CRABS-package: CRABS: Congruent Rate Analyses in Birth-death Scenarios

In CRABS: Congruent Rate Analyses in Birth-Death Scenarios

CRABS: Congruent Rate Analyses in Birth-death Scenarios

Description

Features tools for exploring congruent phylogenetic birth-death models. It can construct the pulled speciation- and net-diversification rates from a reference model. Given alternative speciation- or extinction rates, it can construct new models that are congruent with the reference model. Functionality is included to sample new rate functions, and to visualize the distribution of one congruence class. See also Louca & Pennell (2020) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41586-020-2176-1")}.

References

• Louca, S., & Pennell, M. W. (2020). Extant timetrees are consistent with a myriad of diversification histories. Nature, 580(7804), 502-505. https://doi.org/10.1038/s41586-020-2176-1

• Höhna, S., Kopperud, B. T., & Magee, A. F. (2022). CRABS: Congruent rate analyses in birth–death scenarios. Methods in Ecology and Evolution, 13, 2709– 2718. https://doi.org/10.1111/2041-210X.13997

• Kopperud, B. T., Magee, A. F., & Höhna, S. (2023). Rapidly Changing Speciation and Extinction Rates Can Be Inferred in Spite of Nonidentifiability. Proceedings of the National Academy of Sciences 120 (7): e2208851120. https://doi.org/10.1073/pnas.2208851120

• Andréoletti, J. & Morlon, H. (2023). Exploring congruent diversification histories with flexibility and parsimony. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210X.14240

Author(s)

Maintainer: Bjørn Tore Kopperud [e-mail]

Authors:

• Sebastian Höhna

• Andrew F. Magee

• Jérémy Andréoletti

See Also

Useful links:

• https://github.com/afmagee/CRABS

CRABS documentation built on Oct. 24, 2023, 5:06 p.m.