VegSci.jl is a package containing tools for vegetation science using
Julia (Bezanson et al. 2017), a growing scientific programming language
which solves the ‘two language problem’ (Roesch et al. 2023), offering C
and FORTRAN-like performance alongside the readability and
user-friendliness of higher level languages such as Python. VegSci.jl
aims to collate selected functionality found in popular vegetation
science software programs/packages such as JUICE (Tichý 2002), vegan
(Oksanen et al. 2022), ade4 (Dray and Dufour 2007), vegclust (De
Cáceres, Font, and Oliva 2010; De Cáceres, Legendre, and He 2013), and
vegsoup (Kaiser 2021) into a single location with a user-friendly API
and transparent methodologies. VegSci.jl is being developed with the
aim of assisting in the creation of high-performance, reproducible
analytical pipelines in vegetation research (Sperandii et al. 2024),
developed primarily with the application to the vegetation of Great
Britain in mind, but fully generalisable. Nomenclature follows
Theurillat et al. (2021).
VegSci.jl is structured around the Julia package NamedArrays.jl
facilitating the use of named relevé by species matrices, which
constitute the basic input for most functions.
Dependency Management
Coming soon...
Version Control
Coming soon...
Release Steps
Coming soon...
Testing
To test VegSci.jl
1. Run ] activate . to activate the package environment.
2. Run ] test
2. Run ] activate to exit the package environment.
Documentation
Run quarto check in the terminal to check whether Quarto is ok.
If Julia has been updated you will need to re-install the IJulia kernel
by running using IJulia then installkernel("Julia") in the Julia
terminal.
To render the README run quarto render README.qmd --to md
Bezanson, Jeff, Alan Edelman, Stefan Karpinksi, and Viral B. Shah. 2017. “Julia: A Fresh Approach to Numerical Computing.” SIAM Review 59 (1): 65–98. https://doi.org/10.1137/141000671.
De Cáceres, Miquel, Xavier Font, and Francesc Oliva. 2010. “The Management of Vegetation Classifications with Fuzzy Clustering.” Journal of Vegetation Science 21 (6): 1138–51. https://doi.org/10.1111/j.1654-1103.2010.01211.x.
De Cáceres, Miquel, Pierre Legendre, and Fangliang He. 2013. “Dissimilarity Measurements and the Size Structure of Ecological Communities.” Methods in Ecology and Evolution 4 (12): 1167–77. https://doi.org/10.1111/2041-210X.12116.
Dray, Stéphane, and Anne-Béatrice Dufour. 2007. “The Ade4 Package: Implementing the Duality Diagram for Ecologists.” Journal of Statistical Software 22 (September): 1–20. https://doi.org/10.18637/jss.v022.i04.
Kaiser, Roland. 2021. “Vegsoup: Classes and Methods for Phytosociology.”
Oksanen, Jari, Gavin Simpson, Peter Solymos, Leo Lahti, Geoffrey Hannigan, James Weedon, Eduard Szöcs, et al. 2022. “Vegandevs/Vegan: Vegan 2.6-4 on CRAN.” https://doi.org/10.5281/zenodo.7185692.
Roesch, Elisabeth, Joe G. Greener, Adam L. MacLean, Huda Nassar, Christopher Rackauckas, Timothy E. Holy, and Michael P. H. Stumpf. 2023. “Julia for Biologists.” Nature Methods 20 (5): 655–64. https://doi.org/10.1038/s41592-023-01832-z.
Sperandii, Marta Gaia, Manuele Bazzichetto, Glenda Mendieta-Leiva, Sebastian Schmidtlein, Michael Bott, Renato A. Ferreira de Lima, Valério D. Pillar, Jodi N. Price, Viktoria Wagner, and Milan Chytrý. 2024. “Towards More Reproducibility in Vegetation Research.” Journal of Vegetation Science 35 (1): e13224. https://doi.org/10.1111/jvs.13224.
Theurillat, Jean-Paul, Wolfgang Willner, Federico Fernández-González, Helga Bültmann, Andraž Čarni, Daniela Gigante, Ladislav Mucina, and Heinrich Weber. 2021. “International Code of Phytosociological Nomenclature. 4th Edition.” Applied Vegetation Science 24 (1): e12491. https://doi.org/10.1111/avsc.12491.
Tichý, Lubomír. 2002. “JUICE, Software for Vegetation Classification.” Journal of Vegetation Science 13 (3): 451–53. https://doi.org/10.1111/j.1654-1103.2002.tb02069.x.