Appendix A - Updating Hao et al. 2019 review with biomod2 papers from 2024

In 2019, Hao et al. published a review of 224 peer-reviewed journal articles using biomod2 package version 3.3-7. Even though it was difficult to draw strong conclusions, they highlighted that most papers : did not provide information about the package version used and the model settings used package’s default settings (for cross-validation and tuning) did not provide code or data to reproduce the modelling Since then, biomod2 package has evolved, improving not only the presented functions, but also all the documentation and help support associated with the package. For each function, the parameters are detailed, and examples and tutorials are presented onto the new documentation website. Issues and questions are frequently asked onto the github page. In order to check whether user practices have changed since Hao et al. 2019 review, we decided to redo the review work, searching for biomod2 word within papers published in 2024. All data and code used for this review are presented here. Original review data CITATIONS_GoogleScholar_20250924_SORT.csv GoogleScholar results extraction when searching for biomod2 word for 2024 year. Columns: Authors Title Title CORRECTED STATUS Publication Volume Number Pages Year Publisher Title CORRECTED: correction to match final paper title found when reading the publication STATUS: status of the paper in the review (match the OK column in REVIEW_biomod2_20251112.csv file) REVIEW_biomod2_fields.pdf Description of all the fields used for the review: their potential values ; when not evident, a small description ; and the rules followed.Match the column names in REVIEW_biomod2_20251112.csv file. REVIEW_biomod2_20251112.ods, REVIEW_biomod2_20251112.csv Review data table..ods file allows the user to explore the data more easily, while .csv file is used by the script.All fields are described in REVIEW_biomod2_fields.pdf file. Columns: OK PAPER title PAPER DOI YEAR JOURNAL AUTHOR name last AUTHOR name first AUTHOR country AUTHOR town SPECIES nb SPECIES group SPECIES status SPECIES names SPECIES records time SPECIES records nb pres raw SPECIES records nb abs raw SPECIES records nb pres clean SPECIES records nb abs clean STUDY scale STUDY country STUDY place STUDY coordinates STUDY resolution VARIABLES nb raw VARIABLES nb clean VARIABLES selection COR VARIABLES selection VIF VARIABLES selection other VARIABLES group PROJ past PROJ current PROJ future PROJ climate PROJ GCM PROJ emission scenarios PROJ times R version BIOMOD nb words BIOMOD version BIOMOD citation 2003 BIOMOD citation 2009 BIOMOD citation other BIOMOD use OTHER tool PA strategy PA nb PA run CV strategy CV split CV run EVAL metrics EVAL metrics table EVAL metrics graph MODELS nb 1 MODELS names 1 MODELS nb 2 MODELS names 2 OPTIONS VAR IMPORT VAR IMPORT table VAR IMPORT graph RESP CURVES RESP CURVES graph ENSEMBLE model ENSEMBLE metric ENSEMBLE metric threshold SRC SRC table SRC graph PROJ graph FUNCTIONS mentioned EXTERNAL validation data CLAMPING mask ODMAP, SuppMat Analysis of results PRISMA2020_review_biomod2_20251119.png Summary figure illustrating the number of articles removed at each step of the review process, and the number of articles finally reviewed.Following PRISMA 2020 statement (see Page et al. 2021). SHP_countries Shapefile containing world countries for representation. AppendixA_biomod2_review_20251210.Rmd SCRIPT MARKDOWN used to analyse the review data table.The script is provided for the purposes of transparency, sharing, and reproducibility of analyses. Results AppendixA_biomod2_review_20251210.html HTML OUTPUT file containing the analysis results. Main values or summary statistics are highlighted for each graphic.For some, parallel is made with results of previous review analysis from Passos et al. 2024.