compare: Compare Two Accumulation Curves

In spacc: Fast Spatial Species Accumulation Curves

Compare Two Accumulation Curves

Description

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

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)

spacc documentation built on June 20, 2026, 5:07 p.m.