Changelog

Source: NEWS.md

SHARK4R (development version)

New features

• Add new functions: get_delivery_template() and find_required_fields() to get SHARK delivery templates and required fields from the web.
• Add new function get_shark_datasets() to retrieve available SHARK datasets from API.
• Add new function get_nomp_list() to download and read the latest NOMP biovolume Excel lists.
• Add new function get_peg_list() to download and read the PEG biovolume Excel list.
• Add new function read_ptbx() to read Plankton Toolbox files.
• Add new function get_shark_codes() to download and read the current SHARK code lists.
• Add new function clean_shark4r_cache() to clear cached files.
• Add new function check_setup() and run_qc_app() to download and run SHARK QC scripts and Shiny App.
• Add new function get_shark_statistics() to download SHARK data and extract summary statistics for numeric parameters.
• Add new function translate_shark_datatype() to translate user-facing datatype names to internal SHARK4R names.
• Add new function load_shark4r_stats() to download and load precomputed SHARK4R statistical datasets (e.g., threshold or summary statistics) from a GitHub repository.
• Add new function load_shark4r_fields() to download and load fields definitions from a GitHub repository.

Enhancements

• Re-export functions from the iRfcb package: which_basin() and positions_are_near_land().
• Cache downloaded DwCA files in get_dyntaxa_dwca(), get_shark_codes(), get_nomp_list() and get_peg_list() to avoid repeated downloads.
• Add unit tests for the majority of the package functions.
• Update and correct check_depth().
• Fix bugs in check_* functions.
• Fix various documentation issues.
• Updated several OBIS-dependent functions using lookup_xy().
• Updated scatterplot() function to allow plotting of multiple parameters.
• Added plot_leaflet argument to functions check_station_distance() and check_onland().
• match_worms_taxa() now handles bulk API requests using the bulk argument.
• Add SHARK4R Bio-QC Tool Shiny App to bundle, with improved performance (initialized by run_qc_app()).

Deprecated

• Deprecated functions: ifcb_is_near_land() and ifcb_which_basin() (replaced by re-exported functions with improved cache behavior)
• Deprecated functions: get_algaebase_species(), get_algaebase_genus() and match_algaebase() are now replaced by match_algaebase_species(), match_algaebase_genus() and match_algaebase_taxa().
• Deprecated functions: Parameter and datatype-specific check_*_*_logical() functions replaced by general functions check_parameter_rules and check_logical_parameter() function.
• Deprecated functions: Datatype-specific field check functions check_*() and check_*_deliv() replaced by a general check_fields() function.
• Deprecated functions: Parameter and datatype-specific check_*_*() functions to check for outliers replaced by a general check_outliers() function.
• Deprecated functions: shark_read_deliv() and shark_read_deliv_xls() are now replaced by read_shark_deliv().
• Deprecated functions: shark_read() and shark_read_zip() are now replaced by read_shark().
• Deprecated function: match_dyntaxa() is now replaced by is_in_dyntaxa().
• Deprecated function: plot_map_leaflet_deliv() is now replaced by plot_map_leaflet().
• Deprecated function: check_code_proj() is now replaced by check_codes().
• Deprecated function: match_taxon_name() is now replaced by match_dyntaxa_taxa().
• Deprecated function: get_worms_records_name() is now replaced by match_worms_taxa().
• Deprecated function: nominal_station() is now replaced by check_nominal_station().
• Deprecated function: match_wormstaxa() is now replaced by match_worms_taxa_interactive().
• Deprecated argument: apikey replaced by subscription_key in get_algaebase_genus(), get_algaebase_species() and match_algaebase()

Defunct / Removed

• Defunct function get_shark_table().

Documentation

• Add NEWS.md file.
• Add spell check.

SHARK4R 0.1.7

• Add option to specify row_limits in get_shark_data() to retrieve data in yearly chunks
• Add functions to call APIs to retrieve IOC HAB and IOC IPHAB Toxin lists: get_hab_list() and get_toxin_list()

SHARK4R 0.1.6

Patch release

• Fix issue #16
• Add unparsed output option for get_shark_option()

SHARK4R 0.1.5

Patch release

• Fix issues with construct_dyntaxa_table()
• Fix parsing issue in get_shark_data()
• Add more custom groups to assign_plankton_group()
• Add more flexibility to get_shark_data() parameters, e.g. boundary and year ranges

SHARK4R 0.1.4

• Add algaebase API functions
• Defunct sharkdata functions
• Fix parsing issue in shark_data when data are reported as “-”, which is now a NA pattern
• Cleanup of large files
• UTF-8 encoding

SHARK4R 0.1.3

• Minor bug-fixes and updated documentation

SHARK4R 0.1.2

• Patch release

SHARK4R 0.1.1

• Fix download of large datasets
• Add more WoRMS functionality, including plankton group assignment

SHARK4R 0.1.0

• Add SHARK API functionality
• Improve Dyntaxa API functionality
• Fix documentation issues

SHARK4R 0.0.1

• Initial development version.