further reading
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: