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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 rangesThese binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.