retrieve_data_files: Retrieve data files from the Github repository

Description Usage Arguments Value Examples

View source: R/retrieve_data_files.R

Description

This script downloads relevant data files from the TaxonSampling project repository. It will extract the data into a folder containing directories related multi-fasta files from where sequences should be sampled and metadata files (e.g., table linking NCBI taxon IDs to sequence IDs, etc.). If the 'target.dir' provided does not exist it is created (recursively) by the function.

Usage

1
2
3
4
5
6
retrieve_data_files(
  target.dir,
  method = "auto",
  unzip = getOption("unzip"),
  ...
)

Arguments

target.dir

path to the folder where the files will be saved ( accepts relative and absolute paths)

method

Method to be used for downloading files. Current download methods are "internal", "wininet" (Windows only) "libcurl", "wget" and "curl", and there is a value "auto": see _Details_ and _Note_ in the documentation of utils::download.file().

unzip

The unzip method to be used. See the documentation of utils::unzip() for details.

...

additional attributes (currently ignored)

Value

No return value, called for side effects (see Description).

Examples

1
2
3
4
## Not run: 
  TaxonSampling::retrieve_data_files(target.dir = "data_files/")

## End(Not run)

fcampelo/TaxonSampling documentation built on Jan. 14, 2022, 9:42 p.m.