optim.alpha.stats {BAT}

R Documentation

Efficiency statistics for alpha-sampling.

Description

Average alpha diversity observed with a given number of samples per method.

Usage

optim.alpha.stats(comm, tree, methods, samples, runs = 0)

Arguments

comm	A samples x species x sites array, with either abundance or incidence data.
tree	A phylo or hclust object (used only for PD or FD) or alternatively a species x traits matrix or data.frame to build a functional tree.
methods	A vector specifying the method of each sample (length must be equal to nrow(comm))
samples	A vector defining the number of samples per method to be evaluated (length must be equal to number of methods).
runs	Number of random permutations to be made to the sample order. Default is 1000.

Details

Different combinations of samples per method allow sampling different sub-communities. This function allows knowing the average TD, PD or FD values for a given combination, for one or multiple sites simultaneously. PD and FD are calculated based on a tree (hclust or phylo object, no need to be ultrametric).

Value

A single average alpha diversity value. Rescaled to 0-1 if made for several sites, where 1 is the true diversity of each site.

Examples

comm1 <- matrix(c(1,1,0,2,4,0,0,1,2,0,0,3), nrow = 4, ncol = 3, byrow = TRUE)
comm2 <- matrix(c(2,2,0,3,1,0,0,0,5,0,0,2), nrow = 4, ncol = 3, byrow = TRUE)
comm <- array(c(comm1, comm2), c(4,3,2))
colnames(comm) <- c("Sp1","Sp2","Sp3")
methods <- c("Met1","Met2","Met2","Met3")
tree <- hclust(dist(c(1:3), method="euclidean"), method="average")
tree$labels <- colnames(comm)
optim.alpha.stats(comm,,methods, c(1,1,1))
optim.alpha.stats(comm, tree, methods = methods, samples = c(0,0,1), runs = 100)

---