Introduction
Package indicspecies provides functions to conduct:
Indicator species analysis: Assess the strength and statistical significance of the relationship between species occurrence/abundance and groups of sites (De Cáceres & Legendre 2009; De Cáceres et al. 2010; De Cáceres et al. 2012).
Species niche analysis: Measure species niche metrics using resource categories (De Cáceres et al. 2011).
Package installation
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)Usage
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).
Maintenance
Although not in active development, the R package is maintained by the Ecosystem Modelling Facility unit at CREAF (in Spain).
References
De Cáceres, M., & Legendre, P. (2009). Associations between species and groups of sites: indices and statistical inference. Ecology, 90(12), 3566–3574 (https://doi.org/10.1890/08-1823.1).
De Cáceres, M., Legendre, P., & Moretti, M. (2010). Improving indicator species analysis by combining groups of sites. Oikos, 119(10), 1674–1684 (https://doi.org/10.1111/j.1600-0706.2010.18334.x).
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 (https://doi.org/10.1111/j.2041-210X.2012.00246.x).
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 (https://doi.org/10.1111/J.1600-0706.2011.19679.x).