rotl: get_study_subtree – R documentation

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rotl

get_study_subtree

Study Subtree

Description

Retrieve subtree from a specific tree in the Open Tree of Life data store

Usage

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

Arguments

`study_id`	the study identifier (character)
`tree_id`	the tree identifier (character)
`subtree_id,`	either a node id that specifies a subtree or “ingroup” which returns the ingroup for this subtree.
`object_format`	the class of the object returned by the function (default, and currently only possibility `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`	character, the file format to use to save the results of the query (possible values, ‘newick’ or ‘nexus’).
`file`	character, the path and file name where the output should be written.
`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).

Examples

## Not run: 
small_tr <- get_study_subtree(study_id="pg_1144", tree_id="tree5800", subtree_id="node991044")
ingroup  <- get_study_subtree(study_id="pg_1144", tree_id="tree5800", subtree_id="ingroup")
nexus_file <- tempfile(fileext=".nex")
get_study_subtree(study_id="pg_1144", tree_id="tree5800", subtree_id="ingroup", file=nexus_file,
                  file_format="nexus")

## 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_subtree

Description

Usage

Arguments

Examples

rotl

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