DOI: 10.5061/dryad.wpzgmsbxt
title: Data from: Standardising fossil disparity metrics using sample coverage

description: Estimating past biodiversity using the fossil record is a central goal of
 palaeobiology. Because raw estimates of biodiversity are biased by
 variation in sampling intensity across time, space, environments, and
 taxonomic groups, sampling standardisation is routinely applied when
 estimating taxonomic diversity (e.g., species richness). However, sampling
 standardisation is less commonly used when estimating alternative
 currencies of biological diversity, such as morphological disparity. Here,
 we show the effects of standardising fossil time series of morphological
 disparity to equal sample completeness, or “coverage” of the underlying
 taxon-frequency distribution. We apply coverage-based standardisation to
 three published datasets of discrete morphological characters
 (echinoderms, ichthyosaurs, and ornithischian dinosaurs), and quantify
 disparity using two metrics: weighted mean pairwise dissimilarity (WMPD)
 and the sum of variance (SOV). We also compare the effects of
 coverage-based and sample-size-based standardisation. Our results show
 that coverage standardisation can yield estimates of disparity through
 time that dramatically deviate from raw estimates, both in magnitude and
 direction of changes. These findings demonstrate that future studies of
 morphological disparity should control for variation in sampling intensity
 to make more reliable inferences.
description: # Data from: Standardising fossil disparity metrics using sample coverage
 [https://doi.org/10.5061/dryad.wpzgmsbxt](https://doi.org/10.5061/dryad.wpzgmsbxt) ## Description of the data and file structure ### Files and variables #### File: Nordenetal2018.xlsx **Description:**  This file contains one dataset used in our study: discrete morphological character data for 194 ornithischian species. #### File: SupportingInformation **Description:**  This file contains Figs. S1-S7 that are not contained in the main manuscript. #### File: Jones\_Close\_Data.zip **Description:**  We have deposited the input data files and scripts for the analyses described in our article, 'Standardising fossil disparity metrics using sample coverage'. This article outlines a novel coverage-based rarefaction approach for standardising discrete morphological character data, as opposed to traditional size-based rarefaction. Our approach is trialled on three published datasets for ichthyosaurs, echinoderms, and ornithischian dinosaurs. **Folder: inputs** This folder contains one of the three published datasets used in our study. * novackgottshall2022/EchinoTree_Morph.nex -  Discrete morphological character data for 366 echinoderm species. **Folder: scripts** This folder contains the R scripts to perform the analyses in our study. * 00-format-tibble.R * 01-disparity-timeseries.R * 02-multi-quorum.R * 03-coverage-analysis.R * 04-rarefaction-analysis.R * master-script.R * packages-functions.R * run-coverage-based-rarefaction-analysis-in-rscript.R * run-master-script.R * run-rarefaction-script.R * run-size-based-rarefaction-analysis-in-rscript.R **Subfolder: scripts/plotting:** * generate-coverage-plots.R * generate-disparity-plots.R * generate-multiQ-plots.R * generate-rarefaction-plots.R  **Folder: plots** This is an empty folder where plots saved throughout the analysis will automatically be saved. **Folder: saved-workspaces** This is an empty folder where workspace images saved throughout the analysis will automatically be saved. ## Code/software All computational work was conducted in R v4.3.1 (R Core Team 2023) via RStudio (RStudio Team 2023). The R scripts used to perform the analyses are contained within the 'scripts' folder and are outlined below. **Folder: scripts** * 00-format-tibble.R - Script to load the datasets and create the basic data structure for later analyses. * 01-disparity-timeseries.R - Calculates raw, size-standardised, and coverage-standardised ('SQS") disparity estimates through time for the three datasets. * 02-multi-quorum.R - Generates SQS disparity time series for a range of specified quorum values. * 03-coverage-analysis.R - Calculates sampling and spatial coverage through time. * 04-rarefaction-analysis.R - Sources the scripts for performing size-based and SQS rarefaction analyses. * master-script.R - This 'master' script contains the individual components of the analysis which are run without the script. It generates the necessary workspace images that can be later loaded and used to generate plots. * packages-functions.R - Loads the necessary packages and defines the custom functions used to perform our analyses. * run-coverage-based-rarefaction-analysis-in-rscript.R - Called from within 04-rarefaction-analysis.R to run the SQS rarefaction analysis * run-master-script.R - Run this script to source and work through the master-script.R * run-rarefaction-script.R - Calls the 04-rarefaction-analysis.R script for performing the size-based and SQS disparity analysis. * run-size-based-rarefaction-analysis-in-rscript.R - Called from within 04-rarefaction-analysis.R to run the size-basd rarefaction analysis **Subfolder: scripts/plotting:** * generate-coverage-plots.R - produces plots of sampling and spatial coverage through time (Fig. 5) * generate-disparity-plots.R - produces disparity time series (Figs. 2, S1) * generate-multiQ-plots.R - produces SQS disparity time series for a range of quorum values (Fig. 6) * generate-rarefaction-plots.R - produces size- and coverage-based rarefaction plots for the WMPD and SOV disparity metrics. Bins are plotted together (Figs. 3, 4) and individually (Figs. S2-S7) ## Access information Data was derived from the following sources: Paleobiology Database (CC0 1.0 license) * URL: [https://paleobiodb.org/#/](https://paleobiodb.org/#/) Harvard Dataverse (CC0 1.0 license) * URL: [https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/20BEYV&version=2.1&selectTab=termsTab](https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/20BEYV&version=2.1&selectTab=termsTab) FigShare (CC by 4.0 license). **Note that this data is not included in this Dryad dataset due to conflicting non-CC0 licensing. The link is provided for access to the dataset.** * URL: [https://figshare.com/articles/dataset/A_new_cymbospondylid_ichthyosaur_Ichthyosauria_from_the_Middle_Triassic_Anisian_of_the_Augusta_Mountains_Nevada_USA/12159657](https://figshare.com/articles/dataset/A_new_cymbospondylid_ichthyosaur_Ichthyosauria_from_the_Middle_Triassic_Anisian_of_the_Augusta_Mountains_Nevada_USA/12159657) Dryad (CC0 1.0 license) * URL: [https://doi.org/10.5061/dryad.pp07dm0](https://doi.org/10.5061/dryad.pp07dm0)