R: Study Tree

get_study_tree {rotl} | R Documentation

## 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)

[Package rotl version 3.0.5 Index]