" class="reference-link">shar | Species habitat associations in R

README Last updated: 2025-02-11

CI	Development	CRAN	License

Species-habitat associations in R provides a toolset of
functions in the R programming language to analyze species-habitat
associations. Therefore, information about the location of the species
(as a point pattern) and the environmental conditions (as a raster) is
needed. In order to analyse the data for significant habitat
associations either the location data or the environmental data is
randomized n-times. Then, counts within the habitats are compared
between the observed and the randomized data. Positive or negative
associations are present if the observed counts are higher or lower than
the randomized counts (using quantile thresholds). Methods are described
in Plotkin et al. (2000), Harms et al. (2001) and Wiegand & Moloney
(2014). shar is mainly based on the
spatstat (Baddeley et al. 2015) and
terra (Hijmans 2022) package.

You can find more information and help using the corresponding
homepage.

Installation

You can install the released version of shar from
CRAN with:

install.packages("shar")

And the development version from
GitHub with:

# install.packages("remotes")
remotes::install_github("r-spatialecology/shar")

This also automatically installs all non-base R package dependencies,
namely: classInt, spatstat.explore, spatstat.geom,
spatstat.model, spatstat.random, and terra.

How to use shar

Please refer to vignette("Get started") and the
homepage to get an
introduction to shar.

Citation

The shar package is part of our academic work. To cite the package
or acknowledge its use in publications, please cite the following paper.

Hesselbarth, M.H.K., (2021). shar: A R package to analyze
species-habitat associations using point pattern analysis. Journal of
Open Source Software, 6(67), 3811.
https://doi.org/10.21105/joss.03811.

If you use the reconstruct_pattern_multi() function, please also cite.

Wudel C., Schlicht R., Berger U. (2023). Multi-trait point pattern
reconstruction of plant ecosystems. Methods in Ecology and Evolution,
14, 2668–2679. https://doi.org/10.1111/2041-210X.14206.

The get a BibTex entry, please use citation("shar").

Contributing and Code of Conduct

Contributions to shar are highly welcomed and appreciated. This
includes any form of feedback, bug reports, feature
requests/suggestions, or general questions about the usage.

Please note that the shar package is released with a Contributor
Code of Conduct. By contributing to this project,
you agree to abide by its terms.

To contribute to this project, please see the Contributing
guidelines.