Supplement to Estimating spatial variation in origination and extinction in deep time: a case study using the Permian–Triassic marine invertebrate fossil record

This repository contains the supplementary information for:

Allen BJ, Clapham ME, Saupe EE, Wignall PB, Hill DJ, Dunhill AM. 2023. Estimating spatial variation in origination and extinction in deep time: a case study using the Permian–Triassic marine invertebrate fossil record. Paleobiology.

Description of files

This repository contains the supplementary figures and tables associated with the paper, in pdf format.

This repository also contains all of the R code and files used in the paper:
Evol rate simulation.R - the code that runs the first simulation (without extinction selectivity, with spatial bins)
Plot simulation results.R - code for evaluating and plotting the outputs of the first simulation
Statistical tests.R - the statistical tests used to evaluate simulation performance
Selectivity simulation.R - the code that runs the second simulation (with extinction selectivity)
Wrangle occurrences.R - code for cleaning the PBDB occurrence dataset
Rotating palaeo-occurrences.R - code for pre- and post-processing the occurrences for spatial rotation with GPlates
Sampling through space-time.R - code for generating summary statistics from the occurrence data
Latitudinal rates from fossils.R - applying the metrics to the occurrence data
PT_marine_inverts.csv - uncleaned PBDB occurrence dataset

Permian-Triassic marine invertebrate dataset

Occurrences of marine invertebrates from the Permian and Triassic downloaded from the Paleobiology Database on 10.03.21 using the following URL:
http://paleobiodb.org/data1.2/occs/list.csv?datainfo&rowcount&base_name=Brachiopoda,%20Bivalvia,%20Ammonoidea,%20Gastropoda&taxon_reso=genus&idqual=genus_certain&interval=Artinskian,Norian&private&show=full,entname

The data follows the standard format of Paleobiology Database downloads, described at https://paleobiodb.org/data1.2/. This data is available under a CC-0 International Licence.
An up-to-date version of the dataset can be downloaded using the above URL, or accessed through https://paleobiodb.org/.