tax_bioshifts_pq() attaches, for each taxon of a phyloseq object, a summary of documented range-shift rates from the current BioShifts release (the original BioShifts merged with the CoRE database, Comte et al. 2024) via BioShiftR::get_shifts(), adding mean latitudinal (bioshift_LAT_rate) and elevational (bioshift_ELE_rate) shift rates plus a bioshift_n_records count. Taxa are matched on the taxonomic_rank column(s) of the tax_table; by default the BioShifts names are harmonised with gna_verifier_pq() and the join is made on currentCanonicalSimple (disable with skip_name_verification = TRUE). A pre-fetched table can be supplied via shifts_data to skip the network query.
tax_faprotax_pq() annotates the taxa of a phyloseq object with the ecological/metabolic functional groups of the FAPROTAX database (Louca et al. 2016), matching every group's *level*level* patterns (including the add_group / subtract_group composites) against the taxonomic lineage; it adds a faprotax_groups summary column (and, with binary = TRUE, one 0/1 column per group). The FAPROTAX database is bundled in inst/extdata/FAPROTAX.txt. Its output was validated to be identical, per OTU and per functional group, to the official FAPROTAX Python tool (collapse_table.py) on phyloseq::GlobalPatterns (19216 taxa) and on a GTDB archaeal dataset (541 taxa). A valid_word_symbols argument (default "-") reproduces FAPROTAX's word-boundary rules, so _ acts as a boundary (e.g. *Methanobacterium* matches the GTDB name Methanobacterium_B).
tax_harmonize_backbone_pq() re-derives the higher taxonomic ranks (those above a chosen anchor rank, or above each taxon's deepest assigned rank with anchor = "last_assigned") from a single trusted backbone (GBIF online via rgbif::name_backbone_checklist() or a local backbone data frame), making taxonomies from different reference databases comparable; it harmonises several databases at once through suffix-based tracks (e.g. suffixes = c("", "_Euk")), gates online matches on matchType/confidence, disambiguates homonyms with kingdom, optionally recovers ambiguous names that GBIF backs off to a higher rank via the verbose rgbif::name_backbone() alternatives (resolve_ambiguous = TRUE, e.g. placing a bare Boletus in Boletaceae), and optionally keeps the overwritten values in _orig companion columns.
tax_metatraits_pq() augments the tax_table with harmonised microbial phenotypic traits from the metaTraits resource (Robbani et al. 2026, https://metatraits.embl.de). It matches GTDB names given by the taxonomic_rank column(s) (species-first, with genus fallback), downloads and caches the large summary tables once in tools::R_user_dir("taxinfo", "cache"), and supports filtering by traits, groups (metaTraits group_1 category) and min_consensus_percentage.
tax_spores_volume_pq() annotates the taxa of a phyloseq object with fungal spore volume and morphology (length, width, projected area and length/width ratio) from the spore-trait database of Aguilar-Trigueros et al. (2023), redistributed by the q2-fungal-traits plugin and bundled in inst/extdata/Spore_data_12Nov21.tsv. For each spore type (Mitospores, Meiospores, Multinucleate sexual spores, Multinucleate asexual spores) it matches taxa hierarchically (species binomial, then genus, then family, with genus/family values the geometric mean of the database entries) and records the matched rank in a *_matching_level column, restricting matches to fungal taxa. Species-, genus- and family-level matches were cross-checked against a recomputation of the geometric-mean matching logic on the bundled database.
tax_faprotax_pq() now stores the per-group binary = TRUE columns as logical TRUE/FALSE/NA instead of integer 0/1. Taxa that matched no FAPROTAX group (faprotax_groups is NA) receive NA (not found in the database) rather than 0/FALSE (a real "definitely not in this group"); faprotax_n_groups is likewise NA for those taxa.The phyloseq-augmenting functions gna_verifier_pq(), tax_gbif_occur_pq(), tax_get_wk_info_pq(), tax_globi_pq(), tax_iucn_code_pq(), tax_oa_pq(), tax_occur_check_pq() and tax_photos_pq() now build the tax_table join key with the same "NA"-token cleanup used to query the external database, fixing silently dropped information for genus-only taxa when taxonomic_rank spans several columns (e.g. c("Genus", "Species")).
tax_gbif_occur_pq() and tax_iucn_code_pq() now join GBIF results to the tax_table on the submitted query name rather than GBIF's resolved canonicalName, so occurrence counts and IUCN codes are no longer silently dropped when GBIF maps a name to a different canonical (e.g. a synonym).
gna_verifier_pq() gains a max_age_days parameter (default 365) and reports an informative message when a selected data_sources entry was last updated more than that many days ago; its data_sources documentation now explains how to adapt the source to the downstream database (e.g. data_sources = 11, the GBIF Backbone, before the GBIF-based functions).
tax_ecoregion_occur_pq() now disambiguates colliding tax_table column names by prefixing them, consistent with the other tax_*_pq() functions, instead of overwriting the existing columns.
The GBIF occurrence functions (tax_gbif_occur_coords(), tax_occur_check(), tax_occur_check_pq(), tax_occur_multi_check_pq()) now default to GBIF's Download API (method = "download"), which requires GBIF credentials (GBIF_USER, GBIF_PWD, GBIF_EMAIL in your .Renviron). The previous rgbif::occ_search() behaviour is still available with method = "search" (no credentials, capped at 100,000 records). See https://docs.ropensci.org/rgbif/articles/gbif_credentials.html.
tax_occur_check() (and its *_pq() wrappers) now report the true worldwide georeferenced count in total_count_in_world for taxa with no occurrence in the search radius, where the previous behaviour returned 0.
The WWF/TNC ecoregion layer downloaded on first use by the ecoregion functions (points_to_ecoregions(), tax_check_ecoregion(), tax_ecoregion_occur()) is now written to a stable per-user cache directory (tools::R_user_dir("taxinfo", "cache")) instead of an inst/extdata/downloads folder created under the current working directory.
gna_verifier_pq() removes the stats and main_taxon_threshold parameters. These only affected kingdom-level summary metadata (not per-name results), and main_taxon_threshold was never forwarded to the API by taxize::gna_verifier() anyway.
gna_verifier_pq() gains a problematic_chars parameter (default "[?\\\\#|&]") to detect taxonomic names containing characters that corrupt the GNA Verifier GET URL (?, \, #, |, &), and a clean_problematic_chars parameter (default FALSE). When problematic names are found, a warning reports their count and examples; set clean_problematic_chars = TRUE to replace matching cells with NA before verification, or clean the data upstream (e.g. with MiscMetabar::simplify_taxo()).
gna_verifier_pq() gains a force_recompute parameter (default FALSE). When TRUE, existing result columns matching col_prefix are removed from the tax_table before re-adding them, avoiding duplicate-column errors on re-runs.
select_taxa_pq() aborts with an explicit message naming the requested taxnames when none of them match the tax_table, instead of failing with an obscure OTU abundance data must have non-zero dimensions error; taxa_summary_text() inherits the same clear behaviour.
New function tax_crosscheck_gbif_pq() compares name-verification results from GNA Verifier (taxize::gna_verifier() with data_sources = 11, i.e. GBIF Backbone Taxonomy) and rgbif::name_backbone_checklist(). Returns a per-taxon comparison with status labels (match, mismatch, gna_only, backbone_only, both_na), a summary count vector, and an optional Venn diagram via ggVennDiagram. Discrepancies between the two services highlight taxa that may need manual review.
tax_ecoregion_occur() gains a method argument (forwarded to tax_gbif_occur_coords()) and keeps the credential-free rgbif::occ_search() path as its default, so ecoregion profiling and its wrappers (tax_ecoregion_occur_pq(), tax_check_ecoregion()) do not require GBIF credentials.
tax_gbif_occur_coords() gains a method argument ("download", "download_sql", "search") and server-side filter arguments (country, year_gte, year_lte, geometry). The default "download" collapses the former per-taxon rgbif::occ_search() loop into a single, citable rgbif::occ_download() request and correctly retains infraspecific and higher-rank records.
tax_occur_check() gains a method argument ("download", "search"); with method = "download" it issues a single rgbif::occ_download() constrained to the search bounding box instead of rgbif::occ_search().
tax_occur_check_pq() and tax_occur_multi_check_pq() now issue a single GBIF download for all taxa (and, for tax_occur_multi_check_pq(), all GPS points) when method = "download", instead of one rgbif::occ_search() call per taxon per point, and expose method, circle_form, clean_coord and n_occur arguments.
theme_idest() falls back to the graphics-device default font when a requested font family (Roboto Condensed, Linux Libertine G, Fira Code) is not installed, instead of failing with invalid font type when the plot is printed (for example during R CMD check examples or a pkgdown render).
range_bioreg_pq() and tax_check_ecoregion() now call gbif.range::read_ecoreg() and gbif.range::check_and_get_ecoreg() instead of the removed read_bioreg() / check_and_get_bioreg().theme_idest(): when x_is_species_name = TRUE or y_is_species_name = TRUE is set, a message now indicates which axis will receive italic labels. This helps users catch the common mistake of passing x_is_species_name = TRUE when species names are on the y-axis (e.g. horizontal bar charts with aes(x = n, y = sp)), which previously caused ggplot2 to silently misinterpret the continuous x-axis as discrete and break the chart.tax_check_ecoregion() no longer takes taxa_name as its first argument. The new signature follows the package-wide physeq = NULL, taxnames = NULL, taxonomic_rank pattern. Single-species positional calls like tax_check_ecoregion("Sp.", lon, lat) must become tax_check_ecoregion(taxnames = "Sp.", longitudes = lon, latitudes = lat). The return shape also changes: is_in_ecoregion is always a n_taxa × n_points logical matrix, and the full long tibble of (taxon × ecoregion) counts is available in the new taxon_ecoregions element.add_to_phyloseq parameter now defaults to TRUE when a phyloseq object is provided, and FALSE when using the taxnames parameter. This makes the workflow more intuitive - when working with phyloseq objects, the enriched object is returned by default.Add points_to_ecoregions() to locate a set of GPS points in the WWF/TNC terrestrial ecoregion layer. Returns a tibble with ECO_NAME, biome and realm columns; used internally by tax_check_ecoregion().
tax_check_ecoregion() has been rewritten as a thin comparison wrapper on top of the new tax_ecoregion_occur() and points_to_ecoregions() functions. It now supports a vector of taxa (via taxnames) or a phyloseq object (via physeq + taxonomic_rank), always returns a n_taxa × n_points logical matrix in is_in_ecoregion, and caches the WWF/TNC shapefile across calls instead of re-downloading it through gbif.range::check_and_get_ecoreg() each time. The shapefile is read via sf::st_join() (boundary-safe) instead of sf::st_intersection().
Add tax_ecoregion_occur() to return a long tibble of taxon_name × ECO_NAME × n_occur × prop_occur from GBIF occurrences, with min_nb_occur / min_proportion filters. Zero-occurrence taxa are kept with n_occur = 0L so downstream joins do not silently drop them.
Add tax_ecoregion_occur_pq() as the phyloseq wrapper for tax_ecoregion_occur(). When add_to_phyloseq = TRUE, three columns are added to @tax_table: ecoregion_top (modal ecoregion), ecoregion_n (number of qualifying ecoregions) and ecoregion_list (semicolon-separated, ordered by descending occurrence count).
Add tax_gbif_occur_coords() to fetch georeferenced GBIF occurrences for a vector of taxa (capped by n_occur). Taxa with zero valid occurrences are listed in attr(result, "missing_taxa").
tax_photos_pq() now works correctly with gallery = TRUE regardless of the add_to_phyloseq value: when add_to_phyloseq = TRUE the gallery is printed as a side-effect and the updated phyloseq object is returned invisibly. The pixture package dependency has been removed; the gallery is now built with htmltools (available on CRAN). Two new parameters img_height and img_width replace the previous h/w arguments passed via ... to pixture::pixgallery().
Add fungal_traits_guilds() to enrich a phyloseq tax_table with guild and trait information from both the FungalTraits and FUNGuild databases in a single call. The function automatically calls [gna_verifier_pq()] when currentCanonicalSimple is absent, and optionally produces consensus columns (cons_trophicMode, cons_trophicMode_agreement) comparing the two sources.
All main functions (gna_verifier_pq(), tax_gbif_occur_pq(), tax_get_wk_info_pq(), tax_globi_pq(), tax_info_pq(), tax_iucn_code_pq(), tax_oa_pq(), tax_occur_check_pq(), tax_photos_pq()) now support the taxnames parameter, allowing users to query information for specific taxonomic names without a phyloseq object.
Added comprehensive tests for taxnames parameter usage across all functions.
Add functions extract_spores_mycodb() and tax_spores_size_pq() to retrieve spore size information from MycoDB.
Add params year_col and authorship_col to gna_verifier_pq() to output year of publication and authorship information for each taxa.
Add function intra_taxnames_dist() to compute pairwise DNA distances among taxa with the same taxonomic names.
Add function cluster_sbc() to (post)cluster taxa into SBC (Species bound cluster) defined as "clusters that include all and only ESVs assigned to one species, the sequence similarity threshold can vary between these clusters" by Riley et al. 2025 (https://doi.org/10.1186/s12915-025-02284-x). Also add a new vignette to illustrate the use of cluster_sbc().
Print information when using tax_info_pq() with add_to_phyloseq = TRUE to inform users that the phyloseq object is being updated.
Add an example in tax_info_pq() manual with the EPPO database to determine if pest species regulated in France are found in the example phyloseq object.
Change the result column genus into genusEpithet from the gna_verifier_pq() function to avoid confusion between "Genus" and "genus" columns and to debug the use of duckdb in taxinfo_pq().
gna_verifier_pq() now adds a genusSpeciesEpithet column (when genus_species_canonical_col = TRUE) that copies currentCanonicalSimple but is NA for genus-only names (i.e. when specificEpithet is NA or empty).
gna_verifier_pq() gains a species_only parameter (default TRUE): when TRUE, currentCanonicalSimple is set to NA for uninomial matches (matchedCardinality == 1, i.e. genus or higher-rank names with no species epithet). genusEpithet is always populated regardless of this setting; specificEpithet is always NA for uninomials independently of this parameter.
gna_verifier_pq(): fixed verbose summary always reporting 0 accepted/synonym names when add_to_phyloseq = FALSE (was incorrectly reading dropped columns from res_verifier_clean instead of res_verifier). Fixed matchedCardinality threshold used for "uninomial" reporting (was == 2 instead of == 1). Fixed genusEpithet and specificEpithet being absent from the return value when add_to_phyloseq = FALSE and genus_species_canonical_col = TRUE (the function was returning the raw GNA result instead of the cleaned tibble). Fixed potential many-to-many join when add_to_phyloseq = TRUE by deduplicating on submittedName after select() rather than before.
Fixed issue in functions tax_gbif_occur_pq() and range_bioreg_pq() due to the loss of the column verbatim_index in rgbif::name_backbone_checklist() (commit c74602b).
add_to_phyloseq.list_keywords and n_citation columns in the return of tax_oa_pq().