get_ott_children: Use this instead of 'rotl::tol_subtree()' when taxa are not...

In datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

Use this instead of rotl::tol_subtree() when taxa are not in synthesis tree and you still need to get all species or an induced OpenTree subtree

Description

Use this instead of rotl::tol_subtree() when taxa are not in synthesis tree and you still need to get all species or an induced OpenTree subtree

Usage

get_ott_children(input = NULL, ott_ids = NULL, ott_rank = "species", ...)

Arguments

input	Optional. A character vector of names or a datelifeQuery object.
ott_ids	If not NULL, it takes this argument and ignores input. A numeric vector of ott ids obtained with rotl::taxonomy_taxon_info() or rotl::tnrs_match_names() or tnrs_match().
ott_rank	A character vector with the ranks you wanna get lineage children from.
...	Other arguments to pass to get_valid_children().

Value

A data.frame object.

Examples

# An example with the dog genus:

# It is currently not possible to get an OpenTree subtree of a taxon that is
#  missing from the OpenTree synthetic tree.
# The dog genus is not monophyletic in the OpenTree synthetic tree, so in
#  practice, it has no node to extract a subtree from.
tnrs <- tnrs_match("Canis")

## Not run:  # This is a flag for package development. You are welcome to run the example.
rotl::tol_subtree(tnrs$ott_id[1])
#> Error: HTTP failure: 400
#> [/v3/tree_of_life/subtree] Error: node_id was not found (broken taxon).


## End(Not run) # end dontrun

ids <- tnrs$ott_id[1]
names(ids) <- tnrs$unique_name
children <- get_ott_children(ott_ids = ids) # or
children <- get_ott_children(input = "Canis")
if (!is.na(children)) {
str(children)
ids <- children$Canis$ott_id
names(ids) <- rownames(children$Canis)
tree_children <- datelife::get_otol_synthetic_tree(ott_ids = ids)
plot(tree_children, cex = 0.3)
}

# An example with flowering plants:

## Not run:  # This is a flag for package development. You are welcome to run the example.

oo <- get_ott_children(input = "magnoliophyta", ott_rank = "order")
# Get the number of orders of flowering plants that we have
sum(oo$Magnoliophyta$rank == "order")


## End(Not run) # end dontrun

datelife documentation built on July 10, 2023, 2:02 a.m.