twostagechao {vegan}R Documentation

Multiple-Community Similarity Index

Description

The function implements the two-stage probabilistic approach to multiple-community similarity indices proposed by Chao et al. (2008), extending the traditional pairwise comparisons of sites.

Usage

twostagechao(x, order = 2, N = nrow(x), m = 1, nboot = 200, subset)

Arguments

x A community matrix with rows as sites and columns as species.
order The order of the similarity, see details.
N The number of sites to use. By default it is the number of rows in x. If N < ncol(x), then N and subset must conform (length(subset) == N).
m The exponent used for calculating the NESS index variant, see details.
nboot Number of bootstrap samples to use for calculating standard error of the estimate. If nboot = 0, standard error is not computed.
subset Optional vector defining the subset of sites to use in the calculations. If this argument is provided, its length should equal N.

Details

PUT DETAILS HERE

Value

The result is an object of class 'twostagechao' inheriting its structure from class 'htest'.

Author(s)

P\'eter S\'olymos, solymos@ualberta.ca

References

Chao, A., Jost, L., Chiang, S. C., Jiang, Y.-H., Chazdon, R. L. (2008) A two-stage probabilistic approach to multiple-community similarity indices. Biometrics 64, 1178–1186.

Supplementary material at: http://www.biometrics.tibs.org/datasets/070539.pdf

See Also

dist, vegdist

Examples

data(BCI)
twostagechao(BCI)
res1 <- t(sapply(2:5, function(z) twostagechao(BCI, order=z)$statistic))
rownames(res1) <- paste("Order =", 2:5)
## similarity decreases as rare species get more weights
res1
## original example from Chao et al. 2008
## supplementary material, LSUR Primary Plot
lep1 <- structure(c(7L, 48L, 17L, 0L, 38L, 14L, 31L, 37L, 121L, 6L, 30L, 
16L, 0L, 27L, 10L, 0L, 24L, 5L, 2L, 23L, 6L, 3L, 21L, 6L, 1L, 
19L, 1L, 0L, 19L, 73L, 0L, 19L, 2L, 2L, 17L, 4L, 3L, 17L, 17L, 
2L, 16L, 5L, 0L, 16L, 11L, 0L, 16L, 4L, 2L, 15L, 1L, 0L, 15L, 
9L, 4L, 14L, 7L, 0L, 14L, 2L, 0L, 13L, 4L, 5L, 12L, 0L, 1L, 11L, 
7L, 2L, 11L, 20L, 1L, 9L, 0L, 2L, 9L, 5L, 0L, 9L, 0L, 1L, 8L, 
0L, 0L, 8L, 6L, 0L, 8L, 0L, 0L, 8L, 0L, 0L, 8L, 0L, 3L, 7L, 3L, 
0L, 7L, 17L, 0L, 7L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 
1L, 0L, 0L, 1L, 0L, 0L, 2L, 6L, 1L, 0L, 6L, 6L, 0L, 6L, 2L, 1L, 
5L, 0L, 2L, 5L, 1L, 1L, 5L, 3L, 0L, 5L, 2L, 0L, 5L, 1L, 0L, 5L, 
1L, 1L, 4L, 1L, 1L, 4L, 2L, 0L, 4L, 29L, 0L, 4L, 3L, 0L, 4L, 
1L, 0L, 4L, 0L, 0L, 3L, 2L, 0L, 3L, 1L, 0L, 3L, 0L, 3L, 2L, 0L, 
1L, 2L, 0L, 1L, 2L, 0L, 1L, 2L, 3L, 0L, 2L, 7L, 0L, 2L, 5L, 0L, 
2L, 1L, 0L, 2L, 1L, 0L, 2L, 1L, 0L, 2L, 0L, 0L, 2L, 0L, 0L, 2L, 
0L, 0L, 2L, 0L, 0L, 2L, 0L, 0L, 2L, 0L, 0L, 2L, 0L, 0L, 2L, 0L, 
3L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 3L, 0L, 0L, 54L, 0L, 0L, 3L, 
0L, 2L, 0L, 0L, 2L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 1L, 1L, 
1L, 2L, 0L, 1L, 5L, 0L, 1L, 3L, 0L, 1L, 3L, 0L, 1L, 1L, 0L, 1L, 
1L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 1L, 1L, 0L, 1L, 0L, 
0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 
1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 
0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L, 0L, 
2L, 0L, 0L, 2L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 3L, 0L, 0L, 2L, 0L, 
0L, 1L, 0L, 0L, 1L, 0L, 0L, 1L), .Dim = c(3L, 120L), .Dimnames = list(
    c("Tree", "Sapling", "Seedling"), NULL))
## compare values in Table 3 of Chao et al. 2008
## (4th column, last 6 rows)
## results are different!
Order <- rep(2:3, 3)
m <- c(1, 1, 5, 5, 10, 10)
res2 <- t(sapply(1:6, function(z)
    twostagechao(lep1, order=Order[z], m=m[z])$statistic))
rownames(res2) <- c("Morisita C23", "Morisita C33", "NESS23(5)",
    "NESS33(5)", "NESS23(10)", "NESS33(10)")
res2

[Package vegan version 1.16-32 Index]