Mikrubi: a model for species distributions using region-based records
Author Mikumikunisiteageru
0 Stars
Updated Last
5 Months Ago
Started In
February 2022


Documentation Documentation CI Codecov Aqua.jl Quality Assurance

Mikrubi: a model for species distributions using region-based records

Many species occurrence records from specimens and publications are based on regions such as administrative units (thus sometimes called counties in the codes). These region-based records are accessible and dependable, and sometimes they are the only available data source; however, few species distribution models accept such data as direct input. In Yang et al. (2023), we present a method named Mikrubi for robust prediction of species distributions from region-based occurrence data. This is the Julia package implementing the algorithms.


Mikrubi currently requires Julia v1.7.0 or higher. This registered package can be installed inside the Julia REPL by typing

]add Mikrubi

Input data requirements

To estimate the fine-scale distribution of a species using its presence or absence in each region, the package generally requires three types of input data:


A typical workflow of the package resembles the following lines, where shppath refers to the path to the map file, climpath refers to the directory path to the raster files, and ctlistpath refers to the path to the list containing lines of integer identifiers representing the regions.

using Mikrubi
shptable = readshape(shppath)
layers = readlayers(climpath)
ctlist = readlist(ctlistpath)
field, ylayers = makefield(layers, shptable)
model = fit(field, ctlist)
geodist = predict(ylayers, model)
writelayer("path/to/output/geodist.tif", geodist)


An introduction of this package and the model it implements has been published on Ecography (10.1111/ecog.06283).

If you apply the package or the model in your research, please cite them via the paper above or as the following after substituting the version:

Yang, Y.-C., Zhang, Q. and Chen, Z.-D. 2023. Mikrubi: a model for species distributions using region-based records. – Ecography 2023: e06283 (ver. 1.3.2).

The equivalent BibTeX file for citation is available at CITATION.bib. You may also import this file or the following BibTeX code block to your reference management software.

	author = {Yang, Yu-Chang and Zhang, Qian and Chen, Zhi-Duan},
	title = {Mikrubi: a model for species distributions using region-based records},
	journal = {Ecography},
	year = {2023},
	volume = {2023},
	pages = {e06283},
	doi = {https://doi.org/10.1111/ecog.06283},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ecog.06283},
	eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/ecog.06283},