clade.var: Calculation clade-level beta-dispersion

In willpearse/pez: Phylogenetics for the Environmental Sciences

Description

As described in Pearse et al. (in press), this function calculations phylogenetic beta-dispersion for each clade within a phylogeny. Beta-dispersion is the variation of presences and absences across multiple sites, and by focusing on clades' dispersions patterns it is possible to unpick processes occurring across a system. This method is based around species' variances in While this code reports an analytical expectation (and so p-value) for

Usage

clade.var(data, alpha = 0.05, clade = NULL)

Arguments

data	comparative.comm object
alpha	Critical values (DEFAULT: 5 confidence intervals. See notes for details about this.
clade	If given (by default not: NULL) then values for only these clades will be returned. Should be a numeric vector of any length; negative values are interpreted as excluding certain clades. Rarely, if ever, needed.

Value

a data.frame with each clade's observed variance, Faith's pd (calculated by summing the branch lengths of each clade), the number of species in the clade, the expected variance (from the analytical expectation; see 'notes'), and then the upper and lower confidence interval bounds for expectation of that variance (see also 'notes'; calculated at a critical value of alpha).

Note

As described in Pearse et al. (in press), there are two ways of assessing the statistical significance of this approach: an analytical expectation and through a null permutation test. This code returns the analytical expectation; to perform a bootstrap, simply run this function many times across data you have permuted in some way. The assumptions implicit in the analytical test (e.g., iid and Normally distributed abundances/occurrences) will rarely, if ever, be met, and so I advise against using it as anything other than a general guide.

Author(s)

Will Pearse

References

Pearse WD, Legendre P, Peres-Neto, PR, & Davies TJ (in press). The interaction of phylogeny and community structure: Linking the community composition and trait evolution of clades. Global Ecology & Biogeography (available online at bioRxiv: 404111).

Examples

data(laja)
data <- comparative.comm(invert.tree, river.sites, invert.traits)
clade.var(data)

willpearse/pez documentation built on June 18, 2019, 9:33 p.m.