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.