Stratigraphic Paleobiology Modeling Pipelines
apply niche model
model taphonomic effects
define niche from boundaries
simulate ornstein-uhlenbeck (OU) process (specimen level)
simulate ornstein-uhlenbeck (OU) process
simulate variable rate Poisson point process
simulate Poisson point process
plot pre-paleoTS objects
probabilistic removal of elements
simulate (un)biased random walk (specimen level)
simulate (un)biased random walk
reduce pre-paleoTS format to paleoTS
random numbers from rejection sampling
simple niche model
simulate phenotypic stasis (specimen level)
simulate phenotypic stasis
StratPal: Stratigraphic Paleobiology Modeling Pipelines
simulate strict phenotypic stasis (specimen level)
thin a series of events (e.g. fossil occurrences)
The fossil record is a joint expression of ecological, taphonomic, evolutionary, and stratigraphic processes (Holland and Patzkowsky, 2012, ISBN:978-0226649382). This package allowing to simulate biological processes in the time domain (e.g., trait evolution, fossil abundance), and examine how their expression in the rock record (stratigraphic domain) is influenced based on age-depth models, ecological niche models, and taphonomic effects. Functions simulating common processes used in modeling trait evolution or event type data such as first/last occurrences are provided and can be used standalone or as part of a pipeline. The package comes with example data sets and tutorials in several vignettes, which can be used as a template to set up one's own simulation.
Useful links