Zeta.ddecays: Zeta distance decay for a range of numbers of assemblages or...
In zetadiv: Functions to Compute Compositional Turnover Using Zeta Diversity

Zeta.ddecays

R Documentation

Zeta distance decay for a range of numbers of assemblages or sites

Description

Computes the distance decay of zeta diversity for a range of orders (number of assemblages or sites), using generalised linear models.

Usage

Zeta.ddecays(
  xy,
  data.spec,
  orders = 2:10,
  sam = 1000,
  family = stats::gaussian(),
  distance.type = "Euclidean",
  dist.custom = NULL,
  method = "mean",
  confint.level = 0.95,
  trsf = "NULL",
  cutoff = NULL,
  rescale = FALSE,
  normalize = FALSE,
  plot = TRUE
)

Arguments

`xy`	Site-by-coordinate data frame, with sites as rows and coordinates as columns.
`data.spec`	Site-by-species presence-absence data frame, with sites as rows and species as columns.
`orders`	Range of number of assemblages or sites at which zeta diversity is computed. All the orders must be striclty greater than 1.
`sam`	Number of samples for which the zeta diversity is computed.
`family`	A description of the error distribution and link function to be used in the generalised linear models (see `family` for details of family functions).
`distance.type`	Method to compute distance. Default is "`Euclidean`", for Euclidean distance. The other options are (i) "`ortho`" for orthodromic distance, if xy correspond to longitudes and latitudes (orthodromic distance is computed using the `geodist` function from package `geodist`); and (ii) "`custom`", in which case the user must provide a distance matrix for `dist.custom`.
`dist.custom`	Distance matrix provided by the user when `distance.type` = `"custom"`.
`method`	Name of a function (as a string) indicating how to combine the pairwise differences and distances for more than 3 sites. It can be a basic R-function such as "`mean`" or "`max`", but also a custom function.
`confint.level`	Percentage for the confidence intervals of the coefficients from the linear regression.
`trsf`	Name of a function (as a string) indicating how to transform distance. Default is "NULL" for the identity transformation.
`cutoff`	If specified, maximum distance value for which the linear regression must be performed.
`rescale`	Boolean value (TRUE or FALSE) indicating if the zeta values should be divided by ζ_1, to get a range of values between 0 and 1. Has no effect if `normalize` != `FALSE`.
`normalize`	Indicates if the zeta values for each sample should be divided by the total number of species for this specific sample (`normalize = "Jaccard"`), by the average number of species per site for this specific sample (`normalize = "Sorensen"`), or by the minimum number of species in the sites of this specific sample (`normalize = "Simpson"`). Default value is `FALSE`, indicating that no normalization is performed.
`plot`	Boolean value (TRUE or FALSE) indicating if the outputs must be plotted.

Value

Zeta.ddecays returns a list containing the following components:

`orders`	Range of number of assemblages or sites at which zeta diversity was computed.
`coefs`	A vector of the coefficients from the generalised linear models for the numbers of sites specified by `orders`.
`confint`	The confidence intervals for the coefficients from the generalised linear models.

References

Hui C. & McGeoch M.A. (2014). Zeta diversity as a concept and metric that unifies incidence-based biodiversity patterns. The American Naturalist, 184, 684-694.

Examples

utils::data(bird.spec.coarse)
xy.bird <- bird.spec.coarse[,1:2]
data.spec.bird <- bird.spec.coarse[,3:193]

dev.new()
zeta.ddecays.bird <- Zeta.ddecays(xy.bird, data.spec.bird, sam = 100, orders = 2:5,
    plot = TRUE, confint.level = 0.95)

##########

utils::data(Marion.species)
xy.marion <- Marion.species[,1:2]
data.spec.marion <- Marion.species[,3:33]

dev.new()
zeta.ddecays.marion <- Zeta.ddecays(xy.marion, data.spec.marion, sam = 100,
   orders = 2:5, plot = TRUE, confint.level = 0.95)

zetadiv documentation built on June 11, 2022, 1:12 a.m.