set_safe_dir: Set the local SAFE data directory

Description Usage Arguments Details Examples

View source: R/index.R

Description

This function sets the local directory used to store SAFE dataset files along with record and index metadata. The function can also initialise a new data directory, downloading the required index files. By default, it will update indices if needed and will validate the directory contents. Once set, the location of the directory is stored in options('safedata.dir').

Usage

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set_safe_dir(safedir, update = TRUE, create = FALSE, validate = TRUE)

Arguments

safedir

A path to the directory to set as the SAFE data directory (str).

update

Should the local dataset index be updated (logical)?

create

Should a new data directory be created at the provided path (logical)?

validate

Should the directory structure be validated (logical)?

Details

The safedata package uses a data directory to store local copies of dataset files along with index files. Files for a dataset record are stored in subdirectories using the zenodo concept id for the record and then record id: 3342494/3342495, for example. In addition to data files from these records, these folders can also contain a JSON file containing record metadata (e.g. 3342495.json): this is a structured version of the summary information shown on the Zenodo page.

The root of the data directory also holds three index files:

index.json

, containing a full list of the files and dataset records available in the SAFE data repository;

gazetteer.geojson

, containing the official list of known sampling locations and GIS data; and

location_aliases.csv

, a list of alternative names permitted for some locations.

If create=TRUE, the function will try to create the named directory and populate it with the three index files. This requires an internet connection.

By default, the function also needs an internet connection to check for updates to the three index files. Updating can be turned off for offline use.

The default behaviour is also to validate the directory structure. The function will warn when files other than those found in datasets are present within the data structure and when any dataset files that are present have been modified. Although this can be turned off, it is not recommended to modify or add files within a SAFE data directory.

Examples

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   safedir <- system.file('example_data_dir', package='safedata')
   set_safe_dir(safedir, update=FALSE, validate=FALSE)

ImperialCollegeLondon/safe_data documentation built on Oct. 8, 2019, 4:27 p.m.