DDD: Diversity-Dependent Diversification

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Implements maximum likelihood and bootstrap methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent, under various models including various types of key innovations.

Also contains functions to simulate the diversity-dependent process.

Installing DDD

From CRAN

From within R, do:

install.packages("DDD")

From GitHub

Install DDD from this GitHub repository by running:

install.packages("remotes")
# remotes::install_github("rsetienne/DDD")
install.packages("DDD", repos = c('https://rsetienne.r-universe.dev', 'https://cloud.r-project.org'))

References

• Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, https://doi.org/10.1098/rspb.2011.1439
• Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, https://doi.org/10.1086/667574
• Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, https://doi.org/10.1111/2041-210X.12565
• Laudanno et al. 2021. Syst. Biol. 70: 389–407, https://doi.org/10.1093/sysbio/syaa048