The goal of timber is to facilitate logging in a clinical environment with the goal of making code easily traceable and reproducible.
This package is still in development and currently is only available from GitHub. To install the development version run the following:
devtools::install_github("atorus-research/timber")While many packages to facilitate the logging of code already exist in the R ecosystem, it is hard to find a solution that works well for clinical programming applications. Many logging implementations are more implicit and rely on user input to create the log for the execution of a script. While this is useful for logging specific events of an application, in clinical programming a log has a set purpose.
timber is built around the concept of creating a log for the execution
of an R script that provides an overview of what happened as well as the
environment that it happened in. We set out to create a flexible logging
utility that could provide the necessary information to anyone reviewing
the code execution so they can recreate the execution environment and
run the code for themselves. timber is purpose-built for the needs of
clinical programming to capture necessary elements of the environment
and execution to be able to create a complete view of the program
execution.
timber can be used in a file or through scripting. More information on
how to use timber can be found in vignette("timber")
While this development version has been released, the development team
is still making improvements to the package. This release is intended to
give access to the core functionality of timber while it is still
being developed. While the main functions and functionality have already
been created, there are still many behind the scenes items that need to
be addressed.