Rclade: automated taxonomic collapsing and geological-timescale annotation of time-calibrated phylogenetic trees in R

Rclade is an R package that simplifies the process of taxonomic collapsing and geological-timescale annotation of time-calibrated phylogenetic trees. It streamlines the workflow by providing a single-function interface, eliminating the need for coordination among multiple packages and repetitive coding tasks.

Rclade offers several key features. Firstly, it includes custom ggproto objects (GeomPolygonStraight/GeomSegmentStraight) that render collapsed triangles in circular layouts as straight edges, bypassing the coord_munch() interpolation. Secondly, it automatically detects and parses four different taxonomic-label formats (GTDB, Silva, NCBI, and user-supplied custom regex) with explicit input-validation contracts and parsing-accuracy evaluation on real and derived test sets.

Lastly, Rclade can be easily integrated into workflows using YAML configuration, library-mode APIs, and standard Unix exit codes.

The package has been tested on synthetic and real datasets, ranging from 200 to 10,000 synthetic tips and real reference trees with up to 10,122 tips. The benchmarks show that the full-pipeline overhead is minimal for interactive use, with a median of approximately 0.87 seconds for in-session rendering and around 8.4 seconds for process-level wall-clock time at 10,000 tips.

In conclusion, Rclade serves as a convenient layer over the ggtree/deeptime ecosystem, reducing boilerplate code while introducing targeted technical improvements for circular-layout rendering and managing format heterogeneity.