nussaibahrs/ooet2021

Archived code for Raja and Kiessling (2021) Out of the extratropics: Out of the extratropics: the evolution of the latitudinal diversity gradient of Cenozoic marine plankton

The evolution of the latitudinal diversity gradient of Cenozoic marine plankton

Nussaïbah B. Raja & Wolfgang Kiessling

• Description
• Requirements
• Setup
• Scripts
• Troubleshooting

Description

This repository contains all R scripts (in /scripts) necessary to evaluate the diversification dynamics and selectivity in, and the dispersal of marine plankton over the last 66 million years. The original data files can be downloaded at http://doi.org/10.17605/OSF.IO/NGK54. They were not included in the repository due to file size limits. Please download the data files and replace the contents of the data folder. The outputs of the scripts are provided in the /output and figures in the /figs folder. Please cite the study as:

Raja NB, Kiessling W. 2021 Out of the extratropics: the evolution of the latitudinal diversity gradient of Cenozoic marine plankton. Proc. R. Soc. B 20210545. https://doi.org/10.1098/rspb.2021.0545

Requirements

This code was developed in R 4.0.0. It is therefore recommended to use the same or any more up-to-date version of R for reproducing the analyses in this study.

Setup

You will need to either use the Rstudio project environment or set your working directory to the root of this folder.

To install all required depdendencies (packages), run:

source(file.path("inst","dependencies.R"))

Scripts

The scripts/ folder contains all the code generated for the above mentioned study. The folder contains 5 R scripts and two additional folders, namely, utils which contains scripts for custom functions and paramters used for plotting and supplementary that contains additional scripts for the results in the Supplementary Online Material in the study (Available here: https://royalsocietypublishing.org/doi/suppl/10.1098/rspb.2021.0545). The scripts are numbered in the order in which they should be run.

• 01-prepare_data.R: This script prepared the data files to be used in the analyses from the original download from the Nepture Database. It calculates the first appearance datum and last appearance datum of each species. It also categorises each occurrence into the tropics and extratropics, and calculate when dispersal from one zone to the other may have happened.

• 02-analysis_diversity_dynamics.R: This script calculates the diversity of marine plankton over the last 66 million years per climate zone and hemisphere.

• 03-analysis_LDG_div_overall.R: This script calculates the latitudinal diversity gradients for marine plankton over the last 66 million years, divided into climate phases.

• 04a-preferences_migration.R: This script calculates origination, extinction and diversitfication preferences, and dispersal proportions across climate zones over the last 66 million years, divided into climate phases.

• 04b-plot_prefs_and_migration.R: This script generates the plots of origination, extinction and diversitfication preferences, and dispersal proportions across climate zones over the last 66 million years, divided into climate phases, as per the analyses in 04a-preferences_migration.R.

Troubleshooting

The issue tracker is the preferred channel for bug reports. You may also contact me by email.