The true beauty of pharmaverse (and open source in general) is when efforts from various different developers come together to compliment each other as a whole greater than the sum of the individual parts. By design in R, no single package will ever completely cover all your needs, but by piecing them together we can make complex tasks increasingly simple.
This book contains end-to-end examples of using pharmaverse packages together to achieve common clinical reporting analyses, such as ADaM and Tables/Listings/Graphs. The examples use consistent source test SDTMs and ADaMs from {pharmaversesdtm} and {pharmaverseadam} respectively.
We'll endeavour to include a selection of examples here over time, e.g. to help users when trying out the packages for PK/PD or Therapeutic Area specific (such as Oncology or Vaccines) analyses.
Note that this examples book should only be used to show how collections of packages can be used in conjunction - more thorough examples of individual package usages would always be covered in the package site vignettes and no need to repeat here.
Each example can be explored via a live and interactive Posit Cloud environment (preconfigured with all required package installations). Click here: "Launch Posit Cloud" to try out any of the examples code. You can do this by clicking File: Open File: and then choosing whichever example script, e.g. adam/adsl.R. Feel free to try out customizing any of the examples to better fit any of your own internal clinical reporting workflows!
Individual R scripts are produced automatically when the pages are
rendered.
These standalone scripts can be run in the Posit
Cloud environment, and may be
easier to understand for a new developer than the Quarto files.
New Quarto pages should include the code snippet at the top for the scripts to be produced.
invisible_hook_purl <- function(before, options, ...) {knitr::hook_purl(before, options, ...); NULL}
knitr::knit_hooks$set(purl = invisible_hook_purl)
Anyone can suggest ideas for examples to this repo for usage of any pharmaverse packages. To do this, make an issue here with your idea. Any new issues get automatically added to our project board.
Our team will periodically review and choose which backlog issues are
prioritized. If you'd be willing to contribute towards adding the
example yourself, then let us know in the issue and our team would
provide you the necessary repo access. You can then branch off main
(including the issue # at the start of your feature branch name) and
create a PR where one of our maintainer team would review and approve to
get your contribution published.
If ever unsure about anything and you need input from our team you can tag us in your issue using "@pharmaverse/examples".
A note on dependencies is we don't use renv here to manage this
examples book. If you ever need to use a new package the requirement is
that you will edit the root level DESCRIPTION file and add it to the
Imports. This is a simple dependency management approach, as then during
rendering/deployment our pipeline will pull the latest released version
from CRAN.
You could even use the Posit Cloud environment for these contributions, but if not be sure you have installed the latest CRAN versions of all the packages being used.
We recommend you notify the maintainers of all the packages used in your example, as then they are more likely to help inform us if ever anything changes in their packages that breaks any of our examples.