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sepkoski

Overview

sepkoski is a data R package of Sepkoski’s fossil marine animal genera compendium (Sepkoski, 2002), ported from Shanan Peters’ online database.

The aim of sepkoski is to provide a light and easily-accessible solution to working with Sepkoski’s compendium to support teaching exercises. The package provides access to:

  • sepkoski_raw Sepkoski’s raw fossil marine animal genera compendium (Sepkoski, 2002).
  • sepkoski Sepkoski’s compendium with first and last appearance intervals updated to be consistent with stages from the International Geological Time Scale 2022.
  • interval_table A table linking intervals in Sepkoski’s compendium with the International Geological Time Scale 2022.
  • A function for plotting Sepkoski’s evolutionary fauna for easy reproduction in presentations, articles, etc.

Note: In updating interval names, some interpretation was required. The interval_table dataset documents the linked interval names. If you notice any issue, or disagree with any of these assignments, please feel free to raise a GitHub issue, and I will do my best to address them as soon as possible.

Installation

The stable version of sepkoski can be installed via the CRAN using:

# Install stable version of the package
install.packages("sepkoski")

The development version of sepkoski can be installed via GitHub using:

# Install development version of the package
devtools::install_github("LewisAJones/sepkoski")

Usage 

# Load library
library(sepkoski)

The datasets in sepkoski can be easily accessed via:

# Raw dataset
data("sepkoski_raw")
# Updated interval dataset
data("sepkoski")
# Interval table
data("interval_table")

The only function in the sepkoski package at this time is sepkoski_curve(). This can be used to plot Sepkoski’s evolutionary fauna (Sepkoski, 1981) using the Sepkoski (2002) fossil marine animal genera compendium. Users may provide their own values to function arguments to customise the appearance, or simply use the default arguments:

Plot with default arguments Phanerozoic plot of Sepkoski’s three great evolutionary fauna. Number of genera are counted per international geological stage bin.

References

Sepkoski, J. J. (1981). A factor analytic description of the Phanerozoic marine fossil record. Paleobiology, 7(1), pp. 36-53.

Sepkoski, J. J. (2002). A compendium of fossil marine animal genera. Bulletins of American paleontology, 363, pp. 1-560.

Peters, S. (2022). Sepkoski’s Online Genus Database.