Rclade: automated taxonomic collapsing and geological-timescale annotation of time-calibrated phylogenetic trees in R
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Background
Reproducible taxonomic collapsing and geological-timescale annotation of time-calibrated phylogenetic trees in R often require coordination among several packages and repeated code for label parsing, clade validation, plotting, and export. Workflow-managed analyses additionally benefit from non-interactive configuration, predictable diagnostics, and machine-readable exit status.
Results
We present Rclade, an R package that consolidates the multi-package coordination required for taxonomic collapsing into a streamlined, single-function interface. Rclade provides (1) custom ggproto objects (GeomPolygonStraight/GeomSegmentStraight) that bypass coord_munch() interpolation to achieve straight-edge rendering of collapsed triangles in circular layouts; (2) automatic detection and parsing of four taxonomic-label formats (GTDB, Silva, NCBI, embedded) plus user-supplied custom regex, with explicit input-validation contracts and parsing-accuracy evaluation on real and derived test sets; and (3) workflow embeddability through YAML configuration, library-mode APIs, and standard Unix exit codes. Benchmarks on synthetic and real datasets (200–10,000 synthetic tips and real reference trees up to 10,122 tips; 5 replicates at every scale under a unified fully rendered measurement protocol) show that the full-pipeline overhead is modest for interactive use (median ≈0.87 s in-session rendering and ≈8.4 s process-level wall-clock at 10,000 tips).
Conclusions
Rclade is a convenience layer over the ggtree/deeptime ecosystem that reduces boilerplate while adding targeted technical improvements for circular-layout rendering and format heterogeneity management.
Availability
Rclade is released under the MIT license. Source code, documentation, benchmark scripts, and evaluation data are archived at Zenodo ( https://doi.org/10.5281/zenodo.22106523 (version 1.1.0; all versions: https://doi.org/10.5281/zenodo.22043060 )), with ongoing development at https://github.com/zengzichao/Rclade .
