Description
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) <doi:10.1038/s41586-020-2176-1>.
README.md
CRABS: Congruent Rate Analysis in Birth-death Scenarios
A package for investigating and visualizing the congruence class (Louca & Pennell 2020) of a phylogenetic birth-death model. Previously, this package went by the acronym ACDC.
Installation:
The stable version can be installed from CRAN:
install.packages("CRABS")
The developmental version can be installed from the github repository. The package devtools makes this convenient:
install.packages("devtools")
library(devtools)
install_github("afmagee/CRABS")
Documentation
There is documentation for each function in R (type ?CRABS in the R-console), as well as a long-form vignette with an example workflow.
References
- Louca, S., & Pennell, M. W. (2020). Extant timetrees are consistent with a myriad of diversification histories. Nature, 580(7804), 502-505.
- 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.
- Andreoletti 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.