What have we learned from empirical applications of modern coexistence theory?
Data files
May 06, 2026 version files 50.59 MB
-
data_and_code.zip
50.59 MB
-
README.md
2.08 KB
Abstract
We reviewed empirical applications of modern coexistence theory in ecology. The files and code in this repository show the 84 studies that met our criteria for inclusion along with the data we collected about each study, such as study setting, methodology, and the coexistence metrics quantified. The R code allows users to reproduce the simple analyses we conducted using these data.
Dataset DOI: 10.5061/dryad.ngf1vhj7c
Description of the data and file structure
This repository contains the R script and data files necessary to reproduce the analyses reported in our publication.
Files and variables
File: data_and_code.zip
Description: This zip archive contains the following files and directories:
readme.txt duplicates the text included here.
analysis.R contains all the code to repeat our analysis. Users will need to update the path on line 6.
studydata_Dec_2025.csv describes the 84 studies included in our literature review.
study_locations_Feb2026.csv contains information about latitude and longitude for each field study location as well as a column indicating whether an analysis re-analyzed data previously used for MCT.
mechanisms_Dec_2025.csv contains information we recorded about the purpose and methods for each of the 84 studies.
mechanism_direction_Dec_2025.csv contains information we recorded about the sign and relative magnitude of effect of coexistence mechanisms on invasion growth rates.
metadata.txt describes the fields in the previous four files, as well as the meaning of "NA" values.
The figures directory contains figures (and one table) produced by analysis.R.
The worldclim directory contains climate data used in Fig 3 (map of study locations).
Code/software
Any text editor can be used to view our data.
R is the only software application needed to execute our code. We used R version 4.3.1. Most of the code uses only base R. We used package mgcv for statistical analyses. The following packages are needed only to generate figure 3, the map of study locations:
sf, dplyr, ggplot2, terra, geodata, rnaturalearth, plotbiomes
Access information
Data was derived from the following sources:
- We extracted data from the publications listed in Table S1 of the publication.
- We also extracted data from https://www.worldclim.org/