Data and R script from the paper "Spectral characterisation of plant diversity in a biodiversity-enriched oil palm plantation"

<p dir="ltr">## R Script to calculate plant spectral diversity and partitioning it into alpha and beta components</p><p dir="ltr">Manuscript "Spectral characterisation of plant diversity in a biodiversity-enriched oil palm plantation", Remote Sens Ecol Conserv. (2025).</p><p dir="ltr">The folder Data_Scripts_Montoya-Sanchez et al, contains all the data and R scripts needed to calculate plant spectral diversity and plant diversity as calculated in the manuscript "Spectral characterisation of plant diversity in a biodiversity-enriched oil palm plantation", including the graphs presented in the manuscript.</p><p dir="ltr">This R scripts follows the concept and R functions outlined in Laliberté et al., (2020), https://doi.org/10.1111/ele.13429, including the functions bright_norm(), pca(), and specdiv(), from the custom R code, available online (https://github.com/elaliberte/specdiv), adapted for this study by Prof. Dr. Anna K. Schweiger.</p><p dir="ltr">The folders are:</p><p dir="ltr">1. Codes:</p><p dir="ltr"> - 02_SDiv_landscapes_all.R -> Calculations of plant spectral diversity and the partitioning into alpha and beta components were performed using the R scripts and functions from Etienne Laliberté. Refer to the original version available online: https://github.com/elaliberte/specdiv</p><p dir="ltr"> - specdiv_functions.R -> For the specdiv functions, please refer to the original R script available online at: https://github.com/elaliberte/specdiv</p><p dir="ltr"> - Community_Matrix.R -> The R script to calculate different plant diversity metrics, including rarefied species richness, Shannon and Simpson diversity.</p><p dir="ltr"> - OtherAnalysis.R -> Models to calculate the relationship between the plot characteristics and the different diversity metrics. </p><p dir="ltr">2. Data:</p><p dir="ltr">Contains the initial data required to run the different R scripts. The three most important input data are:</p><p dir="ltr"> - val_all.csv -> Corresponds to the original data from each of the hyperspectral images (rows), including the PlotID; Plot_size; Div_level… and the different bands with the different values (columns).</p><p dir="ltr"> - wvl.txt -> Corresponds to the wavelength from the images, from smaller to larger.</p><p dir="ltr">- Tree_Inventory_2020.csv -> Contains the richness and abundance of all species inventoried in the BEE plots from the 2020 period.</p><p dir="ltr">The other files from the Data folder are calculated along the R code.</p><p dir="ltr">3. R_input:</p><p dir="ltr">Contains .csv; .gri; .rds files that are calculated along the R script and that are input for other calculations. </p><p dir="ltr">contact Vannesa Montoya-Sánchez in case of requiring extra information: vamontoyas@gmail.com</p>