pez (version 1.0-0)

shape: Calculate (phylogenetic) shape: examine assemblage composition

Description

Calculate (phylogenetic) shape: examine assemblage composition

Usage

shape(data, metric = c("all-quick", "all", "psv", "psr", "mpd", "mntd", "pd",
  "colless", "gamma", "taxon", "eigen.sum", "eed", "hed", "dist.fd"),
  sqrt.phy = FALSE, traitgram = NULL, traitgram.p = 2, ext.dist = NULL,
  which.eigen = 1, remove.errors = TRUE, ...)

Arguments

data

comparative.comm object

metric

metrics to calculate. Default (all-quick) calculates everything bar fd.dist, all calculates everything. Individually call-able metrics are: psv, psr, mpd, mntd,

which.eigen

The eigen vector to calculate for the PhyloEigen metric (eigen.sum)

sqrt.phy

If TRUE (default is FALSE) your phylogenetic distance matrix will be square-rooted; specifying TRUE will force the square-root transformation on phylogenetic distance matrices (in the spirit of Leitten and Cornwell, 2014). See `details' for details about

traitgram

If not NULL (default), a number to be passed to funct.phylo.dist (phyloWeight; the `a' parameter), causing analysis on a distance matrix reflecting both traits and phylogeny (0 --> only phylogeny, 1 --> only traits; see fun

traitgram.p

A value for `p' to be used in conjunction with traitgram when calling funct.phylo.dist.

remove.errors

suppress errors about metrics that failed to run (default: TRUE). This will happen for some metrics if you have, for example, only one species in a community.

ext.dist

Supply an external species-level distance matrix for use in calculations. See `details' for comments on the use of distance matrices in different metric calculations.

...

Additional arguments to passed to metric functions (unlikely you will want this!)

Value

• phy.structure list object of metric values. Use coefs to extract a summary metric table, or examine each individual metric (which gives more details for each) by calling print on the output (i.e., type output in the example below).

Details

Calculates various metrics of phylogenetic biodiversity that are categorized as shape metrics by Pearse et al. (2014).

References

Pearse W.D., Purvis A., Cavender-Bares J. & Helmus M.R. (2014). Metrics and Models of Community Phylogenetics. In: Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology. Springer Berlin Heidelberg, pp. 451-464.

PSV,PSR Helmus M.R., Bland T.J., Williams C.K. & Ives A.R. (2007). Phylogenetic measures of biodiversity. American Naturalist, 169, E68-E83.

PD Faith D.P. (1992). Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10.

colless Colless D.H. (1982). Review of phylogenetics: the theory and practice of phylogenetic systematics. Systematic Zoology, 31, 100-104.

gamma Pybus O.G. & Harvey P.H. (2000) Testing macro-evolutionary models using incomplete molecular phylogenies. _Proceedings of the Royal Society of London. Series B. Biological Sciences 267: 2267--2272.

taxon Clarke K.R. & Warwick R.M. (1998). A taxonomic distinctness index and its statistical properties. J. Appl. Ecol., 35, 523-531.

eigen.sum Diniz-Filho J.A.F., Cianciaruso M.V., Rangel T.F. & Bini L.M. (2011). Eigenvector estimation of phylogenetic and functional diversity. Functional Ecology, 25, 735-744.

eed,hed (i.e., Eed, Hed) Cadotte M.W., Davies T.J., Regetz J., Kembel S.W., Cleland E. & Oakley T.H. (2010). Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history. Ecology Letters, 13, 96-105.

See Also

evenness dispersion dissimilarity

Examples

data(laja)
data <- comparative.comm(invert.tree, river.sites, invert.traits)
(output<-shape(data))
str(output)
shape(data, "colless")
shape(data, "eigen.sum", which.eigen=2)