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Load the Fern Tree of Life (FTOL)

ft_tree.Rd

For details on methods used to infer the tree, see Nitta et al. 2022.

Usage

ft_tree(
  branch_len = "ultra",
  consensus = TRUE,
  rooted = TRUE,
  backbone = FALSE,
  drop_og = FALSE,
  label_ages = FALSE,
  decimals = NULL
)

Arguments

branch_len

Character vector of length 1; how to treat branch lengths. Must choose from "ultra" (ultrametric tree, branchlengths in units of time), "raw" (raw branchlengths in units of genetic change), or "clado" (cladogram, no branchlengths). Default "ultra".

consensus

Logical vector of length 1; if TRUE, the majority-rule extended consensus phylogeny will be returned; otherwise returns the maximum-likelihood tree. Default TRUE.

rooted

Logical vector of length 1; if TRUE, the phylogeny will be rooted on bryophytes; otherwise the phylogeny is unrooted. Default TRUE.

backbone

Logical vector of length 1; if TRUE, the backbone phylogeny (only species with complete plastomes available) will be returned; otherwise the phylogeny will include all species. Default FALSE.

drop_og

Logical vector of length 1; if TRUE, the outgroup (non-ferns) will be excluded; otherwise the outgroup is included. Default FALSE.

label_ages

Logical vector of length 1; if TRUE, internal nodes will be labeled with ages. Only works if branch_len is "ultra". Default FALSE.

decimals

Numeric vector of length 1; number of decimals for rounding node labels if label_ages is TRUE; null (default) does no rounding.

Value

List of class "phylo"; a phylogenetic tree.

Details

Not all combinations are possible. For example, branch_len = "ultra" is only available if backbone = FALSE.

References

Nitta JH, Schuettpelz E, Ramírez-Barahona S, Iwasaki W. (2022) An open and continuously updated fern tree of life. https://doi.org/10.3389/fpls.2022.909768

Examples

# Default is the consensus tree with branchlengths in units of time
ft_tree()
#> 
#> Phylogenetic tree with 5868 tips and 5867 internal nodes.
#> 
#> Tip labels:
#>   Acrostichum_danaeifolium, Acrostichum_speciosum, Acrostichum_aureum, Ceratopteris_richardii, Ceratopteris_cornuta, Ceratopteris_pteridoides, ...
#> Node labels:
#>   100/100, 100/100, 100, 100/100, 100/100, 100/100, ...
#> 
#> Rooted; includes branch lengths.