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Convert an Accumulation Curve from Another Package to a spacc Object

Source: R/as_spacc.R
as_spacc.Rd

Bring an existing species accumulation curve into the spacc object system so it can be summarised, plotted, and compared with compare() alongside spatial curves. A vegan specaccum object is currently supported.

Usage

as_spacc(x, ...)

# Default S3 method
as_spacc(x, ...)

# S3 method for class 'specaccum'
as_spacc(x, ...)

Arguments

x

An object to convert. A specaccum object from vegan::specaccum() is supported.

...

Ignored, for method extensibility.

Value

An object of class spacc with print(), summary(), plot(), as.data.frame(), and compare() support.

Details

A specaccum object built with method = "random" stores one richness curve per permutation in its perm matrix. Those curves become the rows of the returned curves matrix and behave exactly like spacc seeds, so the across-curve confidence band and the compare() permutation, bootstrap, and AUC tests carry over unchanged. A specaccum object without a permutation matrix (for example method = "exact" or "collector") contributes its single mean curve.

Coordinates cannot be recovered from a specaccum object, so the result carries no coords: it is a curve container for plotting and comparison, not a re-runnable spatial object.

See also

compare() to test a converted curve against a spatial one.

Examples

# \donttest{
if (requireNamespace("vegan", quietly = TRUE)) {
  data(BCI, package = "vegan")
  classic <- vegan::specaccum(BCI, method = "random")
  sp <- as_spacc(classic)
  summary(sp)
  plot(sp)
}
# }