ConDivSim: Null models for functional-phylogenetic diversity
In willpearse/pez: Phylogenetics for the Environmental Sciences

Description Usage Arguments Details Value Note Author(s) See Also Examples

Simulate expectations (under a null model) of mean pairwise distance for a set of communities with different species richness.

1 2	ConDivSim(object, type = "traits", n.sim = 100, plot = TRUE, disp99 = FALSE)

`object`	a `comparative.comm` object, with presence-absence community data.
`type`	character string giving the type of distance matrix on which the mean pairwise distance is based. Either "trait" or "phy" to a phylogenetic or trait-based distance matrix, or an actual matrix to use (e.g., one from `funct.phylo.dist`)
`n.sim`	The number of permutations of the presence vector used to make the estimations.
`plot`	TRUE or FALSE to make the plot of the expected average mean pairwise distance, and the 5-95% confidence interval.
`disp99`	Display the 99% interval?

If plot == TRUE, then a surface is drawn giving the null distribution. Lighter shades of gray give larger intervals with categories: 0.005-0.995 = 99%, 0.025-0.975 = 95%, 0.05-0.95 = 90%, 0.25-0.75 = 50%.

matrix with quantiles of mean pairwise distances for all quantiles of of mean pairwise distance, with one row for the range of species richnesses in the data (see column SpRich).

No serious checking of user-provided matrices is performed; this is both useful and dangerous!

Steve Walker, wrappers by Will Pearse

sim.phy scape

data(laja)
data <- comparative.comm(invert.tree, river.sites, invert.traits)
#Must have all species present in at least one community!
#...and must be presence-absence data
data <- data[,colSums(data$comm) > 0]
data$comm[data$comm>1] <- 1
sims <- ConDivSim(data)
#...without traits...
sims.phy <- ConDivSim(data, type="phy")