Integration with the FossilSim and paleotree packages

library(StratPal)

This vignette describes how to integrate the StratPal package with the FossilSim and the paleotree packages.

Integration with the FossilSim package

As is, the StratPal package handles fossils objects as constructed by the FossilSim package. These objects represent fossils sampled along a tree (phylogeny). They can be transformed using the functions apply_taphonomy and apply_niche. This will remove fossil occurrences according to preservation potential and change on taphonomic conditions (or niche definition and change in gradient). Note that this corresponds to an nonparametric expansion of the variable recovery model as implemented in FossilSim.

For examples see the documentation of the functions apply_niche and apply_taphonomy.

Integration with paleotree

To combine the StratPal package with the paleotree package, please convert the paleotree format into the FossilSim format as described in the paleotree vignette of the FossilSim vignette:

vignette("paleotree", package = "FossilSim")

After conversion you can proceed as described in the section Integration with the FossilSim package

References

• Barido-Sottani J, Pett W, O’Reilly JE, Warnock RCM. Fossilsim: An r package for simulating fossil occurrence data under mechanistic models of preservation and recovery. Methods Ecol Evol. 2019; 10: 835–840. https://doi.org/10.1111/2041-210X.13170
• Bapst, D.W. (2012), paleotree: an R package for paleontological and phylogenetic analyses of evolution. Methods in Ecology and Evolution, 3: 803-807. https://doi.org/10.1111/j.2041-210X.2012.00223.x
• Warnock R, Barido-Sottani J, Pett W, Joseph O, Stolz U (2024). FossilSim: Simulation and Plots for Fossil and Taxonomy Data. R package version 2.4.1, https://CRAN.R-project.org/package=FossilSim