SHARK4R:::.type_lookup now includes the missing
datatype Jellyfish (#39)extract_complete_toxins() and
repair_toxins_json()README.md.lon and lat arguments to the
lookup_xy() function for more flexible lookup options.get_toxin_list() now handles partial JSON
responses.get_delivery_template() and
find_required_fields() to get SHARK delivery templates and
required fields from the webget_shark_datasets() to retrieve
available SHARK datasets from APIget_nomp_list() to download and read
the latest NOMP biovolume Excel listsget_peg_list() to download and read
the PEG biovolume Excel listread_ptbx() to read Plankton Toolbox
filesget_shark_codes() to download and read
the current SHARK code listsclean_shark4r_cache() to clear cached
filescheck_setup() and
run_qc_app() to download and run SHARK QC scripts and Shiny
Appget_shark_statistics() to download
SHARK data and extract summary statistics for numeric parameterstranslate_shark_datatype() to
translate user-facing datatype names to internal SHARK4R namesload_shark4r_stats() to download and
load precomputed SHARK4R statistical datasets (e.g., threshold or
summary statistics) from a GitHub repositoryload_shark4r_fields() to download and
load fields definitions from a GitHub repositoryget_worms_classification() to retrieve
higher taxonomic information from WoRMS recordsget_worms_taxonomy_tree() to retrieve
and constructs a hierarchical taxonomy tree from WoRMS recordsconvert_ddmm_to_dd() to convert
coordinates from DDMM format to decimal degreesiRfcb package:
which_basin() and
positions_are_near_land()get_dyntaxa_dwca(),
get_shark_codes(), get_nomp_list() and
get_peg_list() to avoid repeated downloadscheck_depth()lookup_xy()scatterplot() function to allow plotting of
multiple parametersmatch_worms_taxa() function to clean taxon
names from problematic special characters before being passed to API
callplot_leaflet argument to functions
check_station_distance() and
check_onland()utv argument to functions
get_shark_options(), get_shark_data(),
get_shark_datasets() and
get_shark_table_counts().add_rank_to_hierarchy argument to the
add_worms_taxonomy() functionmatch_worms_taxa() now handles bulk API requests using
the bulk argumentrun_qc_app())ifcb_is_near_land() and
ifcb_which_basin() (replaced by re-exported functions with
improved cache behavior)get_algaebase_species(),
get_algaebase_genus() and match_algaebase()
are now replaced by match_algaebase_species(),
match_algaebase_genus() and
match_algaebase_taxa()check_*_*_logical() functions replaced by general functions
check_parameter_rules and
check_logical_parameter() functioncheck_*() and check_*_deliv() replaced by a
general check_fields() functioncheck_*_*() functions to check for outliers replaced by a
general check_outliers() functionshark_read_deliv() and
shark_read_deliv_xls() are now replaced by
read_shark_deliv()shark_read() and
shark_read_zip() are now replaced by
read_shark()match_dyntaxa() is now replaced by
is_in_dyntaxa()plot_map_leaflet_deliv() is now
replaced by plot_map_leaflet()check_code_proj() is now replaced
by check_codes()match_taxon_name() is now replaced
by match_dyntaxa_taxa()get_worms_records_name() is now
replaced by match_worms_taxa()nominal_station() is now replaced
by check_nominal_station()match_wormstaxa() is now replaced
by match_worms_taxa()apikey replaced by
subscription_key in get_algaebase_genus(),
get_algaebase_species() and
match_algaebase()aphia_id replaced by
aphia_ids in get_worms_records() and
add_worms_taxonomy()scientific_name replaced by
scientific_names in add_worms_taxonomy() and
parse_scientific_names()genus replaced by
genera in match_algaebase_taxa()get_shark_table()NEWS.md filerow_limits in
get_shark_data() to retrieve data in yearly chunksget_hab_list() and
get_toxin_list()Patch release
get_shark_option()Patch release
construct_dyntaxa_table()get_shark_data()assign_plankton_group()get_shark_data() parameters,
e.g. boundary and year ranges