Title: Data Source Catalogues Online for Southern Ocean Ecosystem Research
Version: 0.6.1
Description: Obtains lists of files of remote sensing collections for Southern Ocean surface properties. Commonly used data sources of sea surface temperature, sea ice concentration, and altimetry products such as sea surface height and sea surface currents are cached in object storage on the Pawsey Supercomputing Research Centre facility. Patterns of working to retrieve data from these object storage catalogues are described. The catalogues include complete collections of datasets Reynolds et al. (2008) "NOAA Optimum Interpolation Sea Surface Temperature (OISST) Analysis, Version 2.1" <doi:10.7289/V5SQ8XB5>, Spreen et al. (2008) "Artist Advanced Microwave Scanning Radiometer for Earth Observing System (AMSR-E) sea ice concentration" <doi:10.1029/2005JC003384>. In future releases helpers will be added to identify particular data collections and target specific dates for earth observation data for reading, as well as helpers to retrieve data set citation and provenance details. This work was supported by resources provided by the Pawsey Supercomputing Research Centre with funding from the Australian Government and the Government of Western Australia. This software was developed by the Integrated Digital East Antarctica program of the Australian Antarctic Division.
License: MIT + file LICENSE
Encoding: UTF-8
Language: en-US
RoxygenNote: 7.3.3
Imports: arrow, curl, S7, tibble
URL: https://github.com/mdsumner/sooty
BugReports: https://github.com/mdsumner/sooty/issues
Suggests: spelling, testthat (≥ 3.0.0), withr
Config/testthat/edition: 3
Depends: R (≥ 2.10)
NeedsCompilation: no
Packaged: 2026-03-10 01:48:47 UTC; mdsumner
Author: Michael D. Sumner [aut, cre], Aleks Terauds [cph, ctb] (Provided logo photo from p116 of 'Subantarctic wilderness: Macquarie Island, 2007(978-1741753028)')
Maintainer: Michael D. Sumner <michael.sumner@aad.gov.au>
Repository: CRAN
Date/Publication: 2026-03-10 06:10:08 UTC

List available datasets

Description

In sooty_files() the data source files are grouped by Dataset, this is the list of unique datasets, values that can be used in datasource(id).

Usage

available_datasets()

Value

character vector of available dataset ids for datasource()

Examples

op <- options("sooty.allow.cache" = FALSE)
available_datasets()
options(op)

Create a datasource object. A data source provides a list of files that together comprise a dataset.

Description

Generates an object whose ⁠@id⁠ property may be set, which then communicates with a dataset of files/objects that sooty knows about.

Usage

datasource(id = NA_character_)

dataset(...)

Arguments

id

a dataset label, see available_datasets()

...

only used by deprecated function, will become defunct

Details

The following properties are available via the @ slot:

By default sooty maintains a local cache of the catalogue used to populate these properties. Set options("sooty.allow.cache" = FALSE) to use only the bundled sysdata, or options("sooty.cache.path" = tempdir()) to redirect the cache directory. See sooty_cache_info() for details.

Note

This was originally called dataset() which usage has now been deprecated.

Examples

op <- options("sooty.allow.cache" = FALSE)
## available dataset names
available_datasets()
## set to one of those
ds <- datasource("ghrsst-tif")
options(op)

Show sooty cache status

Description

Reports the active cache configuration, including the effect of any options that have been set. See the Options section below for details.

Usage

sooty_cache_info()

Value

A data frame (invisibly) with cache details.

Options

Two options control cache behaviour:

sooty.allow.cache

logical, default TRUE. Set to FALSE to skip all disk I/O and use only the bundled sysdata. Suitable for examples, tests, and offline use: options("sooty.allow.cache" = FALSE).

sooty.cache.path

path, default tools::R_user_dir("sooty", "cache"). Override the cache directory. Useful for CI or shared environments: options("sooty.cache.path" = tempdir()).

Examples

sooty_cache_info()

op <- options("sooty.allow.cache" = FALSE)
sooty_cache_info()
options(op)

Obtain object storage catalogues as a dataframe of file/object identifiers.

Description

The object (file) catalogue of available sources is stored in Parquet format on Pawsey object storage. This function retrieves the curated catalogue.

Usage

sooty_files(curated = TRUE)

Arguments

curated

logical TRUE by default, ignored with a warning if FALSE

Details

The returned curated data frame has columns 'date', 'source' which are the main useful fields, these describe the date of the data in the file, and its full URI (Uniform Resource Identifier) source on S3 object storage. There are also fields 'Bucket', 'Key', and 'Protocol' from which 'source' is constructed.

The original publisher URI can be reconstructed by replacing the value of 'Protocol' in 'source' with 'https://'.

The public object URI can be reconstructed by replacing the value of 'Protocol' in 'source' with 'https://projects.pawsey.org.au'.

By default sooty maintains a local cache of the catalogue, refreshed once per session when internet is available. Set options("sooty.allow.cache" = FALSE) to suppress all disk I/O and use only the bundled sysdata, or options("sooty.cache.path" = tempdir()) to redirect the cache directory. See sooty_cache_info() for details.

Value

a data frame, see details

Examples

op <- options("sooty.allow.cache" = FALSE)
sooty_files()
options(op)