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EDGE2 calculating function.

Source: R/EDGE2.R
calculate_EDGE2.Rd

EDGE2 calculating function.

Usage

calculate_EDGE2(
  tree,
  table,
  verbose = TRUE,
  sort.list = FALSE,
  return.all = FALSE
)

Arguments

tree

a phylo object.

table

a tibble or data frame with two columns, named "species" and "RL.cat"

verbose

Logical. Should progress be printed or not.

sort.list

Logical. If TRUE, the EDGE list will be sorted from higher to lower values.

return.all

Logical. If TRUE, an EDGE list, tree and ePDloss list is returned. If FALSE (default), only the list is returned.

Value

A list containing 3 slots if `return.all` is TRUE. If not, only the first item (EDGE list) will be returned.

  • list: will output specific TBL (terminal branch length), pext (sampled probability of extinction), ED (evolutionary distinctiveness), and EDGE (EDGE index).

  • tree: the input tree.

  • ePDloss: complete PD (phylogenetic diversity) and ePDloss (expected PD loss). Units are as in the input tree (generally Million years).

References

Gumbs, R., Gray, C. L., Böhm, M., Burfield, I. J., Couchman, O. R., Faith, D. P., Forest, F., Hoffmann, M., #' Isaac, N. J. B., Jetz, W., Mace, G. M., Mooers, A. O., Safi, K., Scott, O., Steel, M., Tucker, C. M., Pearse, W. D., Owen, N. R. & Rosindell, J. (2023). The EDGE2 protocol: Advancing the prioritisation of Evolutionarily Distinct and Globally Endangered species for practical conservation action. PLoS Biology, 21(2), e3001991. https://doi.org/10.1371/journal.pbio.3001991

Author

I. Ramos-Gutiérrez, R. Gumbs