Skip to contents

Calculate the niche overlap between a set of taxa

Source: R/calc_overlap.R
calc_overlap.Rd

Calculate the niche overlap between all combinations of taxa as present in the 'taxa' argument, or the combinations of taxa present in the 'taxa' and 'taxa_comp' arguments. Two methods are curently provided: "D" - Schoener's D (Schoener, 1968) "I" - Warren's I (Warren et al., 2008)

Usage

calc_overlap(
  taxa,
  taxa_comp = NULL,
  data = elements::HOAData,
  vars = elements::VariableNames,
  method = "D",
  average = FALSE,
  format = "wide"
)

Arguments

taxa

A vector of strings containing taxon codes, see elements::ModelledTaxaCodes.

taxa_comp

A vector of string containing taxon codes, see elements::ModelledTaxaCodes.

data

A data frame containing the univariate responses of the taxa supplied in the 'taxa' and 'taxa_comp' arguments for the variables supplied in the 'vars' argument. elements::HOAData by default.

vars

A vector of strings containing the variables for which to calculate the overlap, one or more of elements::VariableNames.

method

A string, one of "D" or "I" indicating the overlap method (see description).

average

A boolean (TRUE/FALSE) indicating whether to calculate the mean overlap across all variables.

format

A boolean (TRUE/FALSE) indicating whether to return the results in wide of long format.

Value

A data frame containing the overlap values.

References

Schoener, T.W., 1968. The Anolis Lizards of Bimini: Resource Partitioning in a Complex Fauna. Ecology 49, 704–726. https://doi.org/10.2307/1935534 Warren, D.L., Glor, R.E., Turelli, M., 2008. ENVIRONMENTAL NICHE EQUIVALENCY VERSUS CONSERVATISM: QUANTITATIVE APPROACHES TO NICHE EVOLUTION. Evolution 62, 2868–2883. https://doi.org/10.1111/j.1558-5646.2008.00482.x

Examples

elements::calc_overlap(taxa = c("carex_arenaria", "carex_divulsa", "carex_hirta", "carex_sylvatica"))
#>     taxon_code_1    taxon_code_2         M         N         R         L
#> 1 carex_arenaria   carex_divulsa 1.0000000 1.0000000 1.0000000 1.0000000
#> 2 carex_arenaria     carex_hirta 0.7166717 0.7222517 0.6161794 0.7590258
#> 3 carex_arenaria carex_sylvatica 1.0000000 1.0000000 1.0000000 1.0000000
#> 4  carex_divulsa     carex_hirta 1.0000000 1.0000000 1.0000000 1.0000000
#> 5  carex_divulsa carex_sylvatica 1.0000000 1.0000000 1.0000000 1.0000000
#> 6    carex_hirta carex_sylvatica 1.0000000 1.0000000 1.0000000 1.0000000
#>           S        GP        SD   tmax_sm   tmin_wt   prec_sm   prec_wt
#> 1 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
#> 2 0.6477787 0.8676262 0.7001941 0.5306157 0.7514213 0.5589898 0.6319008
#> 3 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
#> 4 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
#> 5 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
#> 6 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000