RPANDA

RPANDA estimates historical species diversity through time from phylogenetic data in R using a probabilistic framework to produce diversity-through-time curves and quantify associated uncertainty.

Key Features:

• Probabilistic Estimation: Employs a probabilistic approach to estimate diversity-through-time curves from phylogenetic trees.
• Uncertainty Quantification: Provides measures of uncertainty around diversity estimates to assess estimate robustness.
• Simulation Validation: Validated by simulation studies demonstrating performance under various diversification scenarios.
• Impact of Tree Size and Undersampling: Includes analyses characterizing how tree size and undersampling affect the accuracy and reliability of diversity estimates.

Scientific Applications:

• Reconstructing historical diversity: Reconstructs temporal patterns of species diversity for evolutionary and macroevolutionary studies.
• Anuran phylogenies: Applied to anuran (frogs and toads) phylogenies to investigate historical diversity dynamics.
• Archaeobatrachia case study: Used to detect a historical decline in diversity in Archaeobatrachia attributed to reduced speciation rather than increased extinction.
• Clade interactions and trait evolution: Supports analyses of competitive interactions between clades and studies of how species richness influences phenotypic divergence.

Methodology:

Probabilistic estimation of diversity-through-time curves from phylogenetic data; quantification of uncertainty around those estimates; validation by simulations; analyses of effects of tree size and undersampling.