Appendix A - Updating Hao et al. 2019 review with biomod2 papers from 2024
Description
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.
Files
AppendixA_biomod2_review_20251211.zip
Files
(20.5 MB)
| Name | Size | Download all |
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md5:fbf95b5880cfb90ee6d3cd3a962257bc
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10.0 MB | Download |
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md5:bfa015fb96d4fd0022a83052f8a78150
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10.5 MB | Preview Download |
Additional details
Software
- Repository URL
- https://biomodhub.github.io/biomod2/
- Programming language
- R
- Development Status
- Active
References
- Hao T, Elith J, Guillera-Arroita G, Lahoz-Monfort JJ. (2019) A review of evidence about use and performance of species distribution modelling ensembles like BIOMOD. Divers Distrib. 25: 839–852. 10.1111/ddi.12892
- Page MJ, McKenzie JE, Bossuyt PM, Boutron I, Hoffmann TC, Mulrow CD, et al. (2021) The PRISMA 2020 statement: An updated guideline for reporting systematic reviews. PLoS Med 18(3): e1003583. 10.1371/journal.pmed.1003583
- Passos I, Figueiredo A, Almeida AM, Ribeiro MM. (2024) Uncertainties in Plant Species Niche Modeling under Climate Change Scenarios. Ecologies, 5, 402-419. 10.3390/ecologies5030025
- Sillero N, Barbosa AM. (2020) Common mistakes in ecological niche models. International Journal of Geographical Information Science, 35(2), 213–226. 10.1080/13658816.2020.1798968
- Kellner KF, Jeffrey WD, Jerrold LB. (2025) Functional R Code is Rare in Species Distribution and Abundance Papers. Ecology 106(1): e4475. 10.1002/ecy.4475