Phylogeny of the species in GIFT

Retrieve a phylogeny of the plant species available in GIFT. The phylogeny table is not available for GIFT_version 1.0, 2.0, 2.1 and 2.2.

Usage

GIFT_phylogeny(
  clade = "Tracheophyta",
  as_tree = TRUE,
  return_work_ID = FALSE,
  work_ID_subset = NULL,
  api = "https://gift.uni-goettingen.de/api/extended/",
  GIFT_version = "latest"
)

Arguments

clade: Character string indicating the taxonomic group of interest corresponding to the node labels in the phylogeny.
as_tree: Logical, whether you want the phylogeny to be returned as a phylogenetic tree (TRUE) or in a table (FALSE). TRUE by default.
return_work_ID: Logical, whether you want to retrieve the species' names or their identification number (work_ID) in the GIFT database. FALSE by default.
work_ID_subset: A vector of work_ID to prune the phylogenetic tree. NULL by default.
api: character string defining from which API the data will be retrieved.
GIFT_version: character string defining the version of the GIFT database to use. The function retrieves by default the latest stable version. If set to beta, the most up-to-date version which is still subject to changes and edits is used.

Value

A data frame with 5 columns or a tree object.

Details

Here is what each column refers to:

taxon_label - Name of the taxonomic group
work_ID - Standardized species name IDs for the species at the tips of the tree
edge_length - Edge length
lft - Left border of a given taxon in the Newick sequence
rgt - Right border of a given taxon in the Newick sequence

References

 Denelle, P., Weigelt, P., & Kreft, H. (2023). GIFT—An R package to
 access the Global Inventory of Floras and Traits. Methods in Ecology
 and Evolution, 14, 2738-2748.
 https://doi.org/10.1111/2041-210X.14213

 Weigelt, P, König, C, Kreft, H. GIFT – A Global Inventory of Floras and
 Traits for macroecology and biogeography. J Biogeogr. 2020; 47: 16– 43.
 https://doi.org/10.1111/jbi.13623

Examples