Divergent effects of native deer and alien wild pigs on forest understories

This repository contains the primary data and code used in the analyses for the paper “Divergent effects of native deer and alien wild pigs on forest understories”, in Proceedings of the Royal Society B. All analyses were conducted in R. The main script, Deer&PigEffects.R, includes the workflow for the study, including package loading, data preparation, statistical analyses, model fitting, and figure generation used in the manuscript. Three compiled datasets are provided: plot_alldata_seedling.rds – Seedling survey data from forest plots across the eastern United States. This dataset was used to analyse the effects of deer on forest regeneration and seedling recruitment. plot_alldata_invafinal.rds – Invasive understory plant data from forest plots across the eastern United States. This dataset was used to analyse the influence of deer on understory plant invasions. plot_boardata_final.rds – Seedling and invasive plant data from forest plots in the southeastern United States. This dataset was used to analyse the effects of wild pigs on forest regeneration and understory plant invasions. Detailed descriptions of each dataset, including variable definitions and units, are provided in the README file. R package informaiton: mapview_2.11.2 viridis_0.6.5 viridisLite_0.4.2 glmmTMB_1.1.9 sf_1.0-16 raster_3.6-20 sp_2.1-3 stringr_1.5.2 dplyr_1.1.4 purrr_1.1.0 readr_2.1.4 tidyr_1.3.1 tibble_3.3.0 ggplot2_4.0.0 tidyverse_2.0.0 data.table_1.17.8