clinify is direct extension of the flextable and officer packages, aimed at supplementing some functionality and simplifying some common tasks in the creation of clinical tables, listings and figures.
You can install the development version of clinify like so:
# Install the development version:
devtools::install_github("https://github.com/atorus-research/clinify.git", ref="development")There’s a large assortment of table packages available, and there are many that are specifically catered to clinical reporting. For many organizations, one of these packages may very well be a great choice, but there are a couple of key motivators we’ve found that lead drove us to start writing clinify:
- Clinical output standards likely exist within an organization, and changing those standards may not be an option
- It’s very likely that certain outputs will require that you deviate from those standards, so flexibility it necessary, sometimes in highly nuanced ways
- Organizations like Contract Research Organizations (CROs) may have to adapt to multiple clients’ reporting standards, which likely don’t look the same
- Regardless of the situation, reuse and repeatability of a given configuration is critical, and changes in configuration must be easily implemented.
Instead of building a new package from the ground up, clinify aims to extend what we see as a best choice for the situation at hand, adding new functionality where necessary and streamlining common tasks to make them more efficient for programmers to implement. We chose flextable for a two key reasons:
- flextable already offers most of the functionality that we’re looking for, particularly with the pairing of officer. For example, word documents have to be a first class priority of output support.
- While creating a table is the focus, the output tends to be more than just a table. We need the capability to modify the underlying document as a whole, which is another place that officer is truly necessary.
Here are some key principles we’re using in building clinify:
- clinify objects should inherit from an underlying flextable or officer object
- clinify functionality must not interfere with flextable or officer functionality, i.e. flextable or officer functions called should operate without error.