collapse_range: Collapse nodes and ranges based on divergence times

In darunabas/phyloregion: Biogeographic Regionalization and Macroecology

Collapse nodes and ranges based on divergence times

Description

This function collapses nodes and geographic ranges based on species' divergence times at various time depths.

Usage

collapse_range(
  x,
  tree,
  n,
  species = "species",
  grids = "grids",
  format = "wide"
)

Arguments

x	A community matrix or data frame.
tree	A phylogenetic tree.
n	Time depth to slice the phylogenetic tree (often in millions of years for dated trees).
species	If format = “long” (the default), the column with the species name.
grids	The column with the sites or grids if format = “long”.
format	Format of the community composition data: “long” or “wide” with species as columns and sites as rows.

Value

Two community data frames: the collapsed community data and original community data

References

Daru, B.H., Farooq, H., Antonelli, A. & Faurby, S. (2020) Endemism patterns are scale dependent. Nature Communications 11: 2115.

Examples

library(ape)
tr1 <- read.tree(text ="(((a:2,(b:1,c:1):1):1,d:3):1,e:4);")
com <- matrix(c(1,0,1,1,0,0,
                1,0,0,1,1,0,
                1,1,1,1,1,1,
                1,0,1,1,0,1,
                0,0,0,1,1,0), 6, 5,
              dimnames=list(paste0("g",1:6), tr1$tip.label))

collapse_range(com, tr1, n=1)

darunabas/phyloregion documentation built on Feb. 3, 2024, 8:59 p.m.