rotl (version 3.1.0)

get_study: Get all the trees associated with a particular study

Description

Returns the trees associated with a given study

Usage

get_study(
  study_id = NULL,
  object_format = c("phylo", "nexml"),
  file_format,
  file,
  ...
)

Value

if file_format is missing, an object of class

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

Arguments

study_id

the study ID for the study of interest (character)

object_format

the class of the object the query should return (either phylo or nexml). Ignored if file_format is specified.

file_format

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

file

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

...

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

Details

If file_format is missing, the function returns an object of the class phylo from the ape package (default), or an object of the class nexml from the RNeXML package.

Otherwise file_format can be either newick, nexus, nexml or json, and the function will generate a file of the selected format. In this case, a file name needs to be provided using the argument file. If a file with the same name already exists, it will be silently overwritten.

See Also

get_study_meta

Examples

if (FALSE) {
that_one_study <- get_study(study_id="pg_719", object_format="phylo")
if (require(RNeXML)) { ## if RNeXML is installed get the object directly
   nexml_study <- get_study(study_id="pg_719", object_format="nexml")
} else { ## otherwise write it to a file
   get_study(study_id="pg_719", file_format="nexml", file=tempfile(fileext=".nexml"))
}
}