Changelog

Source: NEWS.md

SHARK4R 1.0.2

CRAN release: 2025-12-12

Bug fixes

• SHARK4R:::.type_lookup now includes the missing datatype Jellyfish (#39)
• Enhanced documentation and example execution in vignettes - updated examples to run correctly and improved clarity in vignettes and help files
• HTML widgets and interactive objects are now displayed only in pkgdown articles; they are suppressed in CRAN vignettes to reduce size and improve build safety
• Added tests for helper functions – covering extract_complete_toxins() and repair_toxins_json()
• Cache is now cleared after R CMD check

SHARK4R 1.0.1

CRAN release: 2025-12-09

Bug fixes and CRAN compliance

• Corrected formatting of package and software names throughout the package.
• Fixed broken URL in README.md.
• Improved examples to run reliably and quickly.
• Ensured functions and examples no longer write to the user’s home directory.
• Added lon and lat arguments to the lookup_xy() function for more flexible lookup options.
• Minor documentation improvements throughout the package.
• get_toxin_list() now handles partial JSON responses.

SHARK4R 1.0.0

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
• Add new function get_worms_classification() to retrieve higher taxonomic information from WoRMS records
• Add new function get_worms_taxonomy_tree() to retrieve and constructs a hierarchical taxonomy tree from WoRMS records
• Add new function convert_ddmm_to_dd() to convert coordinates from DDMM format to decimal degrees

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
• Updated match_worms_taxa() function to clean taxon names from problematic special characters before being passed to API call
• Added plot_leaflet argument to functions check_station_distance() and check_onland()
• Added utv argument to functions get_shark_options(), get_shark_data(), get_shark_datasets() and get_shark_table_counts().
• Added add_rank_to_hierarchy argument to the add_worms_taxonomy() function
• 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()
• Deprecated argument: apikey replaced by subscription_key in get_algaebase_genus(), get_algaebase_species() and match_algaebase()
• Deprecated argument: aphia_id replaced by aphia_ids in get_worms_records() and add_worms_taxonomy()
• Deprecated argument: scientific_name replaced by scientific_names in add_worms_taxonomy() and parse_scientific_names()
• Deprecated argument: genus replaced by genera in match_algaebase_taxa()

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.