README.md
In vegmod/indicspecies: Relationship Between Species and Groups of Sites

indicspecies

Package indicspecies provides functions to:

Assess the strength and statistical significance of the relationship between species occurrence/abundance and groups of sites: De Cáceres & Legendre (2009) (https://doi.org/10.1890/08-1823.1); De Cáceres et al. (2010) (https://doi.org/10.1111/j.1600-0706.2010.18334.x); De Cáceres et al. (2012) (https://doi.org/10.1111/j.2041-210X.2012.00246.x).
Measure species niche breadth using resource categories: De Cáceres et al. (2011) (https://doi.org/10.1111/J.1600-0706.2011.19679.x).

Packageindicspecies can be found at CRAN package repository. In addition, the latest stable indicspecies R package can be installed from GitHub as follows:

remotes::install_github("emf-creaf/indicspecies")

Additionally, users can have help to run package functions directly as package vignettes, by forcing their inclusion in installation:

remotes::install_github("emf-creaf/indicspecies", 
                        build_opts = c("--no-resave-data", "--no-manual"),
                        build_vignettes = TRUE)

Use strassoc() for assessing strength of associations and signassoc() to assess the statistical significance of the associations (De Cáceres & Legendre 2009). Much more complete functions are multipatt() (De Cáceres et al. 2010) and indicators() (De Cáceres et al. 2012).

Although not in active development, this R package is maintained by the Ecosystem Modelling Facility unit at CREAF (in Spain)

De Cáceres, M., & Legendre, P. (2009). Associations between species and groups of sites: indices and statistical inference. Ecology, 90(12), 3566–3574.
De Cáceres, M., Legendre, P., & Moretti, M. (2010). Improving indicator species analysis by combining groups of sites. Oikos, 119(10), 1674–1684.
De Cáceres, M., Legendre, P., Wiser, S. K., & Brotons, L. (2012). Using species combinations in indicator value analyses. Methods in Ecology and Evolution, 3, 973–982.
De Cáceres, M., Sol, D., Lapiedra, O., & Legendre, P. (2011). A framework for estimating niche metrics using the resemblance between qualitative resources. Oikos, 120(February), 1341–1350.