Simulating Diversification Dynamics
General rate species sampling
General rate Birth-Death simulation
Bin occurrences in geologic intervals
Draw a sim object
Separate a paleobuddy simulation into monophyletic clades
Phylogeny generating
Create a flexible rate for birth-death or sampling simulations
paleobuddy: Simulating diversification dynamics
Converting a phylogeny in a paleobuddy object
General rate exponential and Weibull waiting times
Details, generics, and methods for the sim class
Expected diversity for general exponential rates
Simulation of species diversification, fossil records, and phylogenies. While the literature on species birth-death simulators is extensive, including important software like 'paleotree' and 'APE', we concluded there were interesting gaps to be filled regarding possible diversification scenarios. Here we strove for flexibility over focus, implementing a large array of regimens for users to experiment with and combine. In this way, 'paleobuddy' can be used in complement to other simulators as a flexible jack of all trades, or, in the case of scenarios implemented only here, can allow for robust and easy simulations for novel situations. Environmental data modified from that in 'RPANDA': Morlon H. et al (2016) <doi:10.1111/2041-210X.12526>.