Relationship between species and groups of sites

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")
install.packages("indicspecies", repos = c('https://emf-creaf.r-universe.dev', 'https://cloud.r-project.org'))

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).