This repository contains the required R code and data files to produce most of the analyses and plots in:
‘Anthropogenic disruptions to longstanding patterns of trophic-size structure in vertebrates’
Rob Cooke and William Gearty, Abbie S. A. Chapman, Jillian Dunic, Graham J. Edgar, Jonathan S. Lefcheck, Gil Rilov, Craig R. McClain, Rick D. Stuart-Smith, S. Kathleen Lyons, and Amanda E. Bates
Nature Ecology & Evolution (2022) https://www.nature.com/articles/s41559-022-01726-x
Before running these R scripts, we suggest that you download this folder and set the R folder as your R working directory. Required data files should then load when called in each script, and plot files will save within the figures folder.
Extant analyses (main text figures 2-3; supplementary figures 1-2 and 7):
Run v_plots_rob.R to produce all plots and analyses.
Fossil analyses (main text figures 1 and 4; supplementary figures 3-6):
Run mammal_diet.R to produce all plots and analyses.
Future analyses (main text figure 5):
Run future_v_short.R to produce all plots and analyses.
To replicate the analyses and plots presented here, the following R packages are required:
cowplot
deeptime
dplyr
ggplot2
grImport
gtable
gtools
Hmisc
lemon
nlme
pacman
plyr
rcompanion
stringr
tidyr
tidyverse
vectoR
viridis
The vectoR package is currently only available on GitHub and will need to be installed from there to reproduce these analyses and plots. This can be achieved by running the following commands in your R console (ignore the first line if you already have devtools installed).
install.packages("devtools")
devtools::install_github("richfitz/vectoR")All other packages can be installed from CRAN. These scripts have been tested using R version 4.1.0 - Copyright (C) 2021 The R Foundation for Statistical Computing.