Study Tree

Returns a specific tree from within a study

Usage

get_study_tree(
  study_id = NULL,
  tree_id = NULL,
  object_format = c("phylo"),
  tip_label = c("original_label", "ott_id", "ott_taxon_name"),
  file_format,
  file,
  deduplicate = TRUE,
  ...
)

Arguments

study_id

the identifier of a study (character)

tree_id

the identifier of a tree within the study

object_format

the class of the object to be returned (default and currently only possible value phylo from the ape package).

tip_label

the format of the tip labels. “original_label” (default) returns the original labels as provided in the study, “ott_id” labels are replaced by their ott IDs, “ott_taxon_name” labels are replaced by their Open Tree Taxonomy taxon name.

file_format

the format of the file to be generated (newick default, nexus, or json).

file

the file name where the output of the function will be saved.

deduplicate

logical (default TRUE). If the tree returned by the study contains duplicated taxon names, should they be made unique? It is normally illegal for NEXUS/Newick tree strings to contain duplicated tip names. This is a workaround to circumvent this requirement. If TRUE, duplicated tip labels will be appended _1, _2, etc.

...

additional arguments to customize the API request (see rotl package documentation).

Value

if file_format is missing, an object of class

phylo, otherwise a logical indicating whether the file was successfully created.

Examples

if (FALSE) {
 tree <- get_study_tree(study_id="pg_1144", tree_id="tree2324")

 ## comparison of the first few tip labels depending on the options used
 head(get_study_tree(study_id="pg_1144", tree_id="tree2324", tip_label="original_label")$tip.label)
 head(get_study_tree(study_id="pg_1144", tree_id="tree2324", tip_label="ott_id")$tip.label)
 head(get_study_tree(study_id="pg_1144", tree_id="tree2324", tip_label="ott_taxon_name")$tip.label)
}