rtrees
Deriving Phylogenies from Synthesis Trees
Provides tools to derive species-level phylogenies from large synthesis mega-trees for a wide range of taxonomic groups, including plants, birds, mammals, amphibians, reptiles, fish, bees, butterflies, and sharks. When a queried species is absent from the mega-tree, it is grafted onto the tree using one of two placement strategies: attachment at the basal node of the most closely related genus or family ('at_basal_node'), or random attachment below that basal node with probability proportional to branch length ('random_below_basal'). See Li (2023) <doi:10.1111/ecog.06643> for details. Multiple species from a genus not represented in the mega-tree are placed as a polytomy to preserve clade coherence. The package interfaces with the 'megatrees' data package, which bundles or downloads on demand curated mega-trees. Users can also provide their own mega-trees.
Versions across snapshots
| Version | Repository | File | Size |
|---|---|---|---|
2.0.2 |
rolling linux/jammy R-4.5 | rtrees_2.0.2.tar.gz |
1.9 MiB |
2.0.2 |
rolling linux/noble R-4.5 | rtrees_2.0.2.tar.gz |
1.9 MiB |
2.0.2 |
rolling source/ R- | rtrees_2.0.2.tar.gz |
1.7 MiB |
2.0.2 |
latest linux/jammy R-4.5 | rtrees_2.0.2.tar.gz |
1.9 MiB |
2.0.2 |
latest linux/noble R-4.5 | rtrees_2.0.2.tar.gz |
1.9 MiB |
2.0.2 |
latest source/ R- | rtrees_2.0.2.tar.gz |
1.7 MiB |
2.0.2 |
2026-04-23 source/ R- | rtrees_2.0.2.tar.gz |
0 B |