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

## R Script to calculate plant spectral diversity and partitioning it into alpha and beta componentsManuscript "Spectral characterisation of plant diversity in a biodiversity-enriched oil palm plantation", Remote Sens Ecol Conserv. (2025).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.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.The folders are:1. Codes: - 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 - specdiv_functions.R -> For the specdiv functions, please refer to the original R script available online at: https://github.com/elaliberte/specdiv - Community_Matrix.R -> The R script to calculate different plant diversity metrics, including rarefied species richness, Shannon and Simpson diversity. - OtherAnalysis.R -> Models to calculate the relationship between the plot characteristics and the different diversity metrics. 2. Data:Contains the initial data required to run the different R scripts. The three most important input data are: - 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). - wvl.txt -> Corresponds to the wavelength from the images, from smaller to larger.- Tree_Inventory_2020.csv -> Contains the richness and abundance of all species inventoried in the BEE plots from the 2020 period.The other files from the Data folder are calculated along the R code.3. R_input:Contains .csv; .gri; .rds files that are calculated along the R script and that are input for other calculations. contact Vannesa Montoya-Sánchez in case of requiring extra information: [e-mail]

用于计算植物光谱多样性并将其拆分为α和β多样性组分的R脚本
对应发表于《Remote Sens Ecol Conserv. (2025)》的论文《生物多样性富集油棕种植园植物多样性的光谱表征》。
名为Data_Scripts_Montoya-Sanchez et al.的文件夹包含了该论文中用于计算植物光谱多样性与植物多样性的全部数据和R脚本，同时涵盖论文中呈现的所有图表。
本R脚本参考了Laliberté等人(2020)提出的研究概念与R函数（https://doi.org/10.1111/ele.13429），并采用了其中的bright_norm()、pca()和specdiv()自定义R函数；该函数由Anna K. Schweiger教授为本研究改编，原始代码可在线获取（https://github.com/elaliberte/specdiv）。

文件夹分为以下三类：
1. Codes（代码文件夹）
- 02_SDiv_landscapes_all.R：基于Etienne Laliberté的R脚本与函数完成植物光谱多样性计算及其α、β多样性组分拆分，原始版本可参考https://github.com/elaliberte/specdiv
- specdiv_functions.R：针对specdiv函数的脚本，原始R代码可在线获取：https://github.com/elaliberte/specdiv
- Community_Matrix.R：用于计算多种植物多样性指标的脚本，包括稀疏化物种丰富度、香农（Shannon）多样性与辛普森（Simpson）多样性
- OtherAnalysis.R：用于探究样地特征与不同多样性指标间关联关系的模型脚本
2. Data（数据文件夹）
包含运行各R脚本所需的原始数据，其中三类核心输入数据为：
- val_all.csv：对应各高光谱图像（hyperspectral images）的原始数据，字段包含样地ID（PlotID）、样地面积（Plot_size）、多样性水平（Div_level）等，列则为不同波段的观测值
- wvl.txt：对应图像的波长数据，按波长从小到大排序
- Tree_Inventory_2020.csv：包含2020年BEE样地中所有调查物种的丰富度与多度信息
数据文件夹内其余文件均通过R代码计算生成。
3. R_input文件夹
包含通过R脚本计算得到的.csv、.gri、.rds文件，可作为其他计算的输入文件。
如需获取额外信息，请联系Vannesa Montoya-Sánchez，电子邮箱：[e-mail]