collapse_range function

Collapse nodes and ranges based on divergence times

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

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.

Returns

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

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)

References

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

11 : 2115.