ArchiDART is an R Package Allowing the Automated Computation of Plant Root Architectural Traits and the Topological Analysis of Plant Root Systems

Both root image analysis and root architecture models are powerful tools to help us understand the relationship between root system traits and functions. Often, root systems are characterized using geometric descriptors, such as the total root length, the total root surface, or the number of root tips. However, such descriptors often fail to describe the full complexity of root systems. Additional descriptors able to characterize how individual roots are connected to each other through branching (topology) are also needed. In this context, the R package archiDART offers several tools allowing the automated computation of geometric and topological descriptors using Data Analysis of Root Tracings (DART) and Root System Markup Language (RSML) files.

Since its first release (v1.0), archiDART has contained functions allowing the computation of global root architectural traits, root growth rates, root growth directions and trajectories, and lateral root distribution. In addition, archiDART also includes a set of easy-to-use and flexible plotting functions designed to visualize the dynamics of root system growth and root branching patterns (e.g., branching angles). Recently, we released a new version (v 3.0) of our package on the CRAN repository. This new version now includes several topological analysis methods, such as Fitter indices and persistent homology. Persistent homology is a mathematical framework allowing the quantification of plant morphologies at different scales (from organs to organisms) and increasingly appears as a very promising tool to characterize and compare the topology of plant root systems.

In this communication, we aim to demonstrate how the functions of the R package archiDART can be used to analyse and compare complex root system architectures. We also aim to show that the topological analysis of root systems is highly complementary to the more classical approach that uses a set of geometric descriptors to compare root systems.