Compare Two Accumulation Curves

Test whether two species accumulation curves differ significantly.

Usage

compare(
  x,
  y,
  method = c("permutation", "bootstrap", "auc"),
  normalize = FALSE,
  n_perm = 999L,
  ...
)

Arguments

x: A spacc object.
y: A spacc object.
method: Character. Comparison method: "permutation" (default), "bootstrap", or "auc" (area under curve difference).
normalize: Logical. If TRUE, each seed's curve is divided by its final value before computing AUC, so that curves are compared on a [0, 1] scale (proportion of total species). This compares the shape of accumulation rather than absolute species counts. Default FALSE.
n_perm: Integer. Number of permutations/bootstrap replicates. Default 999.
...: Additional arguments passed to comparison methods.

Value

An object of class spacc_comp containing:

x_name, y_name: Names of compared objects
auc_diff: Difference in area under curve
p_value: P-value from permutation test
saturation_diff: Difference in saturation points
method: Comparison method used
normalized: Whether curves were normalized before comparison

References

Colwell, R.K., Mao, C.X. & Chang, J. (2004). Interpolating, extrapolating, and comparing incidence-based species accumulation curves. Ecology, 85, 2717-2727.

Gotelli, N.J. & Colwell, R.K. (2011). Estimating species richness. In: Biological Diversity: Frontiers in Measurement and Assessment, pp. 39-54. Oxford University Press.

Examples

# \donttest{
coords <- data.frame(x = runif(50), y = runif(50))
sp_a <- matrix(rbinom(50 * 30, 1, 0.3), nrow = 50)
sp_b <- matrix(rbinom(50 * 30, 1, 0.5), nrow = 50)

sac_a <- spacc(sp_a, coords, n_seeds = 10)
sac_b <- spacc(sp_b, coords, n_seeds = 10)
comp <- compare(sac_a, sac_b)
print(comp)
# }