DOI: 10.5281/zenodo.14946419
title: The structure of the end-Cretaceous dinosaur fossil record

description: This dataset contains underlying data, R scripts, and results for the manuscript titled 'The structure of the end-Cretaceous dinosaur fossil record'.

Data S1: Contains data for running analyses, as well as results from analyses to be read into R (.rds format), and R scripts for running analyses.

Data were derived from the following sources. Note that not all of these data are included within the datasets stored here.



Occurrence dataframes were downloaded from The Paleobiology Database (http://paleobiodb.org(opens in new window)).

North American roads compiled by the U.S. Department of Transportation (https://data-usdot.opendata.arcgis.com/datasets/usdot::north-american-roads/about(opens in new window)).

MGVF obtained from Broxton, P. D., Zeng, X., Scheftic, W. & Troch, P. A. A MODIS-based global 1-km maximum green vegetation fraction dataset. Journal of applied Meteorology and Climatology 53, 1996–2004 (2014).

Rainfall obtained from WorldClim (www.worldclim.org(opens in new window)).

Outcrop area obtained from https://macrostrat.org(opens in new window) API.

Land cover obtained from U.S. Geological Survey. 1-Kilometer Resolution, North American Land Cover Characteristics, 1992-1993. USGS (2002).

All paleoclimate model simulations were carried out using a recent version of the UK MetOffice coupled Atmosphere-Ocean General Circulation Model (AOGCM), HadCM3 (specifically HadCM3L-M2.1D), based on palaeogeographies from Scotese, C. R. & Wright, N. PALEOMAP paleodigital elevation models (PaleoDEMS) for the Phanerozoic. URL: https://www(opens in new window). earthbyte. org/paleodem-resource-scotese-and-wright-2018 (2018). These were also used to construct estimates for Sediment Flux.


Occurrences

Contains the following four files:



Distance_roads.csv: A .csv file containing information about the distance from each collection in the dataset from a dataset of North American roads compiled by the U.S. Department of Transportation.

Formations.csv: A .csv file containing information about the geologic formations included within the manuscript, most notably their chronostratigraphic information.

occs_tetrapoda_12_06_2024.csv: A .csv file of occurrences downloaded from the PBDB on 12/06/2024, used in analyses.

scotesebins.csv: A .csv file of the temporal bins used in this study.


R_Scripts

Contains nine scripts in R for formatting data, running analyses, and visualising results.



0.Format_covariate_data: R script for formatting covariate data for the project.

0.Functions: R script containing custom functions necessary to run other files. Called directly from other files.

0.Macrostrat_outcrop: R script for obtaining and formatting relevant outcrop data from the Macrostrat API.

1.Setup_occupancy: R script for setting up data for analyses.

2.Running_Multispecies_Sparta: R script to format and run occupancy models with 'Sparta'.

3.Multispecies_Sparta_posterior_checks: R script to perform posterior checks on models run using 'Sparta'.

4.Setup_spOccupancy: R script for setting up data into required format for 'spOccupancy'. Handles both single and multi-season formats.

5.Run_ms_spOccupancy: R script for automatically running multi-season occupancy models using 'spOccupancy'.

6.Generating_figures: R script for generating figures for manuscript.


Results

Contains the results generated for the manuscript for both Sparta and spOccupancy run occupancy models. Sparta results are saved in either .csv or .rds format. spOccupancy results are saved in .rds format.