High-Performance Open-Source Archive
calc_zooplankton_dry_weight() to calculate
zooplankton dry weight from "Length (mean)" using
AphiaID-based taxa-specific coefficients from
inst/extdata/Mesozooplankton_Kattegat_Skagerrak_taxa_and_biomass_calculations.xlsx.
The function uses adult coefficients for non-NP stages,
taxon-specific nauplii coefficients where available, and otherwise falls
back to the general copepod nauplii coefficients.calc_zooplankton_biomass() to calculate
zooplankton biomass concentration (mg/m3) from
"Abundance" and integrated biomass (mg/m2)
from "Integrated abundance" by combining abundance with
per-individual dry weight on the SHARK observation key
(platform_code, station_name,
sample_date, sample_time,
sample_min_depth_m, sample_max_depth_m,
aphia_id, sex_code,
dev_stage_code, size_class). If dry-weight
rows are not present, they are calculated internally via
calc_zooplankton_dry_weight().create_pie_map(), a general-purpose pie chart map
for station data with automatic pie displacement and leader lines to
prevent overlap in crowded regions. Works with any grouping
(phytoplankton groups, zooplankton orders, microbial phyla, …) and any
numeric value (biomass, biovolume, abundance, …). The optional default
coastline basemap uses rnaturalearth (Suggests);
HTML-formatted legend labels use ggtext (Suggests).shark-qc Shiny app has been rebuilt on
bslib (Bootstrap 5) for a modernized UI, with improved
server-side error handling so transient failures surface as user-facing
notifications instead of crashing the session.get_toxin_list() gains an insecure
argument (default FALSE) to handle periods when the
IOC-UNESCO Toxins Database TLS certificate has lapsed. When a
certificate error is encountered, an interactive session prompts before
retrying without verification, while a non-interactive session aborts
with guidance to set insecure = TRUE. Disabling
verification emits a warning, as it removes protection against
tampering.stop(), warning(), message(),
cat(), txtProgressBar) to the cli
package. Errors use cli_abort(), warnings use
cli_warn(), and informational messages use
cli_inform(), all with structured bullet lists and inline
markup for arguments, values, file paths, and function names. Progress
bars in long-running API functions are replaced with
cli_progress_bar().R/zzz.R are now
bundled as inst/extdata/threshold_values.csv and loaded at
runtime, removing several package-level global variables.tempdir() during R CMD check, extending the
cache_dir() redirect to the remaining call sites in
R/util.R.R/defunct.R and updated their documentation
accordingly.actions/checkout@v6,
actions/upload-artifact@v7,
codecov/codecov-action@v6, and
JamesIves/github-pages-deploy-action@v4.8.0.try()-protected execution chunks, so
transient server errors (502, 503, 500) never cause vignette rebuild
failures. The user-facing code shown on pkgdown remains clean and
uncluttered.skip_if_offline() and
skip_if_resource_unavailable() guards to previously
unprotected tests for deprecated WoRMS wrappers
(match_wormstaxa, update_worms_taxonomy) and
the empty/NA input edge case
(match_worms_taxa(c("", NA))).skip_on_cran() to deprecated WoRMS wrapper tests,
since the base-URL availability check can pass while individual API
endpoints return server errors.skip_if_offline() to the
"wrong url fails" test in
test-xylookup.R.get_nua_media_metadata() to retrieve detailed
metadata for media items from Nordic Microalgaeget_nua_image_labeling_links() to retrieve media
URLs for automated imaging images (e.g., IFCB) from Nordic
Microalgaeget_nua_image_labeling_metadata() to retrieve
detailed metadata for automated imaging images from Nordic
Microalgaeload_shark4r_fields() now downloads field definitions
as a binary .rds file instead of sourcing a remote R
script, eliminating a remote code execution risk.get_shark_data() now validates that
file_path does not contain .. path components,
preventing path traversal when used in downstream applications.get_shark_datasets() now sanitizes dataset names from
the API with basename() before writing to disk.match_algaebase_taxa(). The join between API results and
input data used left_join(by = c("genus", "species")),
which silently dropped results when AlgaeBase returned a reclassified
genus (e.g., querying “Chlorella” but API returns “Auxenochlorella”).
(Part of #47)match_algaebase_genus() returning unrelated
genera when exact_matches_only = TRUE. A variable shadowing
bug inside tibble() caused the input_match
column to always equal 1, making the exact match filter ineffective. For
example, querying “Nitzschia” returned 7 genera (Cymbellonitzschia,
Pseudo-nitzschia, etc.) instead of just Nitzschia. (Part of #47)match_algaebase_species(). When higher taxonomy was
requested, genus = genus_taxonomy$genus was included in the
taxonomy tibble, which could overwrite the species-level genus value.
(Part of #47)match_algaebase_taxa() for
species-level queries. Previously, when a species was not found in
AlgaeBase, the function fell back to a genus-level query. This produced
misleading results where a species record linked to an unrelated genus
page. Species queries that fail now return NA instead. (Part of
#47)get_dyntaxa_records() silently returning a
character string on API error instead of raising a condition with
stop().get_shark_data() silently dropping
municipalities, waterCategories, and
typOmraden parameters when computing the pre-download row
count, which could bypass the chunked download path.nrow(genus > 0) to
nrow(genus) > 0 in
construct_dyntaxa_missing_table().1:length() and 1:nrow()
loops with seq_along() and seq_len() in
construct_dyntaxa_missing_table() and
construct_dyntaxa_table() to prevent errors on zero-length
input.message("ERROR: ...") calls with
warning() in check_value_logical(),
check_zero_value(), check_zero_positions(),
check_codes(), and read_shark_deliv() so
conditions can be caught programmatically with
tryCatch().cachefile assignment in
cache_call() and dead list.files() call in
list_cache().cache_dir()
helper, which redirects to tempdir() during R CMD check.
Previously several functions called tools::R_user_dir()
directly, which could create ~/.cache/R/SHARK4R during CRAN
checks.clean_shark4r_cache()
where search_pattern = NULL (the default) could cause an
error.1.0.0).get_hab_list() documentation.get_hab_list() updated to wrap inline text with
I() in readr::read_delim() for
readr ≥ 2.2.0 compatibility and to remove deprecation
warnings.https://api.obis.org/) which could
return 200 while the /xylookup endpoint itself returned
500.\donttest{} examples that call external APIs are
now wrapped with try() so that transient service outages do
not cause R CMD check --run-donttest failures.quality_control vignette now wraps OBIS-dependent
calls (check_onland(), check_depth()) in
tryCatch() so the vignette builds even when the API is
unavailable.harmful_non_toxic_only argument to
get_hab_list() to download only non-toxigenic harmful
microalgal species from the IOC-UNESCO HABs listspecies_only argument to
get_hab_list() to return only species-level records, which
is now also the default option. This filter is ignored when
harmful_non_toxic_only = TRUEverbose argument to
positions_are_near_land() and
get_hab_list(harmful_non_toxic_only = TRUE) to enable
printing of progress messages during data retrievalpositions_are_near_land(), replacing direct file server
downloads that were unstableSHARK4R:::.type_lookup now includes the missing
datatype Jellyfish (#39)extract_complete_toxins() and
repair_toxins_json()README.mdlon and lat arguments to the
lookup_xy() function for more flexible lookup optionsget_toxin_list() now handles partial JSON
responsesget_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
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