BoundedCoalescent

BoundedCoalescent simulates and computes probabilities of phylogenetic trees under the bounded coalescent model by conditioning the most recent common ancestor (MRCA) to occur after a specified date.

Key Features:

• Direct simulation algorithm: Implements a direct simulation algorithm for the bounded coalescent model that avoids rejection sampling to improve computational efficiency.
• MRCA probability calculation: Computes the probability that the MRCA occurs after a specified date to obtain probability densities for realizations under the bounded coalescent.
• Isochronous and heterochronous support: Supports isochronous sampling (identical collection times) and heterochronous sampling (varying collection dates).
• Temporal-bound influence analysis: Evaluates how imposing a temporal bound on the MRCA alters properties of the resulting phylogenies.
• R implementation: Functions and algorithms are implemented in R.

Scientific Applications:

• Speciation studies: Models and tests hypotheses about speciation events conditioned on MRCA timing.
• Horizontal gene transfer analysis: Applies to analyses of horizontal gene transfer where ancestral timing is constrained.
• Transmission dynamics: Applies to transmission dynamics to condition inference on recent common ancestry after a specified date.
• Phylogenetic studies with time-conditioned ancestral events: Generates and evaluates phylogenies under explicit temporal constraints on ancestral events.

Methodology:

Implements direct simulation from the bounded coalescent model (avoiding rejection sampling), computes the probability that the MRCA is after a specified date, and supports both isochronous and heterochronous sampling.