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What is SecSSE?
SecSSE is an R package designed for multistate data sets under a concealed state and speciation (hisse) framework. In this sense, it is parallel to the ‘MuSSE’ functionality implemented indiversitree, but it accounts for finding possible spurious relationships between traits and diversification rates (“false positives”, Rabosky & Goldberg 2015) by testing against a “hidden trait” (Beaulieu et al. 2013), which is responsible for more variation in diversification rates than the trait being investigated.
Installing secsse
Thesecsse package has a stable version onCRAN and a development version on GitHub.
From GitHub
Install secsse from this GitHub repository by running:
install.packages("remotes")remotes::install_github("rsetienne/secsse")Using secsse as a package dependency
Cite
If you usesecsse in your publications, please cite:
- Herrera-Alsina, Leonel et al. “Detecting the Dependence of Diversification on Multiple Traits from Phylogenetic Trees and Trait Data.” Systematic biology vol. 68,2 (2019): 317-328.https://doi.org/10.1093/sysbio/syy057
References
Beaulieu, Jeremy M et al. “Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms.” Systematic biology vol. 62,5 (2013): 725-37.https://doi.org/.1093/sysbio/syt034
Beaulieu, Jeremy M, and Brian C O’Meara. “Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction.” Systematic biology vol. 65,4 (2016): 583-601.https://doi.org/10.1093/sysbio/syw022
Rabosky, Daniel L., and Emma E. Goldberg. “Model inadequacy and mistaken inferences of trait-dependent speciation.” Systematic biology 64.2 (2015): 340-355.https://doi.org/10.1093/sysbio/syu131