rotl: get_study_tree – R documentation

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Documentation

rotl

get_study_tree

Study Tree

Description

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

## Not run: 
 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)

## End(Not run)

rotl

Interface to the 'Open Tree of Life' API

v3.0.11

BSD_2_clause + file LICENSE

Authors

Francois Michonneau [aut, cre] (<https://orcid.org/0000-0002-9092-966X>), Joseph Brown [aut] (<https://orcid.org/0000-0002-3835-8062>), David Winter [aut] (<https://orcid.org/0000-0002-6165-0029>), Scott Chamberlain [rev] (<https://orcid.org/0000-0003-1444-9135>)

Initial release

get_study_tree

Description

Usage

Arguments

Value

Examples

rotl

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