pez.shape: Calculate (phylogenetic) shape: examine assemblage...

In pez: Phylogenetics for the Environmental Sciences

Calculate (phylogenetic) shape: examine assemblage composition

Description

As described in Pearse et al. (2014), a shape metric is one the examines the phylogenetic structure of species present in each assemblage, ignoring abundances entirely. For completeness, options are provided to calculate these metrics using species traits.

Usage

pez.shape(
  data,
  sqrt.phy = FALSE,
  traitgram = NULL,
  traitgram.p = 2,
  ext.dist = NULL,
  which.eigen = 1,
  quick = TRUE,
  q = 1e-04
)

Arguments

data	comparative.comm object
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 different metric calculations when a distance matrix is used.
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 funct.phylo.dist). If a vector of numbers is given, pez.shape iterates across them and returns a data.frame with coefficients from each iteration. See ‘details’ for details about different metric calculations when a distance matrix is used.
traitgram.p	A value for ‘p’ to be used in conjunction with traitgram when calling funct.phylo.dist.
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.
which.eigen	The eigen vector to calculate for the PhyloEigen metric (eigen.sum)
quick	Only calculate metrics which are quick to calculate (default: TRUE); setting to FALSE will also calculate fd.dist.
q	value for q in scheiner (default 0.0001)

Details

Most of these metrics do not involve comparison with some kind of evolutionary-derived expectation for phylogenetic shape. Those that do, however, such as PSV, make no sense unless applied to a phylogenetic distance matrix - their null expectation *requires* it. Using square-rooted distance matrices, or distance matrices that incorporate trait information, can be an excellent thing to do, but (for the above reasons), pez won't give you an answer for metrics for which WDP thinks it makes no sense. pd, eed & hed can (...up to you whether you should!...) be used with a square-rooted distance matrix, but the results *will always be wrong* if you do not have an ultrametric tree (branch lengths proportional to time) and you will be warned about this. WDP strongly feels you should only be using ultrametric phylogenies in any case, but code to fix this bug is welcome.

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).

Some of the metrics in this wrapper are also in pez.evenness; such metrics can be calculated using species' abundances (making them evenness) metrics or simply using presence/absence of species (making them shape metrics).

Note

As mentioned above, dist.fd is calculated using a phylogenetic distance matrix if no trait data are available, or if you specify sqrt.phy. It is not calculated by default because it generates warning messsages (which WDP is loathe to suppress) which are related to the general tendency for a low rank of phylogenetic distance matrices. Much ink has been written about this, and in part this problem is why the eigen.sum measure came to be suggested.

Many of these metrics, (e.g., eed) will cause (inconsequential) warnings if given assemblages with only one species in them, and return NA/NaN values depending on the metric. I consider these ‘features’, not bugs.

Author(s)

M.R. Helmus, Will Pearse

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.

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.

innd,mipd Ness J.H., Rollinson E.J. & Whitney K.D. (2011). Phylogenetic distance can predict susceptibility to attack by natural enemies. Oikos, 120, 1327-1334.

scheiner Scheiner, S.M. (20120). A metric of biodiversity that integrates abundance, phylogeny, and function. Oikos, 121, 1191-1202.

See Also

pez.evenness pez.dispersion pez.dissimilarity

Examples

data(laja)
data <- comparative.comm(invert.tree, river.sites, invert.traits)
(output<-pez.shape(data))

pez documentation built on Sept. 1, 2022, 1:09 a.m.