Dataset for "Ecological and phylogenetic structuring of wild edible plant species across European vegetation"

Ecological and phylogenetic structuring of wild edible plant species across European vegetation This folder contains the input data and R scripts needed to reproduce the analyses and figures associated with the manuscript. The folder is organised into two main subfolders: 1. data/ The data/ folder contains the basic input data needed to run the analyses. These files include the plot-level metadata, the plot-by-species table, the list of wild edible plant species, plant-part information, and phylogenetic input files. The main input files are: wepe_EVA_header.csv contains plot-level metadata. The table includes the grid-cell identifier, the longitude and latitude of the grid-cell centroid, the biogeographical region, habitat type, and climate variables associated with each plot. wepe_EVA_spp.csv contains the plot-by-species data, linking each PlotObservationID to the vascular plant species recorded in that plot. wepes_filtered_260213.csv contains the filtered list of wild edible plant species used in the analyses, including the corresponding edibility/popularity classification. table_weps_parts_forms.xlsx contains the original wild edible plant species information used to classify species according to the plant parts used. wepe_tpl.csv contains the taxonomic matching information used to link species names to accepted names, genera, and families for the phylogenetic analyses. wepe.phylo.tree.tre contains the phylogenetic tree used in the phylogenetic analyses. 2. code/ The code/ folder contains the R scripts needed to reproduce the figures in the manuscript. The scripts have been cleaned and organised so that they only retain the code required to generate the final figures. The main script is: 00_run_all_figures.R This script runs the full figure-generation workflow. The remaining scripts generate each figure separately: 01_Figure1_spatial_patterns.R 02_Figure2_climate_gams.R 03_Figure3_habitat_bioregion_summary.R 04_Figure4_used_parts_by_habitat.R 05_Figure5_phylogenetic_tree.R The file _helpers.R contains shared helper functions used by several scripts. Output Running the scripts will generate the final figures used in the manuscript: Figure1.png Figure2.png Figure3.png Figure4.png Figure5.png By default, figures are saved in the output folder defined in the scripts. Notes on spatial information The exact coordinates of individual vegetation plots are not included in this dataset. Spatial analyses are instead based on 100 × 100 km grid-cell assignments. Each plot is associated with a grid-cell identifier and with the centroid coordinates of that grid cell. These centroid coordinates are used only to represent broad spatial patterns and to support analyses that require approximate spatial location. For any questions regarding the data or code, please contact the corresponding author at: [e-mail]