Appendix C - Presenting STOC case study with biomod2 v4.3-4

To illustrate the different features of biomod2, both existing and new, this tutorial presents a case study with count data. The example dataset comes from the French Breeding Bird Survey (STOC program) of Vigie-Nature (Fontaine et al. 2020). The original dataset contains 2,948 sites in which more than XX bird species have been observed from 2001 to 2024. Original raw data is not provided here, but might be made available on request by contacting Benoît Fontaine ([e-mail]). Specific sub-dataset has been built for this example, and the data has been integrated to the biomod2 package and can be access through data(DataSTOC) command. 20 bird species present in 1,003 sites have been kept, and their yearly average headcounts have been computed over 2 time periods: 2006-2011 and 2012-2017. These periods ensure both the match with environmental variables availability (especially CORINE habitats, see after) and sufficient records. 6 explanatory variables have been extracted for each site coordinates: annual mean temperature and precipitation (from CHELSA), percentage of agricultural, water and wetland habitat cover around each point (from European Union’s Copernicus Land Monitoring Service information) and Shannon habitat diversity (from CORINE). An example of Material and Methods paragraph, describing this present example, is available below. Italic sentences do not relate directly to this dataset, but have been included for the sake of completeness of the various steps of the modelling workflow. All data and code used for this example are presented here. Original data DATA_biomod2_STOC.csv Dataset used in the example and obtained from STOC.Dataset is also available directly within biomod2 package through data(DataSTOC) command. Columns: site period x_wgs84 y_wgs84 temp precip cover_agri cover_water cover_wet sdiv_hab Cuculus canorus Emberiza citrinella Erithacus rubecula Fulica atra Luscinia megarhynchos Passer domesticus Phylloscopus trochilus Serinus serinus Sitta europaea Streptopelia decaocto Turdus philomelos Alauda arvensis Periparus ater Coccothraustes coccothraustes Phylloscopus bonelli Regulus regulus Perdix perdix Sylvia melanocephala Cettia cetti Analysis of results AppendixC_biomod2_caseStudy_20251211.Rmd SCRIPT MARKDOWN used to produce the example.The script is provided for the purposes of transparency, sharing, and reproducibility of analyses. Results AppendixC_biomod2_caseStudy_20251211.html HTML OUTPUT file containing the example description, code and results. Abstract template for biomod2 study is also provided at the beginning of the file. Periparus.ater/ folder Simulation folder produced by biomod2, containing single and ensemble models, projections, and other simulation information. biomod2_report_Periparus.ater.html, biomod2_code_Periparus.ater.html, biomod2_ODMAP_Periparus.ater.html, biomod2_ODMAP_Periparus.ater_table.csv HTML / CSV OUTPUT files produced by BIOMOD_Report function.为展示biomod2包既有与新增的各项功能，本教程将采用计数数据开展一则案例研究。 本案例所用数据集源自Vigie-Nature发起的法国繁殖鸟类调查（French Breeding Bird Survey，STOC计划）（Fontaine等，2020）。原始数据集涵盖2948个调查样点，2001年至2024年间共记录到逾XX种鸟类。本次演示未提供原始数据，但若联系Benoît Fontaine（邮箱：[e-mail]）申请后可获取。 本案例已专门构建了子数据集，该数据已集成至biomod2包中，可通过`data(DataSTOC)`命令调取。本次筛选出1003个样点中的20种鸟类，并以2006-2011年、2012-2017年两个时间段为周期，计算了各鸟类的年均个体数。这两个时间段既适配环境变量的可获取性（尤其是CORINE生境数据，详见后文），同时也保证了观测记录的充足性。本研究为每个样点提取了6个解释变量：年平均气温与降水量（数据源自CHELSA）、样点周边农业、水域与湿地生境占比（数据源自欧盟哥白尼陆地监测服务（European Union’s Copernicus Land Monitoring Service）），以及香农生境多样性指数（数据源自CORINE）。 下文提供了一则描述本案例的“材料与方法”段落示例。其中斜体语句与本数据集无直接关联，但为完整呈现建模流程的各个步骤而一并纳入。 本案例所用的全部数据与代码均已在此展示。 原始数据 DATA_biomod2_STOC.csv 本案例所用数据集源自STOC，也可直接通过biomod2包中的`data(DataSTOC)`命令调取。 列名： site（样点）、period（时间段）、x_wgs84（WGS84坐标系X坐标）、y_wgs84（WGS84坐标系Y坐标）、temp（年平均气温）、precip（年降水量）、cover_agri（农业生境占比）、cover_water（水域生境占比）、cover_wet（湿地生境占比）、sdiv_hab（香农生境多样性指数） 鸟类物种学名： Cuculus canorus、Emberiza citrinella、Erithacus rubecula、Fulica atra、Luscinia megarhynchos、Passer domesticus、Phylloscopus trochilus、Serinus serinus、Sitta europaea Streptopelia decaocto、Turdus philomelos、Alauda arvensis、Periparus ater、Coccothraustes coccothraustes、Phylloscopus bonelli、Regulus regulus、Perdix perdix、Sylvia melanocephala、Cettia cetti 结果分析 附录C_biomod2_caseStudy_20251211.Rmd 本脚本为Markdown格式，用于生成本案例演示内容。提供该脚本旨在提升分析过程的透明度、便于共享与复现。 结果 附录C_biomod2_caseStudy_20251211.html 该HTML输出文件包含本案例的描述、代码与分析结果。文件开头还提供了biomod2研究的摘要模板。 `Periparus.ater/` 文件夹 该文件夹为biomod2生成的模拟结果文件夹，包含单模型与集成模型、投影结果及其他模拟相关信息。 `biomod2_report_Periparus.ater.html`、`biomod2_code_Periparus.ater.html`、`biomod2_ODMAP_Periparus.ater.html`、`biomod2_ODMAP_Periparus.ater_table.csv`：BIOMOD_Report函数生成的HTML与CSV格式输出文件。