indicspecies R package
Indicator species are species that are used as ecological indicators of community or habitat types, environmental conditions, or environmental changes. In order to determine indicator species, the characteristic to be predicted is represented in the form of a classification of the sites, which is compared to the patterns of distribution of the species found in that set of sites.
Indicspecies is an R package that contains a set of functions to assess the strength of relationship between species and a classification of sites. As such, it includes the well-known IndVal method (Dufrêne & Legendre 1997) and extends it by allowing the user to study combinations of site groups (De Cáceres et al. 2010). Apart from the IndVal index, the package allows computing many other indices suitable for this kind of associations (De Cáceres & Legendre 2009), such as the phi coefficient of association. It is also possible to check the statistical significance of such associations.
About resniche functions
Indicspecies package currently includes the functions formerly included in another R packaged called ‘resniche’. The niche concept underlies most ecological questions, from population growth and geographic expansion to community dynamics and ecosystem functioning. There is not one niche concept, but many, each of which emphasizes a different aspect of a species’ ecological characteristics. The species resource niche refers to the set of resources used by the species, such as food types. Resniche provides functions to estimate resource niche metrics performed on species preference data for a set of qualitative resources (De Cáceres et al. 2011).
Miquel De Cáceres, Florian Jansen