Collapse nodes and ranges based on divergence times — collapse

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.

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)
#> $collapsed_com
#>    grids species
#> 1     g1       a
#> 4     g1       d
#> 6     g3       a
#> 8     g3       d
#> 9     g4       a
#> 12    g4       d
#> 13    g4       e
#> 16    g5       e
#> 18    g6       d
#> 2     g1       b
#> 5     g2       b
#> 7     g3       b
#> 10    g4       b
#> 14    g5       b
#> 17    g6       b
#> 
#> $original_com
#>    grids species
#> 1     g1       a
#> 2     g1       b
#> 3     g1       c
#> 4     g1       d
#> 5     g2       c
#> 6     g3       a
#> 7     g3       c
#> 8     g3       d
#> 9     g4       a
#> 10    g4       b
#> 11    g4       c
#> 12    g4       d
#> 13    g4       e
#> 14    g5       b
#> 15    g5       c
#> 16    g5       e
#> 17    g6       c
#> 18    g6       d
#>