R: Get all the trees associated with a particular study

get_study {rotl} | R Documentation

## 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, ...)

### 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.

### Value

if `file_format` is missing, an object of class `phylo` or `nexml`, otherwise a logical indicating whether the file was successfully created.

### See Also

`get_study_meta`

### Examples

    ## Not run:
    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"))
    }

    ## End(Not run)

[Package rotl version 3.0.4 Index]