EthnoBotaPhyWR stands for ethnobotany, phytochemistry, Wikidata and R (maybe you can also find the bot of robot) It should be pronounced "Ethnobota Fever".
Here is what you minimally need:
Additionally, you can provide:
Or simply use the included orchids datasets for analysis.
EthnoBotaPhyWR provides:
As the package is not (yet) available on CRAN, you will need to install with:
install.packages(
"EthnoBotaPhyWR",
repos = c(
"https://adafede.r-universe.dev",
"https://davidgohel.r-universe.dev", # required for ggiraph, required for ggtree
"https://cran.r-universe.dev",
"https://bioc.r-universe.dev"
)
)
Once installed, you are ready to go through our documentation, with the major steps detailed.
library(EthnoBotaPhyWR)
# Phytochemical data with SMILES and classification
data(orchids_compounds)
head(orchids_compounds)
# NPClassifier taxonomy lookup
data(orchids_compound_classes)
head(orchids_compound_classes)
# Ethnobotanical uses linked to phylogenetics
data(orchids_ethnobotanical)
head(orchids_ethnobotanical)
# Get data for any plant family (requires Wikidata)
result <- ethnobotafever_tree(
taxon_name = "Orchidaceae",
n_multiple_genera = 1,
n_ethnobotanical_count_min = 0,
n_compounds_count_min = 0,
example_family_names = c("Solanaceae", "Fabaceae"),
path_molecules = NULL, # or path to your own
path_classes = NULL,
path_ethnobotanical = NULL,
export_tree_full = "~/orchids_tree_full.pdf",
export_tree_phyto = "~/orchids_tree_phyto.pdf",
export_tree_phyto_sub = "~/orchids_tree_phyto_sub.pdf",
export_table_classified = "~/orchids_classified.tsv",
export_table_counts = "~/orchids_counts.tsv",
export_table_counts_sub = "~/orchids_counts_sub.tsv",
local_cache = "~/.ethnobotaphy_cache",
log_dir = "~/"
)
https://doi.org/10.7554/eLife.70780
https://doi.org/10.3897/BDJ.5.e12581
https://doi.org/10.1021/acs.jnatprod.1c00399
| Package | Version | Citation |
|---|---|---|
| ape | 5.8.1 | Paradis and Schliep (2019) |
| base | 4.6.1 | R Core Team (2026a) |
| BiocManager | 1.30.27 | Morgan and Ramos (2025) |
| BiocVersion | 3.23.1 | Morgan (2025) |
| curl | 8.1.0 | Ooms (2026a) |
| data.table | 1.18.6.1 | Barrett et al. (2026) |
| EthnoBotaPhyWR | 0.0.0.9001 | Rutz (2026) |
| ggtext | 0.2.0 | Wilke and Wiernik (2026) |
| ggtree | 4.2.0 | Yu et al. (2017); Yu et al. (2018); Yu (2020); Yu (2022a); Xu et al. (2022) |
| ggtreeExtra | 1.22.1 | Xu et al. (2021); Yu (2022b) |
| grid | 4.6.1 | R Core Team (2026b) |
| gt | 1.4.0 | Iannone et al. (2026) |
| httr2 | 1.3.0 | Wickham (2026) |
| khroma | 1.17.0 | Frerebeau (2025) |
| knitr | 1.52 | Xie (2014); Xie (2015); Xie (2026) |
| logger | 0.4.3 | Daróczi and Wickham (2026) |
| openssl | 2.4.2 | Ooms (2026b) |
| phangorn | 2.12.1 | Schliep (2011); Schliep et al. (2017) |
| rmarkdown | 2.32 | Xie et al. (2018); Xie et al. (2020); Allaire et al. (2026) |
| rotl | 3.1.1 | Michonneau et al. (2016); OpenTreeOfLife et al. (2019) |
| scales | 1.4.0 | Wickham et al. (2025) |
| spelling | 2.3.2 | Ooms and Hester (2025) |
| testthat | 3.3.2 | Wickham (2011) |
| tidytable | 0.11.2 | Fairbanks (2024) |
| tidytree | 0.4.8 | Yu (2022c) |
| tidyverse | 2.0.0 | Wickham et al. (2019) |
Allaire, JJ, Yihui Xie, Christophe Dervieux, et al. 2026. rmarkdown: Dynamic Documents for r. https://github.com/rstudio/rmarkdown.
Barrett, Tyson, Matt Dowle, Arun Srinivasan, et al. 2026. data.table: Extension of “data.frame”. https://doi.org/10.32614/CRAN.package.data.table.
Daróczi, Gergely, and Hadley Wickham. 2026. logger: A Lightweight, Modern and Flexible Logging Utility. https://doi.org/10.32614/CRAN.package.logger.
Fairbanks, Mark. 2024. tidytable: Tidy Interface to “data.table”. https://doi.org/10.32614/CRAN.package.tidytable.
Frerebeau, Nicolas. 2025. khroma: Colour Schemes for Scientific Data Visualization. Université Bordeaux Montaigne. https://doi.org/10.5281/zenodo.1472077.
Iannone, Richard, Joe Cheng, Barret Schloerke, et al. 2026. gt: Easily Create Presentation-Ready Display Tables. https://doi.org/10.32614/CRAN.package.gt.
Michonneau, Francois, Joseph W. Brown, and David J. Winter. 2016. “rotl: An r Package to Interact with the Open Tree of Life Data.” Methods in Ecology and Evolution 7 (12): 1476–81. https://doi.org/10.1111/2041-210X.12593.
Morgan, Martin. 2025. BiocVersion: Set the Appropriate Version of Bioconductor Packages.
Morgan, Martin, and Marcel Ramos. 2025. BiocManager: Access the Bioconductor Project Package Repository. https://doi.org/10.32614/CRAN.package.BiocManager.
Ooms, Jeroen. 2026a. curl: A Modern and Flexible Web Client for r. https://doi.org/10.32614/CRAN.package.curl.
Ooms, Jeroen. 2026b. openssl: Toolkit for Encryption, Signatures and Certificates Based on OpenSSL. https://doi.org/10.32614/CRAN.package.openssl.
Ooms, Jeroen, and Jim Hester. 2025. spelling: Tools for Spell Checking in r. https://doi.org/10.32614/CRAN.package.spelling.
OpenTreeOfLife, Benjamin Redelings, Luna Luisa Sanchez Reyes, et al. 2019. Open Tree of Life Synthetic Tree. Version 12.3. Zenodo. https://doi.org/10.5281/zenodo.3937741.
Paradis, Emmanuel, and Klaus Schliep. 2019. “Ape 5.0: An Environment for Modern Phylogenetics and Evolutionary Analyses in R.” Bioinformatics 35: 526–28. https://doi.org/10.1093/bioinformatics/bty633.
R Core Team. 2026a. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. https://doi.org/10.32614/R.manuals.
R Core Team. 2026b. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. https://doi.org/10.32614/R.manuals.
Rutz, Adriano. 2026. EthnoBotaPhyWR: Infrastructure for Ethnobotanical and Phytochemical Data Integration with Wikidata. https://doi.org/10.5281/zenodo.TODO.
Schliep, Klaus. 2011. “phangorn: Phylogenetic Analysis in r.” Bioinformatics 27 (4): 592–93. https://doi.org/10.1093/bioinformatics/btq706.
Schliep, Klaus, Alastair J. Potts, David A. Morrison, and Guido W. Grimm. 2017. “Intertwining Phylogenetic Trees and Networks.” Methods in Ecology and Evolution 8 (10): 1212–20.
Wickham, Hadley. 2011. “testthat: Get Started with Testing.” The R Journal 3: 5–10. https://journal.r-project.org/articles/RJ-2011-002/.
Wickham, Hadley. 2026. Httr2: Perform HTTP Requests and Process the Responses. https://doi.org/10.32614/CRAN.package.httr2.
Wickham, Hadley, Mara Averick, Jennifer Bryan, et al. 2019. “Welcome to the tidyverse.” Journal of Open Source Software 4 (43): 1686. https://doi.org/10.21105/joss.01686.
Wickham, Hadley, Thomas Lin Pedersen, and Dana Seidel. 2025. scales: Scale Functions for Visualization. https://doi.org/10.32614/CRAN.package.scales.
Wilke, Claus O., and Brenton M. Wiernik. 2026. ggtext: Improved Text Rendering Support for “ggplot2”. https://doi.org/10.32614/CRAN.package.ggtext.
Xie, Yihui. 2014. “knitr: A Comprehensive Tool for Reproducible Research in R.” In Implementing Reproducible Computational Research, edited by Victoria Stodden, Friedrich Leisch, and Roger D. Peng. Chapman; Hall/CRC.
Xie, Yihui. 2015. Dynamic Documents with R and Knitr. 2nd ed. Chapman; Hall/CRC. https://yihui.org/knitr/.
Xie, Yihui. 2026. knitr: A General-Purpose Package for Dynamic Report Generation in R. https://yihui.org/knitr/.
Xie, Yihui, J. J. Allaire, and Garrett Grolemund. 2018. R Markdown: The Definitive Guide. Chapman; Hall/CRC. https://pkg.yihui.org/rmarkdown-book/.
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Xu, Shuangbin, Lin Li, Xiao Luo, et al. 2022. “Ggtree: A Serialized Data Object for Visualization of a Phylogenetic Tree and Annotation Data.” iMeta 1 (4): e56. https://doi.org/10.1002/imt2.56.
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Yu, Guangchuang. 2022c. Data Integration, Manipulation and Visualization of Phylogenetic Treess. 1st edition. Chapman; Hall/CRC. https://doi.org/10.1201/9781003279242.
Yu, Guangchuang, Tommy Tsan-Yuk Lam, Huachen Zhu, and Yi Guan. 2018. “Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree.” Molecular Biology and Evolution 35: 3041–43. https://doi.org/10.1093/molbev/msy194.
Yu, Guangchuang, David Smith, Huachen Zhu, Yi Guan, and Tommy Tsan-Yuk Lam. 2017. “ggtree: An r Package for Visualization and Annotation of Phylogenetic Trees with Their Covariates and Other Associated Data.” Methods in Ecology and Evolution 8: 28–36. https://doi.org/10.1111/2041-210X.12628.