phyloregion: Calculate evolutionary distinctiveness of phyloregions

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/phyloregion.R

Description

This function estimates evolutionary distinctiveness of each phyloregion by computing the mean value of phylogenetic beta diversity between a focal phyloregion and all other phyloregions in the study area.

Usage

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phyloregion(x, k = 10, method = "average", shp = NULL, ...)

infomap(x, shp = NULL, ...)

Arguments

x

A distance matrix

k

The desired number of phyloregions, often as determined by optimal_phyloregion.

method

the agglomeration method to be used. This should be (an unambiguous abbreviation of) one of “ward.D”, “ward.D2”, “single”, “complete”, “average” (= UPGMA), “mcquitty” (= WPGMA), “median” (= WPGMC) or “centroid” (= UPGMC).

shp

a polygon shapefile of grid cells.

...

Further arguments passed to or from other methods.

Value

An object of class phyloregion containing

Author(s)

Barnabas H. Daru darunabas@gmail.com

References

Daru, B.H., Van der Bank, M., Maurin, O., Yessoufou, K., Schaefer, H., Slingsby, J.A. & Davies, T.J. (2016) A novel phylogenetic regionalization of the phytogeographic zones of southern Africa reveals their hidden evolutionary affinities. Journal of Biogeography 43: 155-166.

Daru, B.H., Elliott, T.L., Park, D.S. & Davies, T.J. (2017) Understanding the processes underpinning patterns of phylogenetic regionalization. Trends in Ecology and Evolution 32: 845-860.

Daru, B.H., Holt, B.G., Lessard, J.P., Yessoufou, K. & Davies, T.J. (2017) Phylogenetic regionalization of marine plants reveals close evolutionary affinities among disjunct temperate assemblages. Biological Conservation 213: 351-356.

See Also

evol_distinct, optimal_phyloregion, evol.distinct for a different approach.

Examples

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library(ape)
tree <- read.tree(text = "((t1:1,t2:1)N2:1,(t3:1,t4:1)N3:1)N1;")
com <- sparseMatrix(c(1,3,4,1,4,5,1,2,3,4,5,6,3,4,6),
  c(1,1,1,2,2,2,3,3,3,3,3,3,4,4,4),x=1,
  dimnames = list(paste0("g", 1:6), tree$tip.label))
pbc <- phylobeta(com, tree)
phyloregion(pbc[[1]], k = 3)

phyloregion documentation built on May 1, 2021, 9:06 a.m.